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Conserved domains on  [gi|1046870203|ref|XP_017456810|]
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peroxisomal coenzyme A diphosphatase NUDT7 isoform X5 [Rattus norvegicus]

Protein Classification

NUDIX hydrolase( domain architecture ID 10130767)

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; such as coenzyme A pyrophosphatase that hydrolyzes the pyrophosphate moiety of coenzyme A

CATH:  3.90.79.10
EC:  3.6.-.-
Gene Ontology:  GO:0016817|GO:0009132|GO:0046872
PubMed:  15581572|16378245
SCOP:  3000098

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUDIX_CoAse_Nudt7 cd03426
coenzyme A pyrophosphatase and similar proteins; Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1) ...
 63-196 1.22e-45

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


:

Pssm-ID: 467532 [Multi-domain]  Cd Length: 158  Bit Score: 149.57  E-value: 1.22e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  63 KYSVLLPLLARGEKLYLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEE--------------------NN 122
Cdd:cd03426     2 RAAVLIPLVEGDGELHVLLTKRASHLRSHPGQIAFPGGKREPGDESPVETALRETEEEiglppesvevlgrldplytpSG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1046870203 123 DLVTPVVGFLDPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSG--YHFVLHCFEYTDpetgskYLIKGMT 196
Cdd:cd03426    82 FVVTPFVGLLDDPPPLRPNPDEVAEVFTVPLSFLLDPEPRRYETFLRSGprGTYRVPFYPYEG------YVIWGLT 151
 
Name Accession Description Interval E-value
NUDIX_CoAse_Nudt7 cd03426
coenzyme A pyrophosphatase and similar proteins; Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1) ...
 63-196 1.22e-45

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


Pssm-ID: 467532 [Multi-domain]  Cd Length: 158  Bit Score: 149.57  E-value: 1.22e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  63 KYSVLLPLLARGEKLYLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEE--------------------NN 122
Cdd:cd03426     2 RAAVLIPLVEGDGELHVLLTKRASHLRSHPGQIAFPGGKREPGDESPVETALRETEEEiglppesvevlgrldplytpSG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1046870203 123 DLVTPVVGFLDPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSG--YHFVLHCFEYTDpetgskYLIKGMT 196
Cdd:cd03426    82 FVVTPFVGLLDDPPPLRPNPDEVAEVFTVPLSFLLDPEPRRYETFLRSGprGTYRVPFYPYEG------YVIWGLT 151
PRK10707 PRK10707
putative NUDIX hydrolase; Provisional
 66-206 1.81e-29

putative NUDIX hydrolase; Provisional


Pssm-ID: 182663  Cd Length: 190  Bit Score: 108.92  E-value: 1.81e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  66 VLLPLLARGEKLyLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEENN---------------D-----LV 125
Cdd:PRK10707   34 VLIPIVRRPQPT-LLLTQRSIHLRKHAGQVAFPGGAVDPTDASLIATALREAQEEVAippsavevigvlppvDsstgyQV 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203 126 TPVVGFLDPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSGYHFVLHCFEYTDpetgskYLIKGMTsklavlAAL 205
Cdd:PRK10707  113 TPVVGIIPPDLPYRANEDEVAAVFEMPLAEALHLGRYHPLDIYRRGQSHRVWLSWYEQ------YFVWGMT------AGI 180


                  .
gi 1046870203 206 I 206
Cdd:PRK10707  181 I 181
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 54-157 4.72e-07

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: 47.72  E-value: 4.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  54 TRYSHLSPSkySVLLPLLARGEklyLLFTVRSDKlRRAPGEVCFPGGKrdpVDADDT--ATALREAQEE---NNDLVTPV 128
Cdd:COG0494     7 SEPEHYRPA--VVVVLLDDDGR---VLLVRRYRY-GVGPGLWEFPGGK---IEPGESpeEAALRELREEtglTAEDLELL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1046870203 129 VGFLDPDFQAQ------------------PNADEVKDVFLVPLDYFL 157
Cdd:COG0494    78 GELPSPGYTDEkvhvflarglgpgeevglDDEDEFIEVRWVPLDEAL 124
NUDIX pfam00293
NUDIX domain;
71-154 7.79e-05

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 41.31  E-value: 7.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  71 LARGEKLYLLFTVRSDklRRAPGEVCFPGGKrdpVDADDT--ATALREAQEE-----NNDLVTPVVGFLDPDFQAQPNAD 143
Cdd:pfam00293   9 VLLNEKGRVLLVRRSK--KPFPGWWSLPGGK---VEPGETpeEAARRELEEEtglepELLELLGSLHYLAPFDGRFPDEH 83

                          90
                  ....*....|.
gi 1046870203 144 EVKDVFLVPLD 154
Cdd:pfam00293  84 EILYVFLAEVE 94
 
Name Accession Description Interval E-value
NUDIX_CoAse_Nudt7 cd03426
coenzyme A pyrophosphatase and similar proteins; Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1) ...
 63-196 1.22e-45

