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Conserved domains on  [gi|9910372|ref|NP_064586|]
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5'(3')-deoxyribonucleotidase, mitochondrial precursor [Homo sapiens]

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) ...
 38-199 6.59e-87

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: 254.23  E-value: 6.59e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587   3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372  118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTAC 197
Cdd:cd02587  81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFTAC 159


                ..
gi 9910372  198 HN 199
Cdd:cd02587 160 HN 161
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 38-199 6.59e-87

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: 254.23  E-value: 6.59e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587   3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372  118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTAC 197
Cdd:cd02587  81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFTAC 159


                ..
gi 9910372  198 HN 199
Cdd:cd02587 160 HN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
38-224 1.04e-47

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 155.03  E-value: 1.04e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQpfIALEDRRGFWVSEQYGrlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:COG4502   5 IAVDMDGVLADFYAAFLDIYNKEYGTN--LTLEDLDGWDLWELVP---PEHRERIREFLNEPGFFRDLPPIPGAQEVLKE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372  118 MasLQNTDVFICTSPIkMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPdiTGAEPtPSWEHVLFTAC 197
Cdd:COG4502  80 L--SDKYEVYIVTAAM-EFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP--KNLEE-FKGKGILFDAP 153

                       170       180
                ....*....|....*....|....*..
gi 9910372  198 HNQHLqlqPPRRRLHSWAdDWKAILDS 224
Cdd:COG4502 154 HNRHI---TGYPRVNNWK-EVEALLLS 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 38-225 8.54e-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: 83.04  E-value: 8.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372     38 VLVDMDGVLADFEGGFLRKFRARF-----PDQpfIALEDRRGFWVSEQYGRLRPGLSEKAisiwesknFFFELEPLPGAV 112
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWFerpllPEE--VSSWGWSEWTNPEQYDSLHRFVTQPG--------FFSDLEPIPGAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372    113 EAVKEMASLqnTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSwehV 192
Cdd:pfam06941  74 EYLRQLSDE--GRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRG---I 148

                         170       180       190
                  ....*....|....*....|....*....|...
gi 9910372    193 LFTACHNQHLQLQpprRRLHSWADDWKAILDSK 225
Cdd:pfam06941 149 LFGNPTNRHIEDE---LRAASWQEVYDMILVAK 178
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 38-199 6.59e-87

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: 254.23  E-value: 6.59e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587   3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372  118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTAC 197
Cdd:cd02587  81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPGWEHILFTAC 159


                ..
gi 9910372  198 HN 199
Cdd:cd02587 160 HN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
38-224 1.04e-47

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 155.03  E-value: 1.04e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQpfIALEDRRGFWVSEQYGrlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:COG4502   5 IAVDMDGVLADFYAAFLDIYNKEYGTN--LTLEDLDGWDLWELVP---PEHRERIREFLNEPGFFRDLPPIPGAQEVLKE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372  118 MasLQNTDVFICTSPIkMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPdiTGAEPtPSWEHVLFTAC 197
Cdd:COG4502  80 L--SDKYEVYIVTAAM-EFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP--KNLEE-FKGKGILFDAP 153

                       170       180
                ....*....|....*....|....*..
gi 9910372  198 HNQHLqlqPPRRRLHSWAdDWKAILDS 224
Cdd:COG4502 154 HNRHI---TGYPRVNNWK-EVEALLLS 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 38-225 8.54e-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: 83.04  E-value: 8.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372     38 VLVDMDGVLADFEGGFLRKFRARF-----PDQpfIALEDRRGFWVSEQYGRLRPGLSEKAisiwesknFFFELEPLPGAV 112
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWFerpllPEE--VSSWGWSEWTNPEQYDSLHRFVTQPG--------FFSDLEPIPGAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372    113 EAVKEMASLqnTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSwehV 192
Cdd:pfam06941  74 EYLRQLSDE--GRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRG---I 148

                         170       180       190
                  ....*....|....*....|....*....|...
gi 9910372    193 LFTACHNQHLQLQpprRRLHSWADDWKAILDSK 225
Cdd:pfam06941 149 LFGNPTNRHIEDE---LRAASWQEVYDMILVAK 178
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
38-131 7.35e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 39.53  E-value: 7.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9910372   38 VLVDMDGVLADFEGGFLRKFRARFPDQ--PFIALEDRRGF-------WVSEQYGRLRPGLSEKAISIWES---KNFFFEL 105
Cdd:COG0546   4 VLFDLDGTLVDSAPDIAAALNEALAELglPPLDLEELRALiglglreLLRRLLGEDPDEELEELLARFRElyeEELLDET 83

                        90       100
                ....*....|....*....|....*.
gi 9910372  106 EPLPGAVEAVKEMASlQNTDVFICTS 131
Cdd:COG0546  84 RLFPGVRELLEALKA-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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