NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488173139|ref|WP_002244347|]
View 

NUDIX hydrolase family protein [Neisseria meningitidis]

Protein Classification

NUDIX hydrolase( domain architecture ID 13599039)

NUDIX hydrolase family protein may catalyze the hydrolysis of nucleoside diphosphates linked to other moieties (X); it would require a divalent cation, such as Mg2+ or Mn2+ for its activity; contains a DUF4743 domain

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

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
 123-272 1.27e-62

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


:

Pssm-ID: 467544  Cd Length: 153  Bit Score: 194.64  E-value: 1.27e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 123 PFGLLSRAVHLNGLTESDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRPVSQ 202
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLRLWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPAAG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488173139 203 LHSLRSVS--RGVHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLDAMLSGNMMHDAQLVTLDAFCR 272
Cdd:cd03676   81 RVSYFYRSdeGGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLDFLIR 152
DUF4743 super family cl38476
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
 94-125 2.74e-03

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


The actual alignment was detected with superfamily member pfam15916:

Pssm-ID: 406365  Cd Length: 119  Bit Score: 36.79  E-value: 2.74e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 488173139   94 LLDGWRNECFDLTDG-GGNPLFTLERAAFRPFG 125
Cdd:pfam15916  84 TLPGWRDECYEVRASfGDPPLFKMERAAAPLFG 116
 
Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
 123-272 1.27e-62

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


Pssm-ID: 467544  Cd Length: 153  Bit Score: 194.64  E-value: 1.27e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 123 PFGLLSRAVHLNGLTESDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRPVSQ 202
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLRLWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPAAG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488173139 203 LHSLRSVS--RGVHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLDAMLSGNMMHDAQLVTLDAFCR 272
Cdd:cd03676   81 RVSYFYRSdeGGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLDFLIR 152
PLN02839 PLN02839
nudix hydrolase
 93-276 3.45e-29

nudix hydrolase


Pssm-ID: 178432 [Multi-domain]  Cd Length: 372  Bit Score: 113.96  E-value: 3.45e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139  93 GLLDGWRNECFDLTDGGGNP-LFTLERAAFRPFGLLSRAVHLNGLTESDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSG 171
Cdd:PLN02839 167 GIIPGIRNELYPVKPSFNAPvFFSLERAAAPYFGIKGYGVHMNGYVERDGQKFLWIGKRSLSKSTYPGMLDHLVAGGLPH 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 172 GEMPSEAVCRESSEEAGLDKTLLPLIRPVSQLHSLRSVSRGVHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLD 251
Cdd:PLN02839 247 GISCGENLVKECEEEAGISKAIADRAIAVGAVSYMDIDQYCFKRDVLFCYDLELPQDFVPKNQDGEVESFKLIPVAQVAN 326

                        170       180
                 ....*....|....*....|....*.
gi 488173139 252 AMLSGNMMHDA-QLVTLDAFCRYGLI 276
Cdd:PLN02839 327 VIRKTSFFKANcSLVIIDFLFRHGFI 352
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 103-256 8.36e-23

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: 91.80  E-value: 8.36e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 103 FDLTDGGGNPLFTLERAAFRPFGLLSRAVHLNgLTESDGRwhFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRE 182
Cdd:COG1443    4 VDLVDEDGRPIGTAERAEVHRKGLLHRAFSVF-VFNSDGR--LLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAAVRE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488173139 183 SSEEAGLdkTLLPLIRPVSQLHSLRSVSRG-VHNEILYVFDAVLPETFLPenQDGEVAGFEKMDIGGLLDAMLSG 256
Cdd:COG1443   81 LEEELGI--TVDDDLRPLGTFRYRAVDANGlVENEFCHVFVARLDGPLTP--QPEEVAEVRWVTLEELLALLEAG 151
NUDIX pfam00293
NUDIX domain;
136-254 9.66e-06

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 44.40  E-value: 9.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139  136 LTESDGRwhFWIGRRSPHKavdPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRPVSQLHSLRSVSRGVHn 215
Cdd:pfam00293  10 LLNEKGR--VLLVRRSKKP---FPGWWSLPGGKVEPGETPEEAARRELEEETGLEPELLELLGSLHYLAPFDGRFPDEH- 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 488173139  216 EILYVFDAVLPETFLPeNQDGEVAGFEKMDIGGLLDAML 254
Cdd:pfam00293  84 EILYVFLAEVEGELEP-DPDGEVEEVRWVPLEELLLLKL 121
DUF4743 pfam15916
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
 94-125 2.74e-03

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


Pssm-ID: 406365  Cd Length: 119  Bit Score: 36.79  E-value: 2.74e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 488173139   94 LLDGWRNECFDLTDG-GGNPLFTLERAAFRPFG 125
Cdd:pfam15916  84 TLPGWRDECYEVRASfGDPPLFKMERAAAPLFG 116
 
Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
 123-272 1.27e-62

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


Pssm-ID: 467544  Cd Length: 153  Bit Score: 194.64  E-value: 1.27e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 123 PFGLLSRAVHLNGLTESDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRPVSQ 202
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLRLWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPAAG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488173139 203 LHSLRSVS--RGVHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLDAMLSGNMMHDAQLVTLDAFCR 272
Cdd:cd03676   81 RVSYFYRSdeGGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLDFLIR 152
PLN02839 PLN02839
nudix hydrolase
 93-276 3.45e-29

nudix hydrolase


Pssm-ID: 178432 [Multi-domain]  Cd Length: 372  Bit Score: 113.96  E-value: 3.45e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139  93 GLLDGWRNECFDLTDGGGNP-LFTLERAAFRPFGLLSRAVHLNGLTESDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSG 171
Cdd:PLN02839 167 GIIPGIRNELYPVKPSFNAPvFFSLERAAAPYFGIKGYGVHMNGYVERDGQKFLWIGKRSLSKSTYPGMLDHLVAGGLPH 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 172 GEMPSEAVCRESSEEAGLDKTLLPLIRPVSQLHSLRSVSRGVHNEILYVFDAVLPETFLPENQDGEVAGFEKMDIGGLLD 251
Cdd:PLN02839 247 GISCGENLVKECEEEAGISKAIADRAIAVGAVSYMDIDQYCFKRDVLFCYDLELPQDFVPKNQDGEVESFKLIPVAQVAN 326

                        170       180
                 ....*....|....*....|....*.
gi 488173139 252 AMLSGNMMHDA-QLVTLDAFCRYGLI 276
Cdd:PLN02839 327 VIRKTSFFKANcSLVIIDFLFRHGFI 352
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 103-256 8.36e-23

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: 91.80  E-value: 8.36e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 103 FDLTDGGGNPLFTLERAAFRPFGLLSRAVHLNgLTESDGRwhFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRE 182
Cdd:COG1443    4 VDLVDEDGRPIGTAERAEVHRKGLLHRAFSVF-VFNSDGR--LLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAAVRE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488173139 183 SSEEAGLdkTLLPLIRPVSQLHSLRSVSRG-VHNEILYVFDAVLPETFLPenQDGEVAGFEKMDIGGLLDAMLSG 256
Cdd:COG1443   81 LEEELGI--TVDDDLRPLGTFRYRAVDANGlVENEFCHVFVARLDGPLTP--QPEEVAEVRWVTLEELLALLEAG 151
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 103-246 1.34e-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: 467574 [Multi-domain]  Cd Length: 142  Bit Score: 63.73  E-value: 1.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 103 FDLTDGGGNPLFTLERAAFRPFGLLSRAVHLNGLTESDGRWHFwiGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRE 182
Cdd:cd04692    1 LDIVDEDGRPIGVATRSEVHRQGLWHRTVHVWLVNPEEGRLLL--QKRSANKDDFPGLWDISAAGHIDAGETYEEAAVRE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488173139 183 SSEEAGLDKTLLPLIRpvsqLHSLRSVSRGVH---NEILYVFDAVLPETFL-PENQDGEVAGFEKMDI 246
Cdd:cd04692   79 LEEELGLTVSPEDLIF----LGVIREEVIGGDfidNEFVHVYLYETDRPLEeFKLQPEEVAGVVFVDL 142
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 104-273 6.84e-08

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: 51.08  E-value: 6.84e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 104 DLTDGGGNPLFTLERAAFRPFGLLSRAVHLNgLTESDGRwhFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRES 183
Cdd:cd04697    2 DIVDENNEVVGAATRAEMRRQKLIHRATYIV-VRNAAGR--LLVQKRTMDKDYCPGYLDPATGGVVGAGESYEENARREL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 184 SEEAGLDKtlLPLIRPVSQLHslrsvsRGVHNEI-LYVFDAVLPETFLPenQDGEVAGFEKMDIGGLLDAMLSGNMMHDa 262
Cdd:cd04697   79 EEELGIDG--VPLRPLFTFYY------EDDRSRVwGALFECVYDGPLKL--QPEEVAEVDWMSEDEILQAARGEEFTPD- 147

                        170
                 ....*....|.
gi 488173139 263 qlvTLDAFCRY 273
Cdd:cd04697  148 ---GRVALERY 155
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 145-196 1.90e-06

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: 46.05  E-value: 1.90e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488173139 145 FWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPL 196
Cdd:cd24154   16 LWIPRRTADKRIFPLALDMSVGGHVSSGETYEQAFVRELQEELNLDLDQLSY 67
NUDIX pfam00293
NUDIX domain;
136-254 9.66e-06

