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Conserved domains on  [gi|281362205|ref|NP_001163673|]
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Isopentenyl-diphosphate delta isomerase, isoform B [Drosophila melanogaster]

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

 Zoom to residue level

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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 ...
 48-256 6.49e-85

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: 253.50  E-value: 6.49e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  48 KEQCILVDANDQAIGAASKADCHRVHPETNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYEIEQE 127
Cdd:PLN02552  22 EDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPN 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 128 RQER-------NAQGIRVAAQRRLNYELGIPTEELQPQDFRYLTRIHY--ADT----GDGVWGEHEIDYILFLQK--DVT 192
Cdd:PLN02552 102 EVDReselidgNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYkaADDvthgPDGKWGEHELDYLLFIRPvrDVK 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362205 193 LRPNSNEVSEVRYLRRDKIDEAVAKFSA-PLTPWFSLILQHRLKLWWDNLHQLEQFEDLSNIQRF 256
Cdd:PLN02552 182 VNPNPDEVADVKYVNREELKEMMRKESGlKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 48-256 6.49e-85

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 253.50  E-value: 6.49e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  48 KEQCILVDANDQAIGAASKADCHRVHPETNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYEIEQE 127
Cdd:PLN02552  22 EDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPN 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 128 RQER-------NAQGIRVAAQRRLNYELGIPTEELQPQDFRYLTRIHY--ADT----GDGVWGEHEIDYILFLQK--DVT 192
Cdd:PLN02552 102 EVDReselidgNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYkaADDvthgPDGKWGEHELDYLLFIRPvrDVK 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362205 193 LRPNSNEVSEVRYLRRDKIDEAVAKFSA-PLTPWFSLILQHRLKLWWDNLHQLEQFEDLSNIQRF 256
Cdd:PLN02552 182 VNPNPDEVADVKYVNREELKEMMRKESGlKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 50-231 2.99e-78

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: 233.16  E-value: 2.99e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  50 QCILVDANDQAIGAASKADCHRvhpetNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYeieqerq 129
Cdd:cd02885    1 EVILVDEDDNPIGTAEKLEAHR-----KGTLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLP------- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 130 ernAQGIRVAAQRRLNYELGIPteelqPQDFRYLTRIHYADTGDGVWGEHEIDYILFLQKDVTLRPNSNEVSEVRYLRRD 209
Cdd:cd02885   69 ---GEGVEDAAQRRLREELGIP-----VCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLE 140

                        170       180
                 ....*....|....*....|..
gi 281362205 210 KIDEAVAKFSAPLTPWFSLILQ 231
Cdd:cd02885  141 ELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 51-230 7.27e-63

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: 194.10  E-value: 7.27e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205   51 CILVDANDQAIGAASKADCHrvhpeTNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYeieqerqe 130
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVH-----LQETPLHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  131 rnaqGIRVAAQRRLNYELGIPTEELqpqDFRYLTRIHY-ADtgDGVWGEHEIDYILFLQKDVTLRPNsNEVSEVRYLRRD 209
Cdd:TIGR02150  68 ----GELEAAIRRLRHELGIPADDV---PLTVLPRFSYrAR--DDAWGEHELCPVFFARANVDLNPN-PEVAEYRWVSLE 137

                         170       180
                  ....*....|....*....|.
gi 281362205  210 KIDEAVAKFSAPLTPWFSLIL 230
Cdd:TIGR02150 138 ELKEILAKPWAGFSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 49-229 1.31e-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: 157.67  E-value: 1.31e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  49 EQCILVDANDQAIGAASKADCHRvhpetnDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYEieqer 128
Cdd:COG1443    2 ELVDLVDEDGRPIGTAERAEVHR------KGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG----- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 129 qernaQGIRVAAQRRLNYELGIPTEElqpqDFRYLTRIHYADTGDGVWGEHEIDYILFLQKDVTLRPNSNEVSEVRYLRR 208
Cdd:COG1443   71 -----ETYEEAAVRELEEELGITVDD----DLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTL 141

                        170       180
                 ....*....|....*....|.
gi 281362205 209 DKIDEAVAKFSAPLTPWFSLI 229
Cdd:COG1443  142 EELLALLEAGPEAFTPWFRLY 162
NUDIX pfam00293
NUDIX domain;
80-226 1.79e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 70.98  E-value: 1.79e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205   80 KLHRAFSVFLFNSQGEMLVQKRSshKITFPNtytnaCCSHPLYEIEQerqernAQGIRVAAQRRLNYELGIPTEELqpqd 159
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPG-----WWSLPGGKVEP------GETPEEAARRELEEETGLEPELL---- 63

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  160 fRYLTRIHYADTGDGVWG-EHEIDYILFLQKDVTLRPNSN-EVSEVRYLRRDKI-DEAVAKFSAPLTPWF 226
Cdd:pfam00293  64 -ELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVPLEELlLLKLAPGDRKLLPWL 132
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 48-256 6.49e-85

