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Conserved domains on  [gi|530410504|ref|XP_005256788|]
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5'(3')-deoxyribonucleotidase, mitochondrial isoform X4 [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) ...
 38-224 7.11e-82

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: 242.29  E-value: 7.11e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587    3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504 118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITgkwpatamwtdamndr 197
Cdd:cd02587   81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL---------------- 143

                        170       180
                 ....*....|....*....|....*..
gi 530410504 198 raeqsscreGAEPTPSWEHVLFTACHN 224
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) ...
 38-224 7.11e-82

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: 242.29  E-value: 7.11e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587    3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504 118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITgkwpatamwtdamndr 197
Cdd:cd02587   81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL---------------- 143

                        170       180
                 ....*....|....*....|....*..
gi 530410504 198 raeqsscreGAEPTPSWEHVLFTACHN 224
Cdd:cd02587  144 ---------EAFEGPGWEHILFTACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
38-249 9.50e-44

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 145.78  E-value: 9.50e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQpfIALEDRRGFWVSEQYGrlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:COG4502    5 IAVDMDGVLADFYAAFLDIYNKEYGTN--LTLEDLDGWDLWELVP---PEHRERIREFLNEPGFFRDLPPIPGAQEVLKE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504 118 MasLQNTDVFICTSPIkMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPditgkwpatamwtdamndr 197
Cdd:COG4502   80 L--SDKYEVYIVTAAM-EFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP------------------- 137

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 530410504 198 raeqsscrEGAEPtPSWEHVLFTACHNQHLqlqPPRRRLHSWAdDWKAILDS 249
Cdd:COG4502  138 --------KNLEE-FKGKGILFDAPHNRHI---TGYPRVNNWK-EVEALLLS 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 38-250 5.28e-17

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: 76.11  E-value: 5.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504   38 VLVDMDGVLADFEGGFLRKFRARF-----PDQpfIALEDRRGFWVSEQYGRLRPGLSEKAisiwesknFFFELEPLPGAV 112
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWFerpllPEE--VSSWGWSEWTNPEQYDSLHRFVTQPG--------FFSDLEPIPGAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  113 EAVKEMASLqnTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGKWPATAmwtd 192
Cdd:pfam06941  74 EYLRQLSDE--GRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRG---- 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 530410504  193 amndrraeqsscregaeptpswehVLFTACHNQHLQLQpprRRLHSWADDWKAILDSK 250
Cdd:pfam06941 148 ------------------------ILFGNPTNRHIEDE---LRAASWQEVYDMILVAK 178
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 38-224 7.11e-82

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: 242.29  E-value: 7.11e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:cd02587    3 ILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504 118 MASlQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITgkwpatamwtdamndr 197
Cdd:cd02587   81 LSD-EGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENL---------------- 143

                        170       180
                 ....*....|....*....|....*..
gi 530410504 198 raeqsscreGAEPTPSWEHVLFTACHN 224
Cdd:cd02587  144 ---------EAFEGPGWEHILFTACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
38-249 9.50e-44

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 145.78  E-value: 9.50e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQpfIALEDRRGFWVSEQYGrlrPGLSEKAISIWESKNFFFELEPLPGAVEAVKE 117
Cdd:COG4502    5 IAVDMDGVLADFYAAFLDIYNKEYGTN--LTLEDLDGWDLWELVP---PEHRERIREFLNEPGFFRDLPPIPGAQEVLKE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504 118 MasLQNTDVFICTSPIkMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPditgkwpatamwtdamndr 197
Cdd:COG4502   80 L--SDKYEVYIVTAAM-EFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNP------------------- 137

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 530410504 198 raeqsscrEGAEPtPSWEHVLFTACHNQHLqlqPPRRRLHSWAdDWKAILDS 249
Cdd:COG4502  138 --------KNLEE-FKGKGILFDAPHNRHI---TGYPRVNNWK-EVEALLLS 176
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 38-250 5.28e-17

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: 76.11  E-value: 5.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504   38 VLVDMDGVLADFEGGFLRKFRARF-----PDQpfIALEDRRGFWVSEQYGRLRPGLSEKAisiwesknFFFELEPLPGAV 112
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWFerpllPEE--VSSWGWSEWTNPEQYDSLHRFVTQPG--------FFSDLEPIPGAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  113 EAVKEMASLqnTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGKWPATAmwtd 192
Cdd:pfam06941  74 EYLRQLSDE--GRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRG---- 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 530410504  193 amndrraeqsscregaeptpswehVLFTACHNQHLQLQpprRRLHSWADDWKAILDSK 250
Cdd:pfam06941 148 ------------------------ILFGNPTNRHIEDE---LRAASWQEVYDMILVAK 178
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
38-131 7.51e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 39.53  E-value: 7.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410504  38 VLVDMDGVLADFEGGFLRKFRARFPDQ--PFIALEDRRGF-------WVSEQYGRLRPGLSEKAISIWES---KNFFFEL 105
Cdd:COG0546    4 VLFDLDGTLVDSAPDIAAALNEALAELglPPLDLEELRALiglglreLLRRLLGEDPDEELEELLARFRElyeEELLDET 83

                         90       100
                 ....*....|....*....|....*.
gi 530410504 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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