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Conserved domains on  [gi|1263710241|gb|PGC67608|]
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NUDIX domain-containing protein [Bacillus safensis]

Protein Classification

NUDIX hydrolase( domain architecture ID 10140399)

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 cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 6-148 2.57e-53

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: 167.35  E-value: 2.57e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   6 LRIFNDQHETIGAAARSVVHAQGHWHETFHFWLLKKEhnTVYLYFQLRSPAKKDFPSLFDITAAGHLLADEQP-SDGLRE 84
Cdd:cd04692     1 LDIVDEDGRPIGVATRSEVHRQGLWHRTVHVWLVNPE--EGRLLLQKRSANKDDFPGLWDISAAGHIDAGETYeEAAVRE 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1263710241  85 VEEELGLSIPFENLTFAGVIQDEIHMPSFIDREFCHVYLYMNQVEHMEVHLQKEEVAGLYRAKL 148
Cdd:cd04692    79 LEEELGLTVSPEDLIFLGVIREEVIGGDFIDNEFVHVYLYETDRPLEEFKLQPEEVAGVVFVDL 142
 
Name Accession Description Interval E-value
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 6-148 2.57e-53

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: 167.35  E-value: 2.57e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   6 LRIFNDQHETIGAAARSVVHAQGHWHETFHFWLLKKEhnTVYLYFQLRSPAKKDFPSLFDITAAGHLLADEQP-SDGLRE 84
Cdd:cd04692     1 LDIVDEDGRPIGVATRSEVHRQGLWHRTVHVWLVNPE--EGRLLLQKRSANKDDFPGLWDISAAGHIDAGETYeEAAVRE 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1263710241  85 VEEELGLSIPFENLTFAGVIQDEIHMPSFIDREFCHVYLYMNQVEHMEVHLQKEEVAGLYRAKL 148
Cdd:cd04692    79 LEEELGLTVSPEDLIFLGVIREEVIGGDFIDNEFVHVYLYETDRPLEEFKLQPEEVAGVVFVDL 142
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 4-158 7.19e-33

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: 115.68  E-value: 7.19e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   4 EKLRIFNDQHETIGAAARSVVHAQGHWHETFHFWLLKKEHNtvyLYFQLRSPAKKDFPSLFDITAAGHLLADEQPSD-GL 82
Cdd:COG1443     2 ELVDLVDEDGRPIGTAERAEVHRKGLLHRAFSVFVFNSDGR---LLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEaAV 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1263710241  83 REVEEELGLSIPfENLTFAGVIQDEIHMPS-FIDREFCHVYLYmnqVEHMEVHLQKEEVAGLYRAKLLDAQQLLTGT 158
Cdd:COG1443    79 RELEEELGITVD-DDLRPLGTFRYRAVDANgLVENEFCHVFVA---RLDGPLTPQPEEVAEVRWVTLEELLALLEAG 151
PLN02791 PLN02791
Nudix hydrolase homolog
 1-141 1.16e-14

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 71.77  E-value: 1.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   1 MEHEKLRIFNDQHETIGAA-ARSVVHAQGHWHETFHFWLLKKehNTVYLYFQLRSPAKKDFPSLFDITAAGHLLA-DEQP 78
Cdd:PLN02791    1 MMEEHLDVLTAAGEKTGVSkPRGEVHRDGDYHRAVHVWIYSE--STQELLLQRRADCKDSWPGQWDISSAGHISAgDTSL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1263710241  79 SDGLREVEEELGLSIPFENLTFAGVIQDE--IHMPSFIDREFCHVYLyMNQVEHMEVH---LQKEEVA 141
Cdd:PLN02791   79 LSAQRELEEELGIILPKDAFELLFVFLQEcvINDGKFINNEYNDVYL-VTTLDPIPLEaftLQESEVS 145
NUDIX pfam00293
NUDIX domain;
56-143 6.21e-03

