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Conserved domains on  [gi|1063715219|ref|NP_001327063|]
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nudix hydrolase homolog 9 [Arabidopsis thaliana]

Protein Classification

NUDIX hydrolase( domain architecture ID 225)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUDIX_Hydrolase super family cl00447
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 108-202 1.03e-06

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 cd04694:

Pssm-ID: 469772 [Multi-domain]  Cd Length: 135  Bit Score: 46.90  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 108 PLGNGAVIETSDKKIIVLRRSNNVGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvtqEMFDSIICEVVEET 187
Cdd:cd04694     2 DVGVVVLIEDSDDRVLLTRRAKHMRTFPGVWVPPGGHVEL----------------GE--------SLLEAGLRELQEET 57

                          90
                  ....*....|....*
gi 1063715219 188 GIPASSLSSPLFIGI 202
Cdd:cd04694    58 GLEVSDIQSLSLLGL 72
 
Name Accession Description Interval E-value
NUDIX_Nudt17 cd04694
nucleoside diphosphate-linked moiety X)) motif 17; Nucleoside diphosphate-linked moiety X)) ...
 108-202 1.03e-06

nucleoside diphosphate-linked moiety X)) motif 17; Nucleoside diphosphate-linked moiety X)) motif 17 (EC 3.6.1.-) encoded by the NUDT17 gene on chromosome 1q21.1 and encodes an enzyme thought to hydrolyse some nucleoside diphosphate derivatives. 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: 467576 [Multi-domain]  Cd Length: 135  Bit Score: 46.90  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 108 PLGNGAVIETSDKKIIVLRRSNNVGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvtqEMFDSIICEVVEET 187
Cdd:cd04694     2 DVGVVVLIEDSDDRVLLTRRAKHMRTFPGVWVPPGGHVEL----------------GE--------SLLEAGLRELQEET 57

                          90
                  ....*....|....*
gi 1063715219 188 GIPASSLSSPLFIGI 202
Cdd:cd04694    58 GLEVSDIQSLSLLGL 72
YjhB COG1051
ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism];
112-227 2.61e-03

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


Pssm-ID: 440671 [Multi-domain]  Cd Length: 125  Bit Score: 36.88  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 112 GAVIETSDKKIIVLRRSNnvGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvtqEMFDSIICEVVEETGIPA 191
Cdd:COG1051    10 DAVIFRKDGRVLLVRRAD--EPGKGLWALPGGKVEP----------------GE--------TPEEAALRELREETGLEV 63

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1063715219 192 SSLSsplFIGISRRELNVRPAMFFYLkCSHHSDDIQ 227
Cdd:COG1051    64 EVLE---LLGVFDHPDRGHVVSVAFL-AEVLSGEPR 95
 
Name Accession Description Interval E-value
NUDIX_Nudt17 cd04694
nucleoside diphosphate-linked moiety X)) motif 17; Nucleoside diphosphate-linked moiety X)) ...
 108-202 1.03e-06

nucleoside diphosphate-linked moiety X)) motif 17; Nucleoside diphosphate-linked moiety X)) motif 17 (EC 3.6.1.-) encoded by the NUDT17 gene on chromosome 1q21.1 and encodes an enzyme thought to hydrolyse some nucleoside diphosphate derivatives. 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: 467576 [Multi-domain]  Cd Length: 135  Bit Score: 46.90  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 108 PLGNGAVIETSDKKIIVLRRSNNVGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvtqEMFDSIICEVVEET 187
Cdd:cd04694     2 DVGVVVLIEDSDDRVLLTRRAKHMRTFPGVWVPPGGHVEL----------------GE--------SLLEAGLRELQEET 57

                          90
                  ....*....|....*
gi 1063715219 188 GIPASSLSSPLFIGI 202
Cdd:cd04694    58 GLEVSDIQSLSLLGL 72
NUDIX_Hydrolase cd02883
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 112-219 2.55e-06

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: 45.09  E-value: 2.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 112 GAVIETSDKKIIVLRRSNnvGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvTQEmfDSIICEVVEETGIPA 191
Cdd:cd02883     4 GAVVFDDEGRVLLVRRSD--GPGPGGWELPGGGVEP----------------GE------TPE--EAAVREVREETGLDV 57

                          90       100
                  ....*....|....*....|....*...
gi 1063715219 192 SSLsSPLFIGISRRELNVRPAMFFYLKC 219
Cdd:cd02883    58 EVL-RLLGVYEFPDPDEGRHVVVLVFLA 84
NUDIX_Hydrolase cd18875
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 111-234 4.78e-06

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: 467587 [Multi-domain]  Cd Length: 144  Bit Score: 45.25  E-value: 4.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 111 NGAVIETSDKKIIVLRRSNnvGEFPGhYVFPGGHPEPtavgidyhqlennvqtGEVLnkkvtqemFDSIICEVVEETGIp 190
Cdd:cd18875     5 NMCMIYDGEDRVLVLDRVK--KDWGG-YTFPGGHVEP----------------GESF--------VDSVIREVKEETGL- 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1063715219 191 asSLSSPLFIGISR--RELNVRPAMFFYlKCSHHSDDIQrlySSAE 234
Cdd:cd18875    57 --TIKNPELCGIKQwiNPDGERYIVFLY-KTDHFSGELL---SSEE 96
NUDIX_AcylCoAdiphos_Nudt19 cd18870
Nucleoside diphosphate-linked moiety X)) motif 19; Acyl CoA diphosphohydrolase (also known as ...
 121-189 6.87e-04

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: 39.15  E-value: 6.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063715219 121 KIIVLRRSNNVGEFPGHYVFPGGHPEPTavgiDYHQLENNVQTGEVLNKKVTQEMFDS----IIC---EVVEETGI 189
Cdd:cd18870    16 EVLLLRRSSTMSFMPGAYVFPGGRVDPA----DRDAPWAGLLPPDVASASRPGKSDPEaralRIAairETFEETGL 87
YjhB COG1051
ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism];
112-227 2.61e-03

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


Pssm-ID: 440671 [Multi-domain]  Cd Length: 125  Bit Score: 36.88  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 112 GAVIETSDKKIIVLRRSNnvGEFPGHYVFPGGHPEPtavgidyhqlennvqtGEvlnkkvtqEMFDSIICEVVEETGIPA 191
Cdd:COG1051    10 DAVIFRKDGRVLLVRRAD--EPGKGLWALPGGKVEP----------------GE--------TPEEAALRELREETGLEV 63

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1063715219 192 SSLSsplFIGISRRELNVRPAMFFYLkCSHHSDDIQ 227
Cdd:COG1051    64 EVLE---LLGVFDHPDRGHVVSVAFL-AEVLSGEPR 95
NUDIX_ADPRase cd04691
ADP-ribose pyrophosphatase and similar proteins; ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1. ...
 109-192 2.86e-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: 467573 [Multi-domain]  Cd Length: 122  Bit Score: 36.89  E-value: 2.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063715219 109 LGNGAVIETsDKKIIVLRRSNNVGEfpGHYVFPGGHpeptavgidyhqlennVQTGEVLNKKVTQEmfdsiiceVVEETG 188
Cdd:cd04691     2 LGVGGVVVK-EGKVLLVKRAYGPGK--GRWTLPGGF----------------VEEGETLDEAIVRE--------VLEETG 54


                  ....
gi 1063715219 189 IPAS 192
Cdd:cd04691    55 IDAK 58
 
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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