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Conserved domains on  [gi|403225015|ref|NP_001258118|]
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5'(3')-deoxyribonucleotidase, cytosolic type [Rattus norvegicus]

Protein Classification

5'-3'-deoxyribonucleotidase( domain architecture ID 11552331)

5'-3'-deoxyribonucleotidase is a HAD (haloacid dehalogenase) family hydrolase that catalyzes the dephosphorylation of the 5' and 2'(3')-phosphates of deoxyribonucleotides

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 7-170 8.24e-86

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: 250.00  E-value: 8.24e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   7 VRVLVDMDGVLADFESGLLQGFRRRFPGEPHVPLEQRRGFLASEQYGAlrPDLAEKVASVYEAPGFFLNLEPIPGALDAL 86
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015  87 REMNAmQDTDVFICTTPLRKYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDDKDNIQGLEETPSWEHILFT 166
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFT 157


                 ....
gi 403225015 167 CCHN 170
Cdd:cd02587  158 ACHN 161
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 7-170 8.24e-86

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: 250.00  E-value: 8.24e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   7 VRVLVDMDGVLADFESGLLQGFRRRFPGEPHVPLEQRRGFLASEQYGAlrPDLAEKVASVYEAPGFFLNLEPIPGALDAL 86
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015  87 REMNAmQDTDVFICTTPLRKYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDDKDNIQGLEETPSWEHILFT 166
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFT 157


                 ....
gi 403225015 167 CCHN 170
Cdd:cd02587  158 ACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
8-187 1.38e-49

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 158.88  E-value: 1.38e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   8 RVLVDMDGVLADFESGLLQGFRRRFPgePHVPLEQRRGFlasEQYGALRPDLAEKVASVYEAPGFFLNLEPIPGALDALR 87
Cdd:COG4502    4 RIAVDMDGVLADFYAAFLDIYNKEYG--TNLTLEDLDGW---DLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015  88 EMNamQDTDVFICTTPLRkYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDdkDNIQGLEEtPSWEHILFTC 167
Cdd:COG4502   79 ELS--DKYEVYIVTAAME-FPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLID--DNPKNLEE-FKGKGILFDA 152

                        170       180
                 ....*....|....*....|
gi 403225015 168 CHNQHLALPPtrrRLLSWSD 187
Cdd:COG4502  153 PHNRHITGYP---RVNNWKE 169
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 5-196 1.30e-20

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: 84.58  E-value: 1.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015    5 RPVrVLVDMDGVLADFESGLLQGFRRRFpGEPHVPlEQRRGFLASEqygALRPDLAEKVASVYEAPGFFLNLEPIPGALD 84
Cdd:pfam06941   1 RSI-IGVDLDGVCADFYGRMRQIANEWF-ERPLLP-EEVSSWGWSE---WTNPEQYDSLHRFVTQPGFFSDLEPIPGARE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   85 ALREMNAmqDTDVFICTTPLRKYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDDKDniQGLEETPSwEHIL 164
Cdd:pfam06941  75 YLRQLSD--EGRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSP--ENLAQLRG-RGIL 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 403225015  165 FTCCHNQHLAlppTRRRLLSWSDDWRGIIESK 196
Cdd:pfam06941 150 FGNPTNRHIE---DELRAASWQEVYDMILVAK 178
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 7-170 8.24e-86

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: 250.00  E-value: 8.24e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   7 VRVLVDMDGVLADFESGLLQGFRRRFPGEPHVPLEQRRGFLASEQYGAlrPDLAEKVASVYEAPGFFLNLEPIPGALDAL 86
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015  87 REMNAmQDTDVFICTTPLRKYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDDKDNIQGLEETPSWEHILFT 166
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFT 157


                 ....
gi 403225015 167 CCHN 170
Cdd:cd02587  158 ACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
8-187 1.38e-49

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 158.88  E-value: 1.38e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   8 RVLVDMDGVLADFESGLLQGFRRRFPgePHVPLEQRRGFlasEQYGALRPDLAEKVASVYEAPGFFLNLEPIPGALDALR 87
Cdd:COG4502    4 RIAVDMDGVLADFYAAFLDIYNKEYG--TNLTLEDLDGW---DLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015  88 EMNamQDTDVFICTTPLRkYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDdkDNIQGLEEtPSWEHILFTC 167
Cdd:COG4502   79 ELS--DKYEVYIVTAAME-FPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLID--DNPKNLEE-FKGKGILFDA 152

                        170       180
                 ....*....|....*....|
gi 403225015 168 CHNQHLALPPtrrRLLSWSD 187
Cdd:COG4502  153 PHNRHITGYP---RVNNWKE 169
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 5-196 1.30e-20

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: 84.58  E-value: 1.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015    5 RPVrVLVDMDGVLADFESGLLQGFRRRFpGEPHVPlEQRRGFLASEqygALRPDLAEKVASVYEAPGFFLNLEPIPGALD 84
Cdd:pfam06941   1 RSI-IGVDLDGVCADFYGRMRQIANEWF-ERPLLP-EEVSSWGWSE---WTNPEQYDSLHRFVTQPGFFSDLEPIPGARE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   85 ALREMNAmqDTDVFICTTPLRKYDHCVGEKYRWVEQNLGPQFVERIILTRDKTVVMGDLLIDDKDniQGLEETPSwEHIL 164
Cdd:pfam06941  75 YLRQLSD--EGRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSP--ENLAQLRG-RGIL 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 403225015  165 FTCCHNQHLAlppTRRRLLSWSDDWRGIIESK 196
Cdd:pfam06941 150 FGNPTNRHIE---DELRAASWQEVYDMILVAK 178
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
9-102 5.32e-05

Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 42.22  E-value: 5.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403225015   9 VLVDMDGVLADFESGLLQGFRRRFP--GEPHVPLEQRRGF-----------LASEQYGALRPDLAEKVASVYEApGFFLN 75
Cdd:COG0546    4 VLFDLDGTLVDSAPDIAAALNEALAelGLPPLDLEELRALiglglrellrrLLGEDPDEELEELLARFRELYEE-ELLDE 82

                         90       100
                 ....*....|....*....|....*..
gi 403225015  76 LEPIPGALDALREMNAmQDTDVFICTT 102
Cdd:COG0546   83 TRLFPGVRELLEALKA-RGIKLAVVTN 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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