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 35.54  E-value: 6.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  56 AKKDFPSLFdITAAGHLLADEQPSDG-LREVEEELGLSIpfENLTFAGVIQDEI-HMPSFIDREFcHVYLYMNQVEHMEV 133
Cdd:pfam00293  23 SKKPFPGWW-SLPGGKVEPGETPEEAaRRELEEETGLEP--ELLELLGSLHYLApFDGRFPDEHE-ILYVFLAEVEGELE 98

                          90
                  ....*....|
gi 1263710241 134 HLQKEEVAGL 143
Cdd:pfam00293  99 PDPDGEVEEV 108
 
Name Accession Description Interval E-value
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 6-148 2.57e-53

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: 167.35  E-value: 2.57e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   6 LRIFNDQHETIGAAARSVVHAQGHWHETFHFWLLKKEhnTVYLYFQLRSPAKKDFPSLFDITAAGHLLADEQP-SDGLRE 84
Cdd:cd04692     1 LDIVDEDGRPIGVATRSEVHRQGLWHRTVHVWLVNPE--EGRLLLQKRSANKDDFPGLWDISAAGHIDAGETYeEAAVRE 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1263710241  85 VEEELGLSIPFENLTFAGVIQDEIHMPSFIDREFCHVYLYMNQVEHMEVHLQKEEVAGLYRAKL 148
Cdd:cd04692    79 LEEELGLTVSPEDLIFLGVIREEVIGGDFIDNEFVHVYLYETDRPLEEFKLQPEEVAGVVFVDL 142
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 4-158 7.19e-33

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: 115.68  E-value: 7.19e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   4 EKLRIFNDQHETIGAAARSVVHAQGHWHETFHFWLLKKEHNtvyLYFQLRSPAKKDFPSLFDITAAGHLLADEQPSD-GL 82
Cdd:COG1443     2 ELVDLVDEDGRPIGTAERAEVHRKGLLHRAFSVFVFNSDGR---LLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEaAV 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1263710241  83 REVEEELGLSIPfENLTFAGVIQDEIHMPS-FIDREFCHVYLYmnqVEHMEVHLQKEEVAGLYRAKLLDAQQLLTGT 158
Cdd:COG1443    79 RELEEELGITVD-DDLRPLGTFRYRAVDANgLVENEFCHVFVA---RLDGPLTPQPEEVAEVRWVTLEELLALLEAG 151
PLN02791 PLN02791
Nudix hydrolase homolog
 1-141 1.16e-14

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 71.77  E-value: 1.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   1 MEHEKLRIFNDQHETIGAA-ARSVVHAQGHWHETFHFWLLKKehNTVYLYFQLRSPAKKDFPSLFDITAAGHLLA-DEQP 78
Cdd:PLN02791    1 MMEEHLDVLTAAGEKTGVSkPRGEVHRDGDYHRAVHVWIYSE--STQELLLQRRADCKDSWPGQWDISSAGHISAgDTSL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1263710241  79 SDGLREVEEELGLSIPFENLTFAGVIQDE--IHMPSFIDREFCHVYLyMNQVEHMEVH---LQKEEVA 141
Cdd:PLN02791   79 LSAQRELEEELGIILPKDAFELLFVFLQEcvINDGKFINNEYNDVYL-VTTLDPIPLEaftLQESEVS 145
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 26-155 9.14e-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: 467575 [Multi-domain]  Cd Length: 157  Bit Score: 66.01  E-value: 9.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  26 AQGHWHETFHFWLLKKEHNtvYLyFQLRSPAKKDFPSLFDITAAGHLLADEQPSDG-LREVEEELGLSIPFENLTFagvI 104
Cdd:cd04693    24 PEGEYHLVVHVWIFNSDGE--IL-IQQRSPDKKGFPGMWEASTGGSVLAGETSLEAaIRELKEELGIDLDADELRP---I 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1263710241 105 QDEIHMPSFIDrefchVYLYMNQVEHMEVHLQKEEVAGlyrAKLLDAQQLL 155
Cdd:cd04693    98 LTIRFDNGFDD-----IYLFRKDVDIEDLTLQKEEVQD---VKWVTLEEIL 140
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
1-122 5.05e-08