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


Pssm-ID: 467532 [Multi-domain]  Cd Length: 158  Bit Score: 149.57  E-value: 1.22e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  63 KYSVLLPLLARGEKLYLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEE--------------------NN 122
Cdd:cd03426     2 RAAVLIPLVEGDGELHVLLTKRASHLRSHPGQIAFPGGKREPGDESPVETALRETEEEiglppesvevlgrldplytpSG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1046870203 123 DLVTPVVGFLDPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSG--YHFVLHCFEYTDpetgskYLIKGMT 196
Cdd:cd03426    82 FVVTPFVGLLDDPPPLRPNPDEVAEVFTVPLSFLLDPEPRRYETFLRSGprGTYRVPFYPYEG------YVIWGLT 151
PRK10707 PRK10707
putative NUDIX hydrolase; Provisional
 66-206 1.81e-29

putative NUDIX hydrolase; Provisional


Pssm-ID: 182663  Cd Length: 190  Bit Score: 108.92  E-value: 1.81e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  66 VLLPLLARGEKLyLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEENN---------------D-----LV 125
Cdd:PRK10707   34 VLIPIVRRPQPT-LLLTQRSIHLRKHAGQVAFPGGAVDPTDASLIATALREAQEEVAippsavevigvlppvDsstgyQV 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203 126 TPVVGFLDPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSGYHFVLHCFEYTDpetgskYLIKGMTsklavlAAL 205
Cdd:PRK10707  113 TPVVGIIPPDLPYRANEDEVAAVFEMPLAEALHLGRYHPLDIYRRGQSHRVWLSWYEQ------YFVWGMT------AGI 180


                  .
gi 1046870203 206 I 206
Cdd:PRK10707  181 I 181
PLN02709 PLN02709
nudix hydrolase
 58-215 1.75e-24

nudix hydrolase


Pssm-ID: 178311  Cd Length: 222  Bit Score: 97.11  E-value: 1.75e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  58 HLSPSKYSVLLPLLA--RGEK--LYLLFTVRSDKLRRAPGEVCFPGGKRDPVDADDTATALREAQEE---NNDLVT---- 126
Cdd:PLN02709   28 HFPAKSSAVLVCLYQeqREDKneLRVILTKRSSTLSSHPGEVALPGGKRDEEDKDDIATALREAREEiglDPSLVTiisv 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203 127 -------------PVVGFL--DPDFQAQPNADEVKDVFLVPLDYFLCPQVYYQSHFTHSGYHFVLHCFEYTDPETGSKYL 191
Cdd:PLN02709  108 lepfvnkkgmsvaPVIGFLhdKKAFKPLPNPAEVEEIFDVPLEMFLKDKNKRAEEREHEGERYLLQYFDYYSEDKERNFI 187

                         170       180
                  ....*....|....*....|....
gi 1046870203 192 IKGMTSKLAVLAALIIFEKSPSFE 215
Cdd:PLN02709  188 IWALTAGILIRVASIVYQRLPEFQ 211
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 54-157 4.72e-07

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: 47.72  E-value: 4.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  54 TRYSHLSPSkySVLLPLLARGEklyLLFTVRSDKlRRAPGEVCFPGGKrdpVDADDT--ATALREAQEE---NNDLVTPV 128
Cdd:COG0494     7 SEPEHYRPA--VVVVLLDDDGR---VLLVRRYRY-GVGPGLWEFPGGK---IEPGESpeEAALRELREEtglTAEDLELL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1046870203 129 VGFLDPDFQAQ------------------PNADEVKDVFLVPLDYFL 157
Cdd:COG0494    78 GELPSPGYTDEkvhvflarglgpgeevglDDEDEFIEVRWVPLDEAL 124
NUDIX pfam00293
NUDIX domain;
71-154 7.79e-05

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 41.31  E-value: 7.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046870203  71 LARGEKLYLLFTVRSDklRRAPGEVCFPGGKrdpVDADDT--ATALREAQEE-----NNDLVTPVVGFLDPDFQAQPNAD 143
Cdd:pfam00293   9 VLLNEKGRVLLVRRSK--KPFPGWWSLPGGK---VEPGETpeEAARRELEEEtglepELLELLGSLHYLAPFDGRFPDEH 83

                          90
                  ....*....|.
gi 1046870203 144 EVKDVFLVPLD 154
Cdd:pfam00293  84 EILYVFLAEVE 94
NUDIX_AcylCoAdiphos_Nudt19 cd18870
Nucleoside diphosphate-linked moiety X)) motif 19; Acyl CoA diphosphohydrolase (also known as ...
 70-120 2.22e-03

Nucleoside diphosphate-linked moiety X)) motif 19; Acyl CoA diphosphohydrolase (also known as NUDIX (nucleoside diphosphate linked moiety X))-type motif 10; Nudt19; testosterone-regulated protein rp2) has activity towards CoA, oxidized CoA and a wide range of CoA esters, including choloyl-CoA and branched-chain fatty-acyl-CoA esters. CoA is the major acyl carrier in mammals and a key cofactor in energy metabolism. Dynamic regulation of CoA in different tissues and organs supports metabolic flexibility. 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: 467582 [Multi-domain]  Cd Length: 159  Bit Score: 37.61  E-value: 2.22e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1046870203  70 LLARGEKLY-LLFTVRSDKLRRAPGEVCFPGGKRDPVDADDT--------------------------ATALREAQEE 120
Cdd:cd18870     7 LLRDGADGLeVLLLRRSSTMSFMPGAYVFPGGRVDPADRDAPwagllppdvasasrpgksdpearalrIAAIRETFEE 84
NUDIX_MTH1_Nudt1 cd03427
MutT homolog-1 (MTH1); MutT homolog-1 (MTH1; EC 3.6.1.- ), also called nucleoside ...
 98-151 9.07e-03

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


Pssm-ID: 467533 [Multi-domain]  Cd Length: 136  Bit Score: 35.58  E-value: 9.07e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1046870203  98 PGGKrdpVDADDT--ATALREAQEENNDLVTPV--VGFLDPDFQAQPNADEVkDVFLV 151
Cdd:cd03427    32 FGGK---VEPGETieEAAVRELEEEAGLTATELekVGRLKFEFPDDPEAMDV-HVFRA 85
 
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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