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 253.50  E-value: 6.49e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  48 KEQCILVDANDQAIGAASKADCHRVHPETNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYEIEQE 127
Cdd:PLN02552  22 EDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPN 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 128 RQER-------NAQGIRVAAQRRLNYELGIPTEELQPQDFRYLTRIHY--ADT----GDGVWGEHEIDYILFLQK--DVT 192
Cdd:PLN02552 102 EVDReselidgNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYkaADDvthgPDGKWGEHELDYLLFIRPvrDVK 181

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362205 193 LRPNSNEVSEVRYLRRDKIDEAVAKFSA-PLTPWFSLILQHRLKLWWDNLHQLEQFEDLSNIQRF 256
Cdd:PLN02552 182 VNPNPDEVADVKYVNREELKEMMRKESGlKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 50-231 2.99e-78

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: 233.16  E-value: 2.99e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  50 QCILVDANDQAIGAASKADCHRvhpetNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYeieqerq 129
Cdd:cd02885    1 EVILVDEDDNPIGTAEKLEAHR-----KGTLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLP------- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 130 ernAQGIRVAAQRRLNYELGIPteelqPQDFRYLTRIHYADTGDGVWGEHEIDYILFLQKDVTLRPNSNEVSEVRYLRRD 209
Cdd:cd02885   69 ---GEGVEDAAQRRLREELGIP-----VCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLE 140

                        170       180
                 ....*....|....*....|..
gi 281362205 210 KIDEAVAKFSAPLTPWFSLILQ 231
Cdd:cd02885  141 ELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 51-230 7.27e-63

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: 194.10  E-value: 7.27e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205   51 CILVDANDQAIGAASKADCHrvhpeTNDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYeieqerqe 130
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVH-----LQETPLHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  131 rnaqGIRVAAQRRLNYELGIPTEELqpqDFRYLTRIHY-ADtgDGVWGEHEIDYILFLQKDVTLRPNsNEVSEVRYLRRD 209
Cdd:TIGR02150  68 ----GELEAAIRRLRHELGIPADDV---PLTVLPRFSYrAR--DDAWGEHELCPVFFARANVDLNPN-PEVAEYRWVSLE 137

                         170       180
                  ....*....|....*....|.
gi 281362205  210 KIDEAVAKFSAPLTPWFSLIL 230
Cdd:TIGR02150 138 ELKEILAKPWAGFSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 49-229 1.31e-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: 157.67  E-value: 1.31e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  49 EQCILVDANDQAIGAASKADCHRvhpetnDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLYEieqer 128
Cdd:COG1443    2 ELVDLVDEDGRPIGTAERAEVHR------KGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG----- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 129 qernaQGIRVAAQRRLNYELGIPTEElqpqDFRYLTRIHYADTGDGVWGEHEIDYILFLQKDVTLRPNSNEVSEVRYLRR 208
Cdd:COG1443   71 -----ETYEEAAVRELEEELGITVDD----DLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTL 141

                        170       180
                 ....*....|....*....|.
gi 281362205 209 DKIDEAVAKFSAPLTPWFSLI 229
Cdd:COG1443  142 EELLALLEAGPEAFTPWFRLY 162
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
49-232 1.68e-40

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 137.79  E-value: 1.68e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  49 EQCILVDANDQAIGAASKADCHrvHPETndvKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLyeieqeR 128
Cdd:PRK03759   6 ELVVLLDEQGVPTGTAEKAAAH--TADT---PLHLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQ------P 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 129 QERNAQgirvAAQRRLNYELGIPTEELQPQ--DFRYltrihYADTGDGVWgEHEIDYILFLQKDVTLRPNSNEVSEVRYL 206
Cdd:PRK03759  75 GESLED----AVIRRCREELGVEITDLELVlpDFRY-----RATDPNGIV-ENEVCPVFAARVTSALQPNPDEVMDYQWV 144

                        170       180
                 ....*....|....*....|....*.
gi 281362205 207 RRDKIDEAVAKFSAPLTPWFSLILQH 232
Cdd:PRK03759 145 DPADLLRAVDATPWAFSPWMVLQAAN 170
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 54-206 5.73e-16

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: 72.59  E-value: 5.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  54 VDANDQAIGAASKADCHRvhpetnDVKLHRAFSVFLFNSQ-GEMLVQKRSSHKITFPNTYTNACCSHplYEIEQERQErn 132
Cdd:cd04692    4 VDEDGRPIGVATRSEVHR------QGLWHRTVHVWLVNPEeGRLLLQKRSANKDDFPGLWDISAAGH--IDAGETYEE-- 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281362205 133 aqgirvAAQRRLNYELGIpteELQPQDFRYLTRIHYADTGDGVWGeHEIDYILFLQKDV---TLRPNSNEVSEVRYL 206
Cdd:cd04692   74 ------AAVRELEEELGL---TVSPEDLIFLGVIREEVIGGDFID-NEFVHVYLYETDRpleEFKLQPEEVAGVVFV 140
NUDIX pfam00293
NUDIX domain;
80-226 1.79e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 70.98  E-value: 1.79e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205   80 KLHRAFSVFLFNSQGEMLVQKRSshKITFPNtytnaCCSHPLYEIEQerqernAQGIRVAAQRRLNYELGIPTEELqpqd 159
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPG-----WWSLPGGKVEP------GETPEEAARRELEEETGLEPELL---- 63