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 44.40  E-value: 9.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139  136 LTESDGRwhFWIGRRSPHKavdPNKLDNTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRPVSQLHSLRSVSRGVHn 215
Cdd:pfam00293  10 LLNEKGR--VLLVRRSKKP---FPGWWSLPGGKVEPGETPEEAARRELEEETGLEPELLELLGSLHYLAPFDGRFPDEH- 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 488173139  216 EILYVFDAVLPETFLPeNQDGEVAGFEKMDIGGLLDAML 254
Cdd:pfam00293  84 EILYVFLAEVEGELEP-DPDGEVEEVRWVPLEELLLLKL 121
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 101-260 1.78e-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: 467575 [Multi-domain]  Cd Length: 157  Bit Score: 44.05  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 101 ECFDLTDGGGNPL-FTLERAAFRPFGLLSRAVH---LNglteSDGRwhFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPS 176
Cdd:cd04693    1 ELWDLYDENRNKTgRTHRRGEPLPEGEYHLVVHvwiFN----SDGE--ILIQQRSPDKKGFPGMWEASTGGSVLAGETSL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 177 EAVCRESSEEAGLDKTLlplirpvSQLHSLRSVsrgVHNEIL---YVFDAVLPETFLpENQDGEVAGFEKMDIGGLLDAM 253
Cdd:cd04693   75 EAAIRELKEELGIDLDA-------DELRPILTI---RFDNGFddiYLFRKDVDIEDL-TLQKEEVQDVKWVTLEEILEMI 143


                 ....*..
gi 488173139 254 LSGNMMH 260
Cdd:cd04693  144 ESGEFIP 150
NUDIX_Hydrolase cd02883
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 144-245 4.07e-05

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: 42.01  E-value: 4.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 144 HFWIGRRSPHKAvdPNKLDnTAAGGVSGGEMPSEAVCRESSEEAGLDktlLPLIRPVSQLHSLRsvSRGVHNEILYVFDA 223
Cdd:cd02883   13 RVLLVRRSDGPG--PGGWE-LPGGGVEPGETPEEAAVREVREETGLD---VEVLRLLGVYEFPD--PDEGRHVVVLVFLA 84

                         90       100
                 ....*....|....*....|..
gi 488173139 224 VLPETFLPENQDGEVAGFEKMD 245
Cdd:cd02883   85 RVVGGEPPPLDDEEISEVRWVP 106
NUDIX_ADPRase cd24160
Adp-ribose pyrophosphatase (ADPRase) found in Thermus thermophilus, and similar proteins; ...
 150-238 6.91e-05

Adp-ribose pyrophosphatase (ADPRase) found in Thermus thermophilus, and similar proteins; ADP-ribose pyrophosphatase (ADPRase) such as found in extreme thermophile Thermus thermophilus (TtADPRase) catalyzes the hydrolysis of ADPR to AMP and ribose 5'-phosphate in the presence of Mg2+ and Zn2+ ions. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site.


Pssm-ID: 467608 [Multi-domain]  Cd Length: 151  Bit Score: 42.11  E-value: 6.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 150 RSPHKAVDPNKLDnTAAGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIRpvsqlhslRSVSRGVHNEILYVFDAV-LPET 228
Cdd:cd24160   38 RQMRPAVGAATLE-IPAGLIDPGETPEEAARRELAEETGLSGDLTYLTR--------FYVSPGFCDEKLHVFLAEnLREV 108

                         90
                 ....*....|
gi 488173139 229 FLPENQDGEV 238
Cdd:cd24160  109 EAHPDEDEAI 118
NUDIX_DHNTPase_like cd04664
dihydroneopterin hydrolase; DHNTP pyrophosphatase (DHNTPase) catalyzes the hydrolysis of ...
 166-232 8.13e-05

dihydroneopterin hydrolase; DHNTP pyrophosphatase (DHNTPase) catalyzes the hydrolysis of dihydroneopterin triphosphate (DHNTP) to dihydroneopterin monophosphate (DHNMP) and pyrophosphate,the second step in the pterin branch of the folate synthesis pathway in bacteria. 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: 467549 [Multi-domain]  Cd Length: 132  Bit Score: 41.47  E-value: 8.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488173139 166 AGGVSGGEMPSEAVCRESSEEAGLDKTLLPLIR-PVSQLHSLRSVSR-GVHNEILYVFDAVLPETFLPE 232
Cdd:cd04664   32 TGGIEDGETPWQAALRELKEETGLDPLELQLIDlNVSNFYEIFDDWRpGVTVNTEHVFAVEVPEEQPIR 100
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
105-256 9.00e-05

