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Conserved domains on  [gi|1083840206|gb|OGJ16816|]
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MAG: hypothetical protein A2632_01950 [Candidatus Pacebacteria bacterium RIFCSPHIGHO2_01_FULL_46_16]

Protein Classification

isopentenyl-diphosphate Delta-isomerase( domain architecture ID 10120965)

isopentenyl-diphosphate Delta-isomerase catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), a key step in the isoprenoid biosynthesis

EC:  5.3.3.2
Gene Ontology:  GO:0008299|GO:0004452
PubMed:  9418296

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 4-170 5.18e-61

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


:

Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 186.55  E-value: 5.18e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   4 QVTLVDKHDRVLGVMNKIEAHRGAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECAR 83
Cdd:cd02885     1 EVILVDEDDNPIGTAEKLEAHRKGTLLHRAFSVFLFN---SKGELLLQRRALSKYTWPGLWTNTCCSHPLPGEGVEDAAQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  84 RRLREELGIVDPELVLQPgaKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRADE 163
Cdd:cd02885    78 RRLREELGIPVCDLEELP--RFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLE-----ELRELLAATP 150


                  ....*....
gi 1083840206 164 WAV--WFEL 170
Cdd:cd02885   151 EAFtpWFRL 159
 
Name Accession Description Interval E-value
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 4-170 5.18e-61

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 186.55  E-value: 5.18e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   4 QVTLVDKHDRVLGVMNKIEAHRGAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECAR 83
Cdd:cd02885     1 EVILVDEDDNPIGTAEKLEAHRKGTLLHRAFSVFLFN---SKGELLLQRRALSKYTWPGLWTNTCCSHPLPGEGVEDAAQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  84 RRLREELGIVDPELVLQPgaKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRADE 163
Cdd:cd02885    78 RRLREELGIPVCDLEELP--RFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLE-----ELRELLAATP 150


                  ....*....
gi 1083840206 164 WAV--WFEL 170
Cdd:cd02885   151 EAFtpWFRL 159
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 3-170 4.48e-53

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 166.53  E-value: 4.48e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   3 DQVTLVDKHDRVLGVMNKIEAHRgAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECA 82
Cdd:COG1443     2 ELVDLVDEDGRPIGTAERAEVHR-KGLLHRAFSVFVFN---SDGRLLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  83 RRRLREELGIvDPELVLQPGAKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRAD 162
Cdd:COG1443    78 VRELEEELGI-TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTLE-----ELLALLEAG 151

                         170
                  ....*....|
gi 1083840206 163 EWAV--WFEL 170
Cdd:COG1443   152 PEAFtpWFRL 161
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
3-180 1.02e-37

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 128.16  E-value: 1.02e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   3 DQVTLVDKHDRVLGVMNKIEAHRGAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECA 82
Cdd:PRK03759    6 ELVVLLDEQGVPTGTAEKAAAHTADTPLHLAFSCYLFD---ADGRLLVTRRALSKKTWPGVWTNSCCGHPQPGESLEDAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  83 RRRLREELG--IVDPELVLqpgAKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTfdkksPTKILEQKR 160
Cdd:PRK03759   83 IRRCREELGveITDLELVL---PDFRYRATDPNGIVENEVCPVFAARVTSALQPNPDEVMDYQWVD-----PADLLRAVD 154

                         170       180
                  ....*....|....*....|..
gi 1083840206 161 ADEWAV--WFELGLNHVVLKER 180
Cdd:PRK03759  155 ATPWAFspWMVLQAANLEAREL 176
NUDIX pfam00293
NUDIX domain;
29-148 2.94e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 68.66  E-value: 2.94e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  29 VLHRAISVFLFRkleDQTELLLQQRSSKKIVGagqWANTVCGNVQPTENYFECARRRLREELGIVDPElvLQPGAKFRYQ 108
Cdd:pfam00293   1 KRRVAVGVVLLN---EKGRVLLVRRSKKPFPG---WWSLPGGKVEPGETPEEAARRELEEETGLEPEL--LELLGSLHYL 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1083840206 109 VVCNEEFG-ENELDQVFIGWYDGEVVPNP-EEVQAVEWLTFD 148
Cdd:pfam00293  73 APFDGRFPdEHEILYVFLAEVEGELEPDPdGEVEEVRWVPLE 114
 
Name Accession Description Interval E-value
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 4-170 5.18e-61

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 186.55  E-value: 5.18e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   4 QVTLVDKHDRVLGVMNKIEAHRGAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECAR 83
Cdd:cd02885     1 EVILVDEDDNPIGTAEKLEAHRKGTLLHRAFSVFLFN---SKGELLLQRRALSKYTWPGLWTNTCCSHPLPGEGVEDAAQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  84 RRLREELGIVDPELVLQPgaKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRADE 163
Cdd:cd02885    78 RRLREELGIPVCDLEELP--RFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLE-----ELRELLAATP 150


                  ....*....
gi 1083840206 164 WAV--WFEL 170
Cdd:cd02885   151 EAFtpWFRL 159
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 3-170 4.48e-53

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 166.53  E-value: 4.48e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   3 DQVTLVDKHDRVLGVMNKIEAHRgAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECA 82
Cdd:COG1443     2 ELVDLVDEDGRPIGTAERAEVHR-KGLLHRAFSVFVFN---SDGRLLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  83 RRRLREELGIvDPELVLQPGAKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRAD 162
Cdd:COG1443    78 VRELEEELGI-TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTLE-----ELLALLEAG 151

                         170
                  ....*....|
gi 1083840206 163 EWAV--WFEL 170
Cdd:COG1443   152 PEAFtpWFRL 161
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
3-180 1.02e-37

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 128.16  E-value: 1.02e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   3 DQVTLVDKHDRVLGVMNKIEAHRGAGVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECA 82
Cdd:PRK03759    6 ELVVLLDEQGVPTGTAEKAAAHTADTPLHLAFSCYLFD---ADGRLLVTRRALSKKTWPGVWTNSCCGHPQPGESLEDAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  83 RRRLREELG--IVDPELVLqpgAKFRYQVVCNEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTfdkksPTKILEQKR 160
Cdd:PRK03759   83 IRRCREELGveITDLELVL---PDFRYRATDPNGIVENEVCPVFAARVTSALQPNPDEVMDYQWVD-----PADLLRAVD 154

                         170       180
                  ....*....|....*....|..
gi 1083840206 161 ADEWAV--WFELGLNHVVLKER 180
Cdd:PRK03759  155 ATPWAFspWMVLQAANLEAREL 176
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 8-147 6.22e-30

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467574 [Multi-domain]  Cd Length: 142  Bit Score: 106.87  E-value: 6.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   8 VDKHDRVLGVMNKIEAHRgAGVLHRAISVFLFRKleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARRRLR 87
Cdd:cd04692     4 VDEDGRPIGVATRSEVHR-QGLWHRTVHVWLVNP--EEGRLLLQKRSANKDDFPGLWDISAAGHIDAGETYEEAAVRELE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083840206  88 EELGIVDPELVLQPGAKFRYQVVcNEEFGENELDQVFIGWYD---GEVVPNPEEVQAVEWLTF 147
Cdd:cd04692    81 EELGLTVSPEDLIFLGVIREEVI-GGDFIDNEFVHVYLYETDrplEEFKLQPEEVAGVVFVDL 142
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 3-170 5.64e-27

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 102.12  E-value: 5.64e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   3 DQVTLVDKHDRVLGVMNKIEAHR-----GAGVLHRAISVFLFrklEDQTELLLQQRSSKKIVGAGQWANTVCGN----VQ 73
Cdd:PLN02552   23 DECILVDENDNVVGHDSKYNCHLfekiePRGLLHRAFSVFLF---NSKYELLLQQRAATKVTFPLVWTNTCCSHplygQD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  74 PTENYFE-------------CARRRLREELGIvDPELVlqPGAKFRY------------QVVCNEEFGENELDQV-FIGW 127
Cdd:PLN02552  100 PNEVDREselidgnvlgvknAAQRKLLHELGI-PAEDV--PVDQFTFltrlhykaaddvTHGPDGKWGEHELDYLlFIRP 176