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  160 fRYLTRIHYADTGDGVWG-EHEIDYILFLQKDVTLRPNSN-EVSEVRYLRRDKI-DEAVAKFSAPLTPWF 226
Cdd:pfam00293  64 -ELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVPLEELlLLKLAPGDRKLLPWL 132
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 51-224 7.17e-14

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: 67.26  E-value: 7.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  51 CILVDANDQAIGAASKADCHRvhpetnDVKLHRAFSVFLFNSQGEMLVQKRSSHKITFPNtYTNACCSHPLYEIEQerqe 130
Cdd:cd04697    1 VDIVDENNEVVGAATRAEMRR------QKLIHRATYIVVRNAAGRLLVQKRTMDKDYCPG-YLDPATGGVVGAGES---- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 131 rnaqgIRVAAQRRLNYELGIpteelQPQDFRYLTRIHYADTGDGVWGE-HEIDYilflqkDVTLRPNSNEVSEVRYLRRD 209
Cdd:cd04697   70 -----YEENARRELEEELGI-----DGVPLRPLFTFYYEDDRSRVWGAlFECVY------DGPLKLQPEEVAEVDWMSED 133

                        170
                 ....*....|....*
gi 281362205 210 KIDEAVAKfsAPLTP 224
Cdd:cd04697  134 EILQAARG--EEFTP 146
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 82-213 3.47e-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: 62.54  E-value: 3.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  82 HRAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPLY-EIEQErqernaqgirvAAQRRLNYELGIpteELQPQDF 160
Cdd:cd04693   29 HLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAgETSLE-----------AAIRELKEELGI---DLDADEL 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 281362205 161 RYLTRIHYadtgdgvwgEHEIDYILFLQKDV---TLRPNSNEVSEVRYLRRDKIDE 213
Cdd:cd04693   95 RPILTIRF---------DNGFDDIYLFRKDVdieDLTLQKEEVQDVKWVTLEEILE 141
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 83-172 2.33e-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: 39.89  E-value: 2.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  83 RAFSVFLFNSQGEMLVQKRSSHKITFPNTYTNACCSHPL----YEieqerqernaqgirVAAQRRLNYELGIpteELQPQ 158
Cdd:cd24154    3 RVVNAFLINSQGQLWIPRRTADKRIFPLALDMSVGGHVSsgetYE--------------QAFVRELQEELNL---DLDQL 65

                         90
                 ....*....|....
gi 281362205 159 DFRYLTRIHYADTG 172
Cdd:cd24154   66 SYRVLGKLTPYEHG 79
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 53-219 1.49e-03

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 38.63  E-value: 1.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  53 LVDANDQAIGAASK----ADCHRvhpetndvklHRAFSVFLFNSQGEMLVQKRSSHKITFPNtYTNACCSHPLYEIEQer 128
Cdd:PRK15393  14 IVNENNEVIAQASReqmrAQCLR----------HRATYIVVHDGMGKILVQRRTETKDFLPG-MLDATAGGVVQAGEQ-- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 129 qernaqgIRVAAQRRLNYELGIPTEELQPQDFRYltrihYADTGDGVWGEheidyiLF---------LQKDvtlrpnsnE 199
Cdd:PRK15393  81 -------LLESARREAEEELGIAGVPFAEHGQFY-----FEDENCRVWGA------LFscvshgpfaLQEE--------E 134

                        170       180
                 ....*....|....*....|
gi 281362205 200 VSEVRYLRRDKIDEAVAKFS 219
Cdd:PRK15393 135 VSEVCWMTPEEITARCDEFT 154
PLN02791 PLN02791
Nudix hydrolase homolog
 70-225 1.72e-03

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 39.42  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205  70 HRVHpetNDVKLHRAFSVFLF-NSQGEMLVQKRSSHKITFPNtytnaccshpLYEIEQERQERNAQGIRVAAQRRLNYEL 148
Cdd:PLN02791  23 GEVH---RDGDYHRAVHVWIYsESTQELLLQRRADCKDSWPG----------QWDISSAGHISAGDTSLLSAQRELEEEL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362205 149 GIpteeLQPQD-----FRYLTRIHyadTGDGVWGEHEIDYILFLqkdVTLRP--------NSNEVSEVRYLRRDKIDEAV 215
Cdd:PLN02791  90 GI----ILPKDafellFVFLQECV---INDGKFINNEYNDVYLV---TTLDPipleaftlQESEVSAVKYMSIEEYKSAL 159

                        170
                 ....*....|
gi 281362205 216 AKFSAPLTPW 225
Cdd:PLN02791 160 AKEDPAYVPY 169
 
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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