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 50.74  E-value: 5.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   1 MEHEKLRIFNDQHETIGAAARSVVH-AQGHWHETFHFWLLkKEHNTVYLyfQLRSPAKKDFPSLFDITAAGHLLADEQPS 79
Cdd:PRK03759    3 METELVVLLDEQGVPTGTAEKAAAHtADTPLHLAFSCYLF-DADGRLLV--TRRALSKKTWPGVWTNSCCGHPQPGESLE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1263710241  80 DG-LREVEEELGLSIPFEnLTFAGVIQDEIHMPSFI-DREFCHVY 122
Cdd:PRK03759   80 DAvIRRCREELGVEITDL-ELVLPDFRYRATDPNGIvENEVCPVF 123
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 1-141 7.17e-06

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 44.79  E-value: 7.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241   1 MEHEKLRIFNDQHETIGAAARSVVHAQGHWHETFHFWLlkkeHNTV-YLYFQLRSPAKKDFPSLFDITAAGHLLADEQPS 79
Cdd:PRK15393    7 ASTEWVDIVNENNEVIAQASREQMRAQCLRHRATYIVV----HDGMgKILVQRRTETKDFLPGMLDATAGGVVQAGEQLL 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1263710241  80 DGL-REVEEELGLS-IPFENltfagviqdeiHMPSFIDREFCHVY-LYMNQVEHMEVHLQKEEVA 141
Cdd:PRK15393   83 ESArREAEEELGIAgVPFAE-----------HGQFYFEDENCRVWgALFSCVSHGPFALQEEEVS 136
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 11-93 1.14e-05

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: 43.76  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  11 DQH-ETIGAAARSVVHAQGHWHE-TFHFWLLKkehnTVYLYFQLRSPAKKDFPSLFDITAAGHLLADEQPSDGL-REVEE 87
Cdd:cd04697     5 DENnEVVGAATRAEMRRQKLIHRaTYIVVRNA----AGRLLVQKRTMDKDYCPGYLDPATGGVVGAGESYEENArRELEE 80


                  ....*.
gi 1263710241  88 ELGLSI 93
Cdd:cd04697    81 ELGIDG 86
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 10-123 6.69e-05

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: 41.71  E-value: 6.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  10 NDQHETIGAAARSVVHAQG-HWHETFHFWLLKKEHNtvyLYFQLRSPAKKDFPSLFDITAAGHLLADEQPSD-GLREVEE 87
Cdd:cd02885     6 DEDDNPIGTAEKLEAHRKGtLLHRAFSVFLFNSKGE---LLLQRRALSKYTWPGLWTNTCCSHPLPGEGVEDaAQRRLRE 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1263710241  88 ELGlsIPFENLTFAGVIQ-----DEIhmpsFIDREFCHVYL 123
Cdd:cd02885    83 ELG--IPVCDLEELPRFRyratdDNG----LVEHEIDHVFV 117
NUDIX_Hydrolase cd04683
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 38-106 1.46e-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: 467566 [Multi-domain]  Cd Length: 137  Bit Score: 37.58  E-value: 1.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  38 LLKKEHNTVYLYFQLRSPAkkdfpslfditaaGHLLADEQPSDGL-REVEEELGLSIPFENLTFAGVIQD 106
Cdd:cd04683    14 LLLRRANTGYDDGWWHLPA-------------GHVEAGETVRAAAvREAKEELGVEIDPEDLRLVHTMHR 70
NUDIX pfam00293
NUDIX domain;
56-143 6.21e-03

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 35.54  E-value: 6.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1263710241  56 AKKDFPSLFdITAAGHLLADEQPSDG-LREVEEELGLSIpfENLTFAGVIQDEI-HMPSFIDREFcHVYLYMNQVEHMEV 133
Cdd:pfam00293  23 SKKPFPGWW-SLPGGKVEPGETPEEAaRRELEEETGLEP--ELLELLGSLHYLApFDGRFPDEHE-ILYVFLAEVEGELE 98

                          90
                  ....*....|
gi 1263710241 134 HLQKEEVAGL 143
Cdd:pfam00293  99 PDPDGEVEEV 108
 
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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