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Conserved domains on  [gi|1747199295|ref|NP_001361267|]
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cytosolic 5'-nucleotidase 3A isoform 5 [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 ...
 59-264 1.82e-130

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 cd07504:

Pssm-ID: 473868 [Multi-domain]  Cd Length: 273  Bit Score: 370.11  E-value: 1.82e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  59 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVE 138
Cdd:cd07504     1 DPTRVEEKICGLVKGGADKLQIISDFDMTLSRFRYNGGRCPTCHNIFDNCKLLTEECRAKLVQLKEKYYPIEIDPHLTIE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 139 EKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPN 218
Cdd:cd07504    81 EKVPYMEEWWTKSHELLIEQGFQKDAIDQIVAESDIALRDGYEEFFEKLQQHGIPVLIFSAGLGDIIEEVLRQAGVYHPN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 219 VKVVSNFMDFDET------------------------------------------------------------------- 231
Cdd:cd07504   161 VKVVSNFMDFDDNgvltgfkgplihvfnknesalkntdyfkqlkgrtniillgdsigdlrmadgvpnvehilkigflndk 240

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1747199295 232 VDELLEKYMDSYDIVLVQDESLEVANSILQKIL 264
Cdd:cd07504   241 VEELLEKYMDSYDIVLVNDETLDVPNSILQKIL 273
 
Name Accession Description Interval E-value
HAD_5NT cd07504
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB; 5 ...
 59-264 1.82e-130

haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB; 5'-nucleotidases dephosphorylate nucleoside 5prime-monophosphates. This family includes human 5'-nucleotidase, cytosolic IIIA (cN-IIIA, previously called cN-III; NT5C3A) the main pyrimidine 5'-nucleotidase in erythrocytes which dephosphorylates the pyrimidine nucleotides CMP, UMP, TMP, and the purine 7-methylguanosine monophosphate (m7GM), and possesses phosphotransferase activity. It also includes human 5'-nucleotidase, cytosolic IIIB (cN-IIIB; NT5C3B) which has a strong preference for m7GMP, dephosphorylates CMP and UMP and, with significantly lower efficiency, GMP and AMP, and can also act as a phosphotransferase. 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: 319807 [Multi-domain]  Cd Length: 273  Bit Score: 370.11  E-value: 1.82e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  59 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVE 138
Cdd:cd07504     1 DPTRVEEKICGLVKGGADKLQIISDFDMTLSRFRYNGGRCPTCHNIFDNCKLLTEECRAKLVQLKEKYYPIEIDPHLTIE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 139 EKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPN 218
Cdd:cd07504    81 EKVPYMEEWWTKSHELLIEQGFQKDAIDQIVAESDIALRDGYEEFFEKLQQHGIPVLIFSAGLGDIIEEVLRQAGVYHPN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 219 VKVVSNFMDFDET------------------------------------------------------------------- 231
Cdd:cd07504   161 VKVVSNFMDFDDNgvltgfkgplihvfnknesalkntdyfkqlkgrtniillgdsigdlrmadgvpnvehilkigflndk 240

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1747199295 232 VDELLEKYMDSYDIVLVQDESLEVANSILQKIL 264
Cdd:cd07504   241 VEELLEKYMDSYDIVLVNDETLDVPNSILQKIL 273
HAD-SF-IE TIGR01544
haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544; This model represents a ...
 50-263 1.96e-122

haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544; This model represents a small group of metazoan sequences. The sequences from mouse are annotated as Pyrimidine 5'-nucleotidases, aparrently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.


Pssm-ID: 273683 [Multi-domain]  Cd Length: 283  Bit Score: 350.31  E-value: 1.96e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  50 FQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYK-GKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYA 128
Cdd:TIGR01544   1 LTQDHCRMRDPTEVERIINEFVIGGAEKMQIISDFDYTLSRFRTEdGGRVPTSHGIFDACQSLPEEFKAKTDKLKHKYYP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 129 IEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEV 208
Cdd:TIGR01544  81 IEIDPHLTIEEKVPYMIEWWTKSHELTVGFPFDKSEIDQIVSKSTHALKDGTEEFFADLQRHGIPTLIFSAGIGNSVESV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 209 IRQAGVYHPNVKVVSNFMDFDET--------------------------------------------------------- 231
Cdd:TIGR01544 161 LRQANVLHPNVKVVSNFLQFDEDglldgfqqplihtfnknetvlnetteyfdlvhtrdniillgdsigdadmasgvpass 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1747199295 232 -----------VDELLEKYMDSYDIVLVQDESLEVANSILQKI 263
Cdd:TIGR01544 241 hilkigylndhVDANLKKYMDTYDIVLVDDQTLDVARTILSLI 283
UMPH-1 pfam05822
Pyrimidine 5'-nucleotidase (UMPH-1); This family consists of several eukaryotic pyrimidine 5 ...
 86-264 1.56e-95

Pyrimidine 5'-nucleotidase (UMPH-1); This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterized by the ability to dephosphorylate nucleic acids. P5'N-1 catalyzes the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans.


Pssm-ID: 310424 [Multi-domain]  Cd Length: 246  Bit Score: 280.79  E-value: 1.56e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  86 MTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKL 165
Cdd:pfam05822   1 MTLSKFRVNGERCPSSHGIFDNCKSIPEECRKKLRELYHKYYPIEIDPHMPIEEKVPYMVEWWTKSHALLIGQGLQKEAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 166 KEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDET-------------- 231
Cdd:pfam05822  81 AEVVAESDIMLRDGTHEFFDDLQQLNVPVLIFSAGLGDVLEEVLRQANVMHPNVKVVSNFMDFDDDgvlngfkgplihtf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 232 -----------------------------------------------------VDELLEKYMDSYDIVLVQDESLEVANS 258
Cdd:pfam05822 161 nknetvldgteyfdqlhtrdniillgdslgdlgmadgvpsvehilkigflndkVEENLDKYMDAFDIVLVDDQTMDVPNA 240


                  ....*.
gi 1747199295 259 ILQKIL 264
Cdd:pfam05822 241 ILEMIL 246
 
Name Accession Description Interval E-value
HAD_5NT cd07504
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB; 5 ...
 59-264 1.82e-130

haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB; 5'-nucleotidases dephosphorylate nucleoside 5prime-monophosphates. This family includes human 5'-nucleotidase, cytosolic IIIA (cN-IIIA, previously called cN-III; NT5C3A) the main pyrimidine 5'-nucleotidase in erythrocytes which dephosphorylates the pyrimidine nucleotides CMP, UMP, TMP, and the purine 7-methylguanosine monophosphate (m7GM), and possesses phosphotransferase activity. It also includes human 5'-nucleotidase, cytosolic IIIB (cN-IIIB; NT5C3B) which has a strong preference for m7GMP, dephosphorylates CMP and UMP and, with significantly lower efficiency, GMP and AMP, and can also act as a phosphotransferase. 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: 319807 [Multi-domain]  Cd Length: 273  Bit Score: 370.11  E-value: 1.82e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  59 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVE 138
Cdd:cd07504     1 DPTRVEEKICGLVKGGADKLQIISDFDMTLSRFRYNGGRCPTCHNIFDNCKLLTEECRAKLVQLKEKYYPIEIDPHLTIE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 139 EKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPN 218
Cdd:cd07504    81 EKVPYMEEWWTKSHELLIEQGFQKDAIDQIVAESDIALRDGYEEFFEKLQQHGIPVLIFSAGLGDIIEEVLRQAGVYHPN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 219 VKVVSNFMDFDET------------------------------------------------------------------- 231
Cdd:cd07504   161 VKVVSNFMDFDDNgvltgfkgplihvfnknesalkntdyfkqlkgrtniillgdsigdlrmadgvpnvehilkigflndk 240

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1747199295 232 VDELLEKYMDSYDIVLVQDESLEVANSILQKIL 264
Cdd:cd07504   241 VEELLEKYMDSYDIVLVNDETLDVPNSILQKIL 273
HAD-SF-IE TIGR01544
haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544; This model represents a ...
 50-263 1.96e-122

haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544; This model represents a small group of metazoan sequences. The sequences from mouse are annotated as Pyrimidine 5'-nucleotidases, aparrently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.


Pssm-ID: 273683 [Multi-domain]  Cd Length: 283  Bit Score: 350.31  E-value: 1.96e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  50 FQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYK-GKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYA 128
Cdd:TIGR01544   1 LTQDHCRMRDPTEVERIINEFVIGGAEKMQIISDFDYTLSRFRTEdGGRVPTSHGIFDACQSLPEEFKAKTDKLKHKYYP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 129 IEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEV 208
Cdd:TIGR01544  81 IEIDPHLTIEEKVPYMIEWWTKSHELTVGFPFDKSEIDQIVSKSTHALKDGTEEFFADLQRHGIPTLIFSAGIGNSVESV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 209 IRQAGVYHPNVKVVSNFMDFDET--------------------------------------------------------- 231
Cdd:TIGR01544 161 LRQANVLHPNVKVVSNFLQFDEDglldgfqqplihtfnknetvlnetteyfdlvhtrdniillgdsigdadmasgvpass 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1747199295 232 -----------VDELLEKYMDSYDIVLVQDESLEVANSILQKI 263
Cdd:TIGR01544 241 hilkigylndhVDANLKKYMDTYDIVLVDDQTLDVARTILSLI 283
UMPH-1 pfam05822
Pyrimidine 5'-nucleotidase (UMPH-1); This family consists of several eukaryotic pyrimidine 5 ...
 86-264 1.56e-95

Pyrimidine 5'-nucleotidase (UMPH-1); This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterized by the ability to dephosphorylate nucleic acids. P5'N-1 catalyzes the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans.


Pssm-ID: 310424 [Multi-domain]  Cd Length: 246  Bit Score: 280.79  E-value: 1.56e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295  86 MTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKL 165
Cdd:pfam05822   1 MTLSKFRVNGERCPSSHGIFDNCKSIPEECRKKLRELYHKYYPIEIDPHMPIEEKVPYMVEWWTKSHALLIGQGLQKEAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 166 KEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDET-------------- 231
Cdd:pfam05822  81 AEVVAESDIMLRDGTHEFFDDLQQLNVPVLIFSAGLGDVLEEVLRQANVMHPNVKