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Conserved domains on  [gi|356874780|ref|NP_001239306|]
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5'(3')-deoxyribonucleotidase, cytosolic type isoform 2 [Homo sapiens]

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

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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 ...
 5-128 3.68e-54

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: 168.34  E-value: 3.68e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   5 VRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAlrPDLADKVASVYEAPGFFLDLEPIPGALDAV 84
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780  85 REMNDlPDTQVFICTSPLLKYHHCVGEK----------------------------------------EETPSWEHILFT 124
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKyewveehfpplfyqrivltrdktvvladiliddnpenleaFEGPGWEHILFT 157


                 ....
gi 356874780 125 CCHN 128
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) ...
 5-128 3.68e-54

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: 168.34  E-value: 3.68e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   5 VRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAlrPDLADKVASVYEAPGFFLDLEPIPGALDAV 84
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780  85 REMNDlPDTQVFICTSPLLKYHHCVGEK----------------------------------------EETPSWEHILFT 124
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKyewveehfpplfyqrivltrdktvvladiliddnpenleaFEGPGWEHILFT 157


                 ....
gi 356874780 125 CCHN 128
Cdd:cd02587  158 ACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
6-152 3.25e-30

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 107.65  E-value: 3.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   6 RVLVDMDGVLADFEAGLLRGFRRRFPEepHVPLEQRRGFlarEQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVR 85
Cdd:COG4502    4 RIAVDMDGVLADFYAAFLDIYNKEYGT--NLTLEDLDGW---DLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780  86 EMNDLPDtqVFICTSPLLkYHHCVGEKE-------------------------------------ETPSWEHILFTCCHN 128
Cdd:COG4502   79 ELSDKYE--VYIVTAAME-FPNSLEEKYewldehfpfipwqniifcgdkslvggdyliddnpknlEEFKGKGILFDAPHN 155

                        170       180
                 ....*....|....*....|....
gi 356874780 129 RHLvlpPTRRRLlswsDNWREILD 152
Cdd:COG4502  156 RHI---TGYPRV----NNWKEVEA 172
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 7-132 3.06e-09

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: 52.99  E-value: 3.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780    7 VLVDMDGVLADFEAGLLRGFRRRFpEEPHVPlEQRRGFLAREqyrALRPDLADKVASVYEAPGFFLDLEPIPGALDAVRE 86
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWF-ERPLLP-EEVSSWGWSE---WTNPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQ 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 356874780   87 MNDlpDTQVFICTSPLLKYHHCVGEKEE--------TPSWEHILftcCHNRHLV 132
Cdd:pfam06941  79 LSD--EGRIVIITHRLFQHYTAVQQKVNwldshlpgIPYWNLCF---VKEKTQV 127
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 5-128 3.68e-54

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: 168.34  E-value: 3.68e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   5 VRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAlrPDLADKVASVYEAPGFFLDLEPIPGALDAV 84
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780  85 REMNDlPDTQVFICTSPLLKYHHCVGEK----------------------------------------EETPSWEHILFT 124
Cdd:cd02587   79 RELSD-EGTDVYICTSPLNKYPTCVEEKyewveehfpplfyqrivltrdktvvladiliddnpenleaFEGPGWEHILFT 157


                 ....
gi 356874780 125 CCHN 128
Cdd:cd02587  158 ACHN 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
6-152 3.25e-30

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 107.65  E-value: 3.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   6 RVLVDMDGVLADFEAGLLRGFRRRFPEepHVPLEQRRGFlarEQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVR 85
Cdd:COG4502    4 RIAVDMDGVLADFYAAFLDIYNKEYGT--NLTLEDLDGW---DLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780  86 EMNDLPDtqVFICTSPLLkYHHCVGEKE-------------------------------------ETPSWEHILFTCCHN 128
Cdd:COG4502   79 ELSDKYE--VYIVTAAME-FPNSLEEKYewldehfpfipwqniifcgdkslvggdyliddnpknlEEFKGKGILFDAPHN 155

                        170       180
                 ....*....|....*....|....
gi 356874780 129 RHLvlpPTRRRLlswsDNWREILD 152
Cdd:COG4502  156 RHI---TGYPRV----NNWKEVEA 172
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 7-132 3.06e-09

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: 52.99  E-value: 3.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780    7 VLVDMDGVLADFEAGLLRGFRRRFpEEPHVPlEQRRGFLAREqyrALRPDLADKVASVYEAPGFFLDLEPIPGALDAVRE 86
Cdd:pfam06941   4 IGVDLDGVCADFYGRMRQIANEWF-ERPLLP-EEVSSWGWSE---WTNPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQ 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 356874780   87 MNDlpDTQVFICTSPLLKYHHCVGEKEE--------TPSWEHILftcCHNRHLV 132
Cdd:pfam06941  79 LSD--EGRIVIITHRLFQHYTAVQQKVNwldshlpgIPYWNLCF---VKEKTQV 127
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
7-106 1.62e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 40.30  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 356874780   7 VLVDMDGVLADFEAGLLRGFRRRFPEE--PHVPLEQRRGFL---AREQYRAL--------RPDLADKVASVYEApGFFLD 73
Cdd:COG0546    4 VLFDLDGTLVDSAPDIAAALNEALAELglPPLDLEELRALIglgLRELLRRLlgedpdeeLEELLARFRELYEE-ELLDE 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 356874780  74 LEPIPGALDAVREMNDLpDTQVFICTS-------PLLKYH 106
Cdd:COG0546   83 TRLFPGVRELLEALKAR-GIKLAVVTNkprefaeRLLEAL 121
 
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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