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Conserved domains on  [gi|657873446|ref|WP_029578007|]
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5'-3'-deoxyribonucleotidase [Bordetella hinzii]

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) ...
 1-159 1.52e-67

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: 203.39  E-value: 1.52e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRHPDIAPVAFDDRRSFHILEDY-PPALRAQAEAIYTEPGFIRNLPPVPGALEAVGE 79
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYkAPELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  80 LMALGMEVRFCSSPLRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPRIEGAARPR-WQHVIYDAPY 158
Cdd:cd02587   81 LSDEGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPgWEHILFTACH 160


                 .
gi 657873446 159 N 159
Cdd:cd02587  161 N 161
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 1-159 1.52e-67

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: 203.39  E-value: 1.52e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRHPDIAPVAFDDRRSFHILEDY-PPALRAQAEAIYTEPGFIRNLPPVPGALEAVGE 79
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYkAPELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  80 LMALGMEVRFCSSPLRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPRIEGAARPR-WQHVIYDAPY 158
Cdd:cd02587   81 LSDEGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPgWEHILFTACH 160


                 .
gi 657873446 159 N 159
Cdd:cd02587  161 N 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
1-183 2.96e-64

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 195.47  E-value: 2.96e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRHPDiaPVAFDDRRSFHILEDYPPALRAQAEAIYTEPGFIRNLPPVPGALEAVGEL 80
Cdd:COG4502    3 PRIAVDMDGVLADFYAAFLDIYNKEYGT--NLTLEDLDGWDLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLKEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  81 MALgMEVRFCSSPlRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPRieGAARPRWQHVIYDAPYNR 160
Cdd:COG4502   81 SDK-YEVYIVTAA-MEFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNPK--NLEEFKGKGILFDAPHNR 156

                        170       180
                 ....*....|....*....|...
gi 657873446 161 QETGRLRLTwqNWRNVLAGALYQ 183
Cdd:COG4502  157 HITGYPRVN--NWKEVEALLLSL 177
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 1-171 4.80e-24

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: 93.06  E-value: 4.80e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446    1 MLILLDQDGVLADFEHAFIDAWRRRHPDiaPVAFDDRRSFHILEDYPPALRAQAEAIYTEPGFIRNLPPVPGALEAVGEL 80
Cdd:pfam06941   2 SIIGVDLDGVCADFYGRMRQIANEWFER--PLLPEEVSSWGWSEWTNPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   81 MALGmEVRFCSSPLRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPriEGAARPRWQHVIYDAPYNR 160
Cdd:pfam06941  80 SDEG-RIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSP--ENLAQLRGRGILFGNPTNR 156

                         170
                  ....*....|..
gi 657873446  161 QETGRLRL-TWQ 171
Cdd:pfam06941 157 HIEDELRAaSWQ 168
 
Name Accession Description Interval E-value
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 1-159 1.52e-67

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: 203.39  E-value: 1.52e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRHPDIAPVAFDDRRSFHILEDY-PPALRAQAEAIYTEPGFIRNLPPVPGALEAVGE 79
Cdd:cd02587    1 IVILVDMDGVLADFEGALVRAIRERFPDEPHVLLESRRGFWVIEQYkAPELSRKAADILEEPGFFRNLEPIPGAVEALRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  80 LMALGMEVRFCSSPLRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPRIEGAARPR-WQHVIYDAPY 158
Cdd:cd02587   81 LSDEGTDVYICTSPLNKYPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGPgWEHILFTACH 160


                 .
gi 657873446 159 N 159
Cdd:cd02587  161 N 161
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
1-183 2.96e-64

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


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 195.47  E-value: 2.96e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRHPDiaPVAFDDRRSFHILEDYPPALRAQAEAIYTEPGFIRNLPPVPGALEAVGEL 80
Cdd:COG4502    3 PRIAVDMDGVLADFYAAFLDIYNKEYGT--NLTLEDLDGWDLWELVPPEHRERIREFLNEPGFFRDLPPIPGAQEVLKEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  81 MALgMEVRFCSSPlRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPRieGAARPRWQHVIYDAPYNR 160
Cdd:COG4502   81 SDK-YEVYIVTAA-MEFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNPK--NLEEFKGKGILFDAPHNR 156

                        170       180
                 ....*....|....*....|...
gi 657873446 161 QETGRLRLTwqNWRNVLAGALYQ 183
Cdd:COG4502  157 HITGYPRVN--NWKEVEALLLSL 177
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 1-171 4.80e-24

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: 93.06  E-value: 4.80e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446    1 MLILLDQDGVLADFEHAFIDAWRRRHPDiaPVAFDDRRSFHILEDYPPALRAQAEAIYTEPGFIRNLPPVPGALEAVGEL 80
Cdd:pfam06941   2 SIIGVDLDGVCADFYGRMRQIANEWFER--PLLPEEVSSWGWSEWTNPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   81 MALGmEVRFCSSPLRQYDNCVLEKYQWIERHFGRAATERLILTRDKTLVQGDLLIDDRPriEGAARPRWQHVIYDAPYNR 160
Cdd:pfam06941  80 SDEG-RIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSP--ENLAQLRGRGILFGNPTNR 156

                         170
                  ....*....|..
gi 657873446  161 QETGRLRL-TWQ 171
Cdd:pfam06941 157 HIEDELRAaSWQ 168
YcjU COG0637
Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];
3-92 1.05e-04

Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440402 [Multi-domain]  Cd Length: 208  Bit Score: 41.35  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   3 ILLDQDGVLADFEHAFIDAWR----RRHPDIAPvafDDRRSFH----------ILEDY-----PPALRAQAEAIYTEPGF 63
Cdd:COG0637    5 VIFDMDGTLVDSEPLHARAWReafaELGIDLTE---EEYRRLMgrsredilryLLEEYgldlpEEELAARKEELYRELLA 81

                         90       100
                 ....*....|....*....|....*....
gi 657873446  64 IRNLPPVPGALEAVGELMALGMEVRFCSS 92
Cdd:COG0637   82 EEGLPLIPGVVELLEALKEAGIKIAVATS 110
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
2-112 2.34e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 40.30  E-value: 2.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   2 LILLDQDGVLADFEHAFIDAWRR--RHPDIAPVAFDDRRSF----------HILEDYPPALRAQAEAIYTE---PGFIRN 66
Cdd:COG0546    3 LVLFDLDGTLVDSAPDIAAALNEalAELGLPPLDLEELRALiglglrellrRLLGEDPDEELEELLARFRElyeEELLDE 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 657873446  67 LPPVPGALEAVGELMALGMEVRFCSSPLRQYDNCVLEKYQWiERHF 112
Cdd:COG0546   83 TRLFPGVRELLEALKARGIKLAVVTNKPREFAERLLEALGL-DDYF 127
YqfW COG5663
Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];
1-160 1.90e-03

Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];


Pssm-ID: 444382 [Multi-domain]  Cd Length: 187  Bit Score: 37.52  E-value: 1.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446   1 MLILLDQDGVLADFEHAFIDAWRRRH-PDIAPvafDDRRSFHILEDYPPAlRAQAEAIY--TEPGFIRNLPPVPGALEAV 77
Cdd:COG5663    1 MRIGIDIDGTITDPYPYFIPLLNKYFgKNITL---EDITTYDLHEVLGLT-EEEFDKFFeeNEEEIYTEAPPVPGAKEVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 657873446  78 GELMALGmEVRFCSS-PLRQYDncvlEKYQWIERHFGRAATERLILTRDKT-LVQG---DLLIDDRP----RIEGAARPr 148
Cdd:COG5663   77 NKLKDQH-ELYYITArPKHLEE----VTENWLEKHGIPYDELILLGSHDKVeAAKElgiDLFIEDKPdnalQLAEEGIP- 150

                        170
                 ....*....|...
gi 657873446 149 wqhVI-YDAPYNR 160
Cdd:COG5663  151 ---VLlFDTPYNR 160
 
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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