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 42.26  E-value: 9.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 105 LTDGGGNPLFTLER-AAFRPFGLLSRA--VHLnglTESDGRwhFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPSEAVCR 181
Cdd:PRK03759  10 LLDEQGVPTGTAEKaAAHTADTPLHLAfsCYL---FDADGR--LLVTRRALSKKTWPGVWTNSCCGHPQPGESLEDAVIR 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488173139 182 ESSEEAGLDKTLLPLIRPVsqlHSLRSV-SRG-VHNEILYVFDAVLPETFLPEnqDGEVAGFEKMDIGGLLDAMLSG 256
Cdd:PRK03759  85 RCREELGVEITDLELVLPD---FRYRATdPNGiVENEVCPVFAARVTSALQPN--PDEVMDYQWVDPADLLRAVDAT 156
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 144-256 2.07e-04

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


Pssm-ID: 440260 [Multi-domain]  Cd Length: 143  Bit Score: 40.79  E-value: 2.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 144 HFWIGRRSPHkAVDPNKLDnTAAGGVSGGEMPSEAVCRESSEEAGLDktllplIRPVSQLHSLRSVSRGVHNEILYVFDA 223
Cdd:COG0494   26 RVLLVRRYRY-GVGPGLWE-FPGGKIEPGESPEEAALRELREETGLT------AEDLELLGELPSPGYTDEKVHVFLARG 97

                         90       100       110
                 ....*....|....*....|....*....|...
gi 488173139 224 VLPETFLPENQDGEVAGFEKMDIGGLLDAMLSG 256
Cdd:COG0494   98 LGPGEEVGLDDEDEFIEVRWVPLDEALALVTAG 130
NUDIX_ADPRase cd04691
ADP-ribose pyrophosphatase and similar proteins; ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1. ...
 135-260 3.46e-04

ADP-ribose pyrophosphatase and similar proteins; ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer.


Pssm-ID: 467573 [Multi-domain]  Cd Length: 122  Bit Score: 39.59  E-value: 3.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 135 GLTESDGRWHFwigrrsPHKAVDPNKLDNTAAGG-VSGGEMPSEAVCRESSEEAGLDktllplIRPVSQLhSLRS-VSRG 212
Cdd:cd04691    6 GVVVKEGKVLL------VKRAYGPGKGRWTLPGGfVEEGETLDEAIVREVLEETGID------AKPVGII-GVRSgVIRD 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488173139 213 VHNEILYVF--DAVLPEtflPENQDGEVAGFEKMDIGGLLDAMLSGNMMH 260
Cdd:cd04691   73 GKSDNYVVFllEYVGGE---PKPDERENSEAGFLTLEEALANEDIADMSR 119
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 101-189 2.04e-03

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 38.24  E-value: 2.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 101 ECFDLTDGGGNPLFTLERAAFRPFGLLSRA----VHlngltesDGRWHFWIGRRSPHKAVDPNKLDNTAAGGVSGGEMPS 176
Cdd:PRK15393  10 EWVDIVNENNEVIAQASREQMRAQCLRHRAtyivVH-------DGMGKILVQRRTETKDFLPGMLDATAGGVVQAGEQLL 82

                         90
                 ....*....|...
gi 488173139 177 EAVCRESSEEAGL 189
Cdd:PRK15393  83 ESARREAEEELGI 95
YjhB COG1051
ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism];
166-254 2.16e-03

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


Pssm-ID: 440671 [Multi-domain]  Cd Length: 125  Bit Score: 37.27  E-value: 2.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488173139 166 AGGVSGGEMPSEAVCRESSEEAGLDktllplIRPVSQLHSLRSVSRGVHNEILYVFDAVLPEtflpENQDGEVAGFEKMD 245
Cdd:COG1051   38 GGKVEPGETPEEAALRELREETGLE------VEVLELLGVFDHPDRGHVVSVAFLAEVLSGE----PRADDEIDEARWFP 107


                 ....*....
gi 488173139 246 IGGLLDAML 254
Cdd:COG1051  108 LDELPELAF 116
DUF4743 pfam15916
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
 94-125 2.74e-03

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


Pssm-ID: 406365  Cd Length: 119  Bit Score: 36.79  E-value: 2.74e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 488173139   94 LLDGWRNECFDLTDG-GGNPLFTLERAAFRPFG 125
Cdd:pfam15916  84 TLPGWRDECYEVRASfGDPPLFKMERAAAPLFG 116
NUDIX_ADPRase cd18880
ADP-ribose pyrophosphatase and similar proteins; ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1. ...
 166-206 4.45e-03

ADP-ribose pyrophosphatase and similar proteins; ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer.


Pssm-ID: 467591 [Multi-domain]  Cd Length: 126  Bit Score: 36.35  E-value: 4.45e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488173139 166 AGGVSGGEMPSEAVCRESSEEAGLDKTLLPL------IRPVSQLHSL 206
Cdd:cd18880   31 GGGQEHGETLPEALKRECLEETGLDVEVGDLlfvreyIGPNKPVHQV 77
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH