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Conserved domains on  [gi|964748907|ref|NP_001304885|]
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isopentenyl-diphosphate Delta-isomerase 1 isoform b [Homo sapiens]

Protein Classification

NUDIX hydrolase( domain architecture ID 225)

NUDIX hydrolase catalyzes the hydrolysis of nucleoside diphosphates linked to other moieties (X); it requires a divalent cation, such as Mg2+ or Mn2+ for its activity

CATH:  3.90.79.10
EC:  3.6.1.-
Gene Ontology:  GO:0016817|GO:0009132|GO:0046872
PubMed:  15581572|16378245|27936487
SCOP:  3000098

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUDIX_Hydrolase super family cl00447
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 22-228 2.16e-93

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.


The actual alignment was detected with superfamily member PLN02552:

Pssm-ID: 469772 [Multi-domain]  Cd Length: 247  Bit Score: 273.92  E-value: 2.16e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  22 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 92
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  93 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 164
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 964748907 165 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 228
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 22-228 2.16e-93

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 273.92  E-value: 2.16e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  22 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 92
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  93 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 164
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 964748907 165 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 228
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 21-203 1.52e-79

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: 235.47  E-value: 1.52e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  21 MCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAElees 100
Cdd:cd02885    1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE---- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907 101 dalGVRRAAQRRLKAELGIpleevPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeL 180
Cdd:cd02885   71 ---GVEDAAQRRLREELGI-----PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---L 139

                        170       180
                 ....*....|....*....|...
gi 964748907 181 KELLKKAASGEIKITPWFKIIAA 203
Cdd:cd02885  140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 22-202 8.48e-77

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 228.38  E-value: 8.48e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907   22 CILIDENDNKIGAETKKNCHLNENIekglLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSnpaeleesd 101
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  102 alGVRRAAQRRLKAELGIPLEEVPpeeINYLTRIHYKAQsDGIWGEHEIDYILLVRKNVTLNPDPnEIKSYCYVSKEELK 181
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRAR-DDAWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 964748907  182 ELLKKAASGeikITPWFKIIA 202
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 23-201 2.15e-48

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: 156.13  E-value: 2.15e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  23 ILIDENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESda 102
Cdd:COG1443    5 DLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET-- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907 103 lgVRRAAQRRLKAELGIpleeVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKE 182
Cdd:COG1443   73 --YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEE 143

                        170
                 ....*....|....*....
gi 964748907 183 LLKKAASGEIKITPWFKII 201
Cdd:COG1443  144 LLALLEAGPEAFTPWFRLY 162
NUDIX pfam00293
NUDIX domain;
50-198 9.50e-17

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 73.67  E-value: 9.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907   50 LLHRAFSVFLFNTENKLLLQQRSdaKITFPGCFtntccshplSNPA-ELEESDAlgVRRAAQRRLKAELGIpleevPPEE 128
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWW---------SLPGgKVEPGET--PEEAARRELEEETGL-----EPEL 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 964748907  129 INYLTRIHYKAQSDGIWG-EHEIDYILLVRKNVTLNPDPN-EIKSYCYVSkeELKELLKKAASGEIKITPWF 198
Cdd:pfam00293  63 LELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVP--LEELLLLKLAPGDRKLLPWL 132
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 22-228 2.16e-93

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 273.92  E-value: 2.16e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  22 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 92
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  93 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 164
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 964748907 165 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 228
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 21-203 1.52e-79

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: 235.47  E-value: 1.52e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  21 MCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAElees 100
Cdd:cd02885    1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE---- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907 101 dalGVRRAAQRRLKAELGIpleevPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeL 180
Cdd:cd02885   71 ---GVEDAAQRRLREELGI-----PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---L 139

                        170       180
                 ....*....|....*....|...
gi 964748907 181 KELLKKAASGEIKITPWFKIIAA 203
Cdd:cd02885  140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 22-202 8.48e-77

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 228.38  E-value: 8.48e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907   22 CILIDENDNKIGAETKKNCHLNENIekglLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSnpaeleesd 101
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  102 alGVRRAAQRRLKAELGIPLEEVPpeeINYLTRIHYKAQsDGIWGEHEIDYILLVRKNVTLNPDPnEIKSYCYVSKEELK 181
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRAR-DDAWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 964748907  182 ELLKKAASGeikITPWFKIIA 202
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 23-201 2.15e-48

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: 156.13  E-value: 2.15e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  23 ILIDENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESda 102
Cdd:COG1443    5 DLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET-- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907 103 lgVRRAAQRRLKAELGIpleeVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKE 182
Cdd:COG1443   73 --YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEE 143

                        170
                 ....*....|....*....
gi 964748907 183 LLKKAASGEIKITPWFKII 201
Cdd:COG1443  144 LLALLEAGPEAFTPWFRLY 162
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
19-198 1.15e-34

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 122.00  E-value: 1.15e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  19 AEMCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAEle 98
Cdd:PRK03759   5 TELVVLLDEQGVPTGTAEKAAAHTAD----TPLHLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQ--PGE-- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  99 esdalGVRRAAQRRLKAELGIPLEEVPPEeinyLTRIHYKA-QSDGIWgEHEIDYILLVRKNVTLNPDPNEIKSYCYVSk 177
Cdd:PRK03759  77 -----SLEDAVIRRCREELGVEITDLELV----LPDFRYRAtDPNGIV-ENEVCPVFAARVTSALQPNPDEVMDYQWVD- 145

                        170       180
                 ....*....|....*....|.
gi 964748907 178 eeLKELLKKAASGEIKITPWF 198
Cdd:PRK03759 146 --PADLLRAVDATPWAFSPWM 164
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 26-169 4.05e-22

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: 88.00  E-value: 4.05e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  26 DENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTEN-KLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESdalg 104
Cdd:cd04692    5 DEDGRPIGVATRSEVH-----RQGLWHRTVHVWLVNPEEgRLLLQKRSANKDDFPGLWDISAAGHIDAG-----ET---- 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 964748907 105 VRRAAQRRLKAELGIpleEVPPEEINYLTRIHYKAQSDGIWGeHEIDYILLVRKNVTLN---PDPNEI 169
Cdd:cd04692   71 YEEAAVRELEEELGL---TVSPEDLIFLGVIREEVIGGDFID-NEFVHVYLYETDRPLEefkLQPEEV 134
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 26-176 7.08e-17

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: 74.87  E-value: 7.08e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  26 DENDNKIGaETKKNchlNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESdalgv 105
Cdd:cd04693    7 DENRNKTG-RTHRR---GEPLPEGEYHLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAG----ETS----- 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 964748907 106 RRAAQRRLKAELGIpleEVPPEEINYLTRIHYkaqsdgiwgEHEIDYILLVRKNVTLN---PDPNEIKSYCYVS 176
Cdd:cd04693   74 LEAAIRELKEELGI---DLDADELRPILTIRF---------DNGFDDIYLFRKDVDIEdltLQKEEVQDVKWVT 135
NUDIX pfam00293
NUDIX domain;
50-198 9.50e-17

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 73.67  E-value: 9.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907   50 LLHRAFSVFLFNTENKLLLQQRSdaKITFPGCFtntccshplSNPA-ELEESDAlgVRRAAQRRLKAELGIpleevPPEE 128
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWW---------SLPGgKVEPGET--PEEAARRELEEETGL-----EPEL 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 964748907  129 INYLTRIHYKAQSDGIWG-EHEIDYILLVRKNVTLNPDPN-EIKSYCYVSkeELKELLKKAASGEIKITPWF 198
Cdd:pfam00293  63 LELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVP--LEELLLLKLAPGDRKLLPWL 132
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 22-176 1.08e-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: 467578 [Multi-domain]  Cd Length: 157  Bit Score: 63.41  E-value: 1.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  22 CILIDENDNKIGAETKKnchlnENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGcFTNTCCShplsnpaeleesd 101
Cdd:cd04697    1 VDIVDENNEVVGAATRA-----EMRRQKLIHRATYIVVRNAAGRLLVQKRTMDKDYCPG-YLDPATG------------- 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907 102 alGV-------RRAAQRRLKAELGIplEEVPPEeinYLTRIHYKAQSDGIWGE-HEIDYillvRKNVTlnPDPNEIKSYC 173
Cdd:cd04697   62 --GVvgagesyEENARRELEEELGI--DGVPLR---PLFTFYYEDDRSRVWGAlFECVY----DGPLK--LQPEEVAEVD 128


                 ...
gi 964748907 174 YVS 176
Cdd:cd04697  129 WMS 131
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 53-133 1.13e-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: 40.66  E-value: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  53 RAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESDAlgvrrAAQRRLKAELGIPLEEVPPEEINYL 132
Cdd:cd24154    3 RVVNAFLINSQGQLWIPRRTADKRIFPLALDMSVGGHVSSG----ETYEQ-----AFVRELQEELNLDLDQLSYRVLGKL 73


                 .
gi 964748907 133 T 133
Cdd:cd24154   74 T 74
PLN02791 PLN02791
Nudix hydrolase homolog
 49-168 4.16e-04

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 40.96  E-value: 4.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  49 GLLHRAFSVFLF-NTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELeesdalgvrRAAQRRLKAELGIPLEEVPPE 127
Cdd:PLN02791  29 GDYHRAVHVWIYsESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSL---------LSAQRELEEELGIILPKDAFE 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 964748907 128 EI-NYLTRIhykAQSDGIWGEHEIDYILLVrknVTLNPDPNE 168
Cdd:PLN02791 100 LLfVFLQEC---VINDGKFINNEYNDVYLV---TTLDPIPLE 135
NUDIX_Hydrolase cd02883
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 56-176 3.40e-03

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: 35.84  E-value: 3.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 964748907  56 SVFLFNTENKLLLQQRSDA----KITFPGCFtntccshplsnpAELEESdalgVRRAAQRRLKAELGIPLEEVPPEEINY 131
Cdd:cd02883    4 GAVVFDDEGRVLLVRRSDGpgpgGWELPGGG------------VEPGET----PEEAAVREVREETGLDVEVLRLLGVYE 67

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 964748907 132 LTRIHYKAQSDGIWgeheidYILLVRKNVTLNPDPNEIKSYCYVS 176
Cdd:cd02883   68 FPDPDEGRHVVVLV------FLARVVGGEPPPLDDEEISEVRWVP 106
 
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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