NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958656995|ref|XP_038941328|]
View 

5'(3')-deoxyribonucleotidase, mitochondrial isoform X1 [Rattus norvegicus]

Protein Classification

HAD family hydrolase( domain architecture ID 229399)

HAD (haloacid dehalogenase) family hydrolase; the HAD family includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates

EC:  3.6.3.-
Gene Ontology:  GO:0005524|GO:0016887|GO:0005215

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HAD_like super family cl21460
Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes ...
 37-125 2.84e-27

Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes carbon and phosphorus hydrolases such as 2-haloalkonoate dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, among others. These proteins catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a conserve alpha/beta core domain, and many also possess a small cap domain, with varying folds and functions.


The actual alignment was detected with superfamily member cd02587:

Pssm-ID: 473868  Cd Length: 161  Bit Score: 99.77  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  37 FFRG---VPGG----KTISSHKSQITI--HHRGTSHMSKKIEYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDIT 107
Cdd:cd02587    64 FFRNlepIPGAvealRELSDEGTDVYIctSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL 143

                          90
                  ....*....|....*...
gi 1958656995 108 GAESHPSWEHILFTSCHN 125
Cdd:cd02587   144 EAFEGPGWEHILFTACHN 161
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 37-125 2.84e-27

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319786  Cd Length: 161  Bit Score: 99.77  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  37 FFRG---VPGG----KTISSHKSQITI--HHRGTSHMSKKIEYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDIT 107
Cdd:cd02587    64 FFRNlepIPGAvealRELSDEGTDVYIctSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL 143

                          90
                  ....*....|....*...
gi 1958656995 108 GAESHPSWEHILFTSCHN 125
Cdd:cd02587   144 EAFEGPGWEHILFTACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
70-150 2.57e-18

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 76.83  E-value: 2.57e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  70 YAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPdiTGAEsHPSWEHILFTSCHNYHLqlqPPRRRLHSWAdDWKAILD 149
Cdd:COG4502   103 YEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP--KNLE-EFKGKGILFDAPHNRHI---TGYPRVNNWK-EVEALLL 175


                  .
gi 1958656995 150 S 150
Cdd:COG4502   176 S 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 47-151 1.05e-08

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 51.45  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  47 ISSHKSQITIHHRGTSHM-SKKIEYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDitGAESHPSwEHILFTSCHN 125
Cdd:pfam06941  79 LSDEGRIVIITHRLFQHYtAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPE--NLAQLRG-RGILFGNPTN 155

                          90       100
                  ....*....|....*....|....*.
gi 1958656995 126 YHLQLQpprRRLHSWADDWKAILDSK 151
Cdd:pfam06941 156 RHIEDE---LRAASWQEVYDMILVAK 178
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 37-125 2.84e-27

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319786  Cd Length: 161  Bit Score: 99.77  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  37 FFRG---VPGG----KTISSHKSQITI--HHRGTSHMSKKIEYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDIT 107
Cdd:cd02587    64 FFRNlepIPGAvealRELSDEGTDVYIctSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL 143

                          90
                  ....*....|....*...
gi 1958656995 108 GAESHPSWEHILFTSCHN 125
Cdd:cd02587   144 EAFEGPGWEHILFTACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
70-150 2.57e-18

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 76.83  E-value: 2.57e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  70 YAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPdiTGAEsHPSWEHILFTSCHNYHLqlqPPRRRLHSWAdDWKAILD 149
Cdd:COG4502   103 YEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP--KNLE-EFKGKGILFDAPHNRHI---TGYPRVNNWK-EVEALLL 175


                  .
gi 1958656995 150 S 150
Cdd:COG4502   176 S 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 47-151 1.05e-08

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 51.45  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656995  47 ISSHKSQITIHHRGTSHM-SKKIEYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDitGAESHPSwEHILFTSCHN 125
Cdd:pfam06941  79 LSDEGRIVIITHRLFQHYtAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPE--NLAQLRG-RGILFGNPTN 155

                          90       100
                  ....*....|....*....|....*.
gi 1958656995 126 YHLQLQpprRRLHSWADDWKAILDSK 151
Cdd:pfam06941 156 RHIEDE---LRAASWQEVYDMILVAK 178
 
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