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1083840206 128 Y-DGEVVPNPEEVQAVEWLTFDKKSptKILEQKRADEWAVWFEL 170
Cdd:PLN02552  177 VrDVKVNPNPDEVADVKYVNREELK--EMMRKESGLKLSPWFRL 218
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 5-164 2.65e-21

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467578 [Multi-domain]  Cd Length: 157  Bit Score: 84.98  E-value: 2.65e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   5 VTLVDKHDRVLGVMNKIEAHRGaGVLHRAISVFLFRKledQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARR 84
Cdd:cd04697     1 VDIVDENNEVVGAATRAEMRRQ-KLIHRATYIVVRNA---AGRLLVQKRTMDKDYCPGYLDPATGGVVGAGESYEENARR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  85 RLREELGIVDpeLVLQPGAKFRYQVVCNEEFGeneldQVFIGWYDGEVVPNPEEVQAVEWLTFDkksptKILEQKRADEW 164
Cdd:cd04697    77 ELEEELGIDG--VPLRPLFTFYYEDDRSRVWG-----ALFECVYDGPLKLQPEEVAEVDWMSED-----EILQAARGEEF 144
NUDIX pfam00293
NUDIX domain;
29-148 2.94e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 68.66  E-value: 2.94e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  29 VLHRAISVFLFRkleDQTELLLQQRSSKKIVGagqWANTVCGNVQPTENYFECARRRLREELGIVDPElvLQPGAKFRYQ 108
Cdd:pfam00293   1 KRRVAVGVVLLN---EKGRVLLVRRSKKPFPG---WWSLPGGKVEPGETPEEAARRELEEETGLEPEL--LELLGSLHYL 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1083840206 109 VVCNEEFG-ENELDQVFIGWYDGEVVPNP-EEVQAVEWLTFD 148
Cdd:pfam00293  73 APFDGRFPdEHEILYVFLAEVEGELEPDPdGEVEEVRWVPLE 114
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 28-149 1.63e-12

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467575 [Multi-domain]  Cd Length: 157  Bit Score: 61.77  E-value: 1.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  28 GVLHRAISVFLFRkleDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARRRLREELGI-VDPElvlQPGAKFR 106
Cdd:cd04693    26 GEYHLVVHVWIFN---SDGEILIQQRSPDKKGFPGMWEASTGGSVLAGETSLEAAIRELKEELGIdLDAD---ELRPILT 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1083840206 107 YqvvcneeFGENELDQVFIGWYD---GEVVPNPEEVQAVEWLTFDK 149
Cdd:cd04693   100 I-------RFDNGFDDIYLFRKDvdiEDLTLQKEEVQDVKWVTLEE 138
PLN02791 PLN02791
Nudix hydrolase homolog
 22-148 1.40e-09

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 56.37  E-value: 1.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  22 EAHRGaGVLHRAISVFLFrkLEDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARRRLREELGIVDPELVLQP 101
Cdd:PLN02791   24 EVHRD-GDYHRAVHVWIY--SESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSLLSAQRELEEELGIILPKDAFEL 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1083840206 102 GAKFRYQVVCNE-EFGENELDQVFIGwydGEVVPNP--------EEVQAVEWLTFD 148
Cdd:PLN02791  101 LFVFLQECVINDgKFINNEYNDVYLV---TTLDPIPleaftlqeSEVSAVKYMSIE 153
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 5-163 3.40e-08

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 50.95  E-value: 3.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206   5 VTLVDKHDRVLGVMNKiEAHRGAGVLHRAISVFLfrkLEDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARR 84
Cdd:PRK15393   12 VDIVNENNEVIAQASR-EQMRAQCLRHRATYIVV---HDGMGKILVQRRTETKDFLPGMLDATAGGVVQAGEQLLESARR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  85 RLREELGIVDpeLVLQPGAKFRYqvvcneefgENELDQVFIGW----YDGEVVPNPEEVQAVEWLTfdkksPTKILEqkR 160
Cdd:PRK15393   88 EAEEELGIAG--VPFAEHGQFYF---------EDENCRVWGALfscvSHGPFALQEEEVSEVCWMT-----PEEITA--R 149


                  ...
gi 1083840206 161 ADE 163
Cdd:PRK15393  150 CDE 152
NUDIX_CoAse_Nudt7 cd03426
coenzyme A pyrophosphatase and similar proteins; Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1) ...
 38-176 2.93e-07

coenzyme A pyrophosphatase and similar proteins; Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1), also called nucleoside diphosphate-linked moiety X)) motif 7, is a member of the NUDIX hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative stress. CoAse has a conserved NUDIX fold and requires a single divalent cation for catalysis. In addition to a signature NUDIX motif G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val, CoAse contains an additional motif upstream called the NuCoA motif (LLTXT(SA)X3RX3GX3FPGG) which is postulated to be involved in CoA recognition. CoA plays a central role in lipid metabolism. It is involved in the initial steps of fatty acid sythesis in the cytosol, in the oxidation of fatty acids and the citric acid cycle in the mitochondria, and in the oxidation of long-chain fatty acids in peroxisomes. CoA has the important role of activating fatty acids for further modification into key biological signalling molecules.


Pssm-ID: 467532 [Multi-domain]  Cd Length: 158  Bit Score: 47.87  E-value: 2.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  38 LFRKLEDQTELLLQQRSSKKivgaGQWANTVC---GNVQPT-ENYFECARRRLREELGIvDPELVlqpgakfryQVVCne 113
Cdd:cd03426     8 PLVEGDGELHVLLTKRASHL----RSHPGQIAfpgGKREPGdESPVETALRETEEEIGL-PPESV---------EVLG-- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206 114 efgenELDQV----------FIGWYDGE--VVPNPEEVQAVEWLTFD------KKSPTKILEQKRADEWAVWFELGLNHV 175
Cdd:cd03426    72 -----RLDPLytpsgfvvtpFVGLLDDPppLRPNPDEVAEVFTVPLSflldpePRRYETFLRSGPRGTYRVPFYPYEGYV 146


                  .
gi 1083840206 176 V 176
Cdd:cd03426   147 I 147
NUDIX_Hydrolase cd02883
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 32-146 1.01e-06

NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467528 [Multi-domain]  Cd Length: 106  Bit Score: 45.47  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  32 RAISVFLFRkleDQTELLLQQRSSKKivGAGQWAnTVCGNVQPTENYFECARRRLREELGIVDPELVLQPGAKFRYqvvc 111
Cdd:cd02883     1 VAVGAVVFD---DEGRVLLVRRSDGP--GPGGWE-LPGGGVEPGETPEEAAVREVREETGLDVEVLRLLGVYEFPD---- 70

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1083840206 112 nEEFGENELDQVFIGWYDGEVVPN--PEEVQAVEWLT 146
Cdd:cd02883    71 -PDEGRHVVVLVFLARVVGGEPPPldDEEISEVRWVP 106
NUDIX_Ap4A_Nudt2 cd03428
diadenosine tetraphosphate; Diadenosine tetraphosphate (Ap4A; EC 3.6.1.17), also called NUDIX ...
 32-148 9.61e-06

diadenosine tetraphosphate; Diadenosine tetraphosphate (Ap4A; EC 3.6.1.17), also called NUDIX (nucleoside diphosphate-linked moiety X)) motif 2/Nudt2, is a member of the NUDIX hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature NUDIX motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and catalytic site, and a required divalent cation, Ap4A hydrolase is structurally similar to the other members of the NUDIX hydrolase superfamily with some degree of variation. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies.


Pssm-ID: 467534 [Multi-domain]  Cd Length: 132  Bit Score: 43.31  E-value: 9.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  32 RAISVFLFRKLEDQTE-LLLQQRSSkkivgaGQWAntvC--GNVQPTENYFECARRRLREELGIvdPELVLQPGakFRYq 108
Cdd:cd03428     3 KSAGAIIYRRDNGEIEfLLLQHSYG------GHWD---FpkGHVEPGESELETALRETKEETGL--TVDDLPPG--FRE- 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1083840206 109 vVCNEEFGENELDQV--FIGWYDGEVVPNP-EEVQAVEWLTFD 148
Cdd:cd03428    69 -TLTYSFKEGVEKTVvyFLAELTPDVEVKLsEEHQDYKWLPYE 110
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
 28-164 1.95e-05

thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a bifunctional enzyme composed of a C-terminal thiamine pyrophosphokinase domain, which transfers pyrophosphate from ATP to thiamine and an N-terminal NUDIX hydrolase domain that converts oxidized derivatives of thiamine diphosphate (oxothiamine and oxythiamine) to their respective monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467544  Cd Length: 153  Bit Score: 42.48  E-value: 1.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  28 GVLHRAISVFLFRKLEDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARRRLREELGIvdPELVLQPGAKF-- 105
Cdd:cd03676     3 GIVTYGVHLNGYVRDGDGLRLWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGL--PEDLARQARPAag 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083840206 106 --RYQVVCNEEFGENELdqvfIGWYDGEV----VPNPE--EVQAvewltFDKKSPTKILEQKRADEW 164
Cdd:cd03676    81 rvSYFYRSDEGGLQPEV----LYVYDLELpedfVPKPQdgEVES-----FELMSVDEVLEALRAGEF 138
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 42-148 2.62e-05

8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX family [Defense mechanisms];


Pssm-ID: 440260 [Multi-domain]  Cd Length: 143  Bit Score: 42.33  E-value: 2.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  42 LEDQTELLLQQRSSKKiVGAGQWAnTVCGNVQPTENYFECARRRLREELGIvDPElVLQPGAKFRYQVVCNEEFgeneld 121
Cdd:COG0494    21 LDDDGRVLLVRRYRYG-VGPGLWE-FPGGKIEPGESPEEAALRELREETGL-TAE-DLELLGELPSPGYTDEKV------ 90

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1083840206 122 QVFIGWYDGEV----VPNPEEVQAVEWLTFD 148
Cdd:COG0494    91 HVFLARGLGPGeevgLDDEDEFIEVRWVPLD 121
YjhB COG1051
ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism];
18-149 2.72e-05

ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism];


Pssm-ID: 440671 [Multi-domain]  Cd Length: 125  Bit Score: 41.89  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  18 MNKIEAHRGAGVLHRaisvflfrkleDQTELLLQQRSSKkiVGAGQWAnTVCGNVQPTENYFECARRRLREELGI--VDP 95
Cdd:COG1051     1 MTKVPKVAVDAVIFR-----------KDGRVLLVRRADE--PGKGLWA-LPGGKVEPGETPEEAALRELREETGLevEVL 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1083840206  96 ELVLQPGAKFRYQVVcneefgenelDQVFIGWYDGEVVPNPEEVQAVEWLTFDK 149
Cdd:COG1051    67 ELLGVFDHPDRGHVV----------SVAFLAEVLSGEPRADDEIDEARWFPLDE 110
NUDIX_Hydrolase cd18882
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 43-146 1.59e-04

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467593 [Multi-domain]  Cd Length: 130  Bit Score: 39.55  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  43 EDQTELLLQQRSSK-KIVGAGQWAnTVCGNVQPTENYFECARRRLREELGivdpelvLQPGaKFRYQVVCNEEFGENELD 121
Cdd:cd18882    10 DDRGKVLLQLRDDKpGIPYPGYWG-LFGGHLEPGETPEEAIRRELEEEIG-------YEPG-EFRFFLLYTEDDGEDRIR 80

                          90       100
                  ....*....|....*....|....*...
gi 1083840206 122 QVFIGWYDG---EVVPNpeEVQAVEWLT 146
Cdd:cd18882    81 HVFHAPLDVdlsDLVLN--EGQALRLFS 106
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 32-163 2.37e-04

NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus radiodurans protein DR_0079 is one of 21 NUDIX hydrolases that it encodes, and it has been observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP), and for their corresponding deoxyribose nucleotides, dCDP and dCTP, to a lesser degree. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467602 [Multi-domain]  Cd Length: 121  Bit Score: 39.12  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  32 RAISVFLFrklEDQTELLLQQRSSKKIVGAGQWANTVCGNVQPTENYFECARRRLREELGIVDPELVLQPGAKFRyqvvc 111
Cdd:cd24154     3 RVVNAFLI---NSQGQLWIPRRTADKRIFPLALDMSVGGHVSSGETYEQAFVRELQEELNLDLDQLSYRVLGKLT----- 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1083840206 112 NEEFGENELDQVFIGWYDGEVVPNPEEVQAVEWLTfdkksPTKILEQKRADE 163
Cdd:cd24154    75 PYEHGVSAFMKVYEIRSDETPDYNPDDFSEAFWLT-----PEELLKRIAAGE 121
NUDIX_Hydrolase cd04683
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 34-96 5.53e-04

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467566 [Multi-domain]  Cd Length: 137  Bit Score: 38.35  E-value: 5.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1083840206  34 ISVFLFrkLEDQTELLLQQRSSKKIVGaGQWAnTVCGNVQPTENYFECARRRLREELGI-VDPE 96
Cdd:cd04683     1 VDVHLL--LVRGDEVLLLRRANTGYDD-GWWH-LPAGHVEAGETVRAAAVREAKEELGVeIDPE 60
NUDIX_MutT_NudA_like cd03425
MutT pyrophosphohydrolase; The MutT pyrophosphohydrolase is a prototypical NUDIX hydrolase ...
 42-148 8.83e-04

MutT pyrophosphohydrolase; The MutT pyrophosphohydrolase is a prototypical NUDIX hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi). This enzyme requires two divalent cations for activity; one coordinates the phosphoryl groups of the NTP/dNTP substrate, and the other coordinates to the enzyme. It also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as metal binding and catalytic site. MutT pyrophosphohydrolase is important in preventing errors in DNA replication by hydrolyzing mutagenic nucleotides such as 8-oxo-dGTP (a product of oxidative damage), which can mispair with template adenine during DNA replication, to guanine nucleotides.


Pssm-ID: 467531 [Multi-domain]  Cd Length: 123  Bit Score: 37.43  E-value: 8.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  42 LEDQTELLLQQRSSKKIVgAGQWantvcGNVQPTENYFECARRRLREELGIvdpelVLQPGAKFRyQVVCNEEFGENELD 121
Cdd:cd03425     8 IVDDGRVLIAQRPEGKHL-AGLWef-pgGKVEPGETPEQALVRELREELGI-----EVEVGEPLG-TVEHDYPDFHVRLH 79

                          90       100
                  ....*....|....*....|....*..
gi 1083840206 122 QVFIGWYDGEvvPNPEEVQAVEWLTFD 148
Cdd:cd03425    80 VYLCTLWSGE--PQLLEHQELRWVTPE 104
NUDIX_Hydrolase cd18879
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 42-144 9.83e-04

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467590 [Multi-domain]  Cd Length: 142  Bit Score: 37.56  E-value: 9.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  42 LEDQTELLLQQRSSkkivgAGQWAnTVCGNVQPTENYFECARRRLREELGI-----------VDPELVLQPGAKFRYqvv 110
Cdd:cd18879    26 LRDAGRVLLVRRAD-----NGRWT-PVTGIVEPGEQPADAAVREVLEETGVdveverlasvgASPPVTYPNGDQCQY--- 96

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1083840206 111 cneefgeneLDQVFIG-WYDGEVVPNPEEVQAVEW 144
Cdd:cd18879    97 ---------LDLTFRCrPVGGEARVNDDESLEVGW 122
NUDIX_Hydrolase cd04685
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 47-99 1.65e-03

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467568 [Multi-domain]  Cd Length: 138  Bit Score: 37.17  E-value: 1.65e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1083840206  47 ELLLQQRSSKKIVGAGQWAnTVCGNVQPTENYFECARRRLREELGIVDPELVL 99
Cdd:cd04685    13 RVLLFRFHDPDDPGRSWWF-TPGGGVEPGESPEQAAVRELREETGLRLEPDDL 64
NUDIX_MutT_Nudt1 cd18886
MutT homolog-1 and similar proteins; MutT homolog-1 (MTH1), also known as NUDIX (nucleoside ...
 42-138 1.88e-03

MutT homolog-1 and similar proteins; MutT homolog-1 (MTH1), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 1/Nudt1, is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases.


Pssm-ID: 467596 [Multi-domain]  Cd Length: 147  Bit Score: 36.83  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  42 LEDQTELLLQQRSSKKivGAGQWaNTVCGNVQPTENYFECARRRLREELGIVDPELVLQPGAKFRYqvvcnEEFGENELD 121
Cdd:cd18886     7 IIRDDEVLLLNRNKKP--NMGKW-NGVGGKLEPGESPEECAIREVFEETGLELEDLQLRGIVTFPS-----FDGGEDWLM 78

                          90
                  ....*....|....*...
gi 1083840206 122 QVFIG-WYDGEVVPNPEE 138
Cdd:cd18886    79 YVFLAeAFSGELVESDRE 96
NUDIX_MTH2_Nudt15 cd04678
MutT homolog 2; MutT Homolog 2 (MTH2; EC 3.6.1.9), also known as NUDIX (nucleoside ...
 34-93 2.80e-03

MutT homolog 2; MutT Homolog 2 (MTH2; EC 3.6.1.9), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 15/Nudt15, may catalyze the hydrolysis of nucleoside diphosphates, triphosphates including dGTP, dTTP, dCTP, their oxidized forms like 8-oxo-dGTP, and prodrug thiopurine derivatives 6-thio-dGTP and 6-thio-GTP. MTH2 may also play a role in DNA synthesis and cell cycle progression by stabilizing PCNA. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467561 [Multi-domain]  Cd Length: 128  Bit Score: 36.00  E-value: 2.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  34 ISVFLFRkleDQTELLLQQRssKKIVGAGQWAnTVCGNVQPTENYFECARRRLREELGIV 93
Cdd:cd04678     5 VGVIVLN---DDGKVLLGRR--KGSHGAGTWA-LPGGHLEFGESFEECAAREVLEETGLE 58
NUDIX_MTH1_Nudt1 cd03427
MutT homolog-1 (MTH1); MutT homolog-1 (MTH1; EC 3.6.1.- ), also called nucleoside ...
 36-97 5.52e-03

MutT homolog-1 (MTH1); MutT homolog-1 (MTH1; EC 3.6.1.- ), also called nucleoside diphosphate-linked moiety X)) motif 1 (Nudt1), is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases.


Pssm-ID: 467533 [Multi-domain]  Cd Length: 136  Bit Score: 35.58  E-value: 5.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1083840206  36 VFLFRkleDQTELLLQQRssKKIVGAGQWaNTVCGNVQPTENYFECARRRLREELGIVDPEL 97
Cdd:cd03427     6 VFVLR---GDDRVLLGLK--KRGFGAGKW-NGFGGKVEPGETIEEAAVRELEEEAGLTATEL 61
NUDIX_Ap6A_hydrolase cd03673
diadenosine hexaphosphate (Ap6A) hydrolase; Diadenosine hexaphosphate (Ap6A) hydrolase is a ...
 70-149 9.02e-03

diadenosine hexaphosphate (Ap6A) hydrolase; Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the NUDIX hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most preferred substrate, hydrolyzes to produce two ATP molecules, which is a novel hydrolysis mode for Ap6A. These results indicate that Ap6A hydrolase is a diadenosine polyphosphate hydrolase. It requires the presence of a divalent cation, such as Mn2+, Mg2+, Zn2+, and Co2+, for activity. Members of the NUDIX hydrolase superfamily are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site.


Pssm-ID: 467541 [Multi-domain]  Cd Length: 131  Bit Score: 34.84  E-value: 9.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083840206  70 GNVQPTENYFECARRRLREELGIvdPELVLQPGAKFRYQVVCNEEFGENELDqvfigWY-----DGEVVPNP-EEVQAVE 143
Cdd:cd03673    34 GKLEPGETPEEAAVREVEEETGL--RVRLGRPLGTTRYTYTRKGKGILKKVH-----YWlmralGGEFLPQPeEEIDEVR 106


                  ....*.
gi 1083840206 144 WLTFDK 149
Cdd:cd03673   107 WLPPDE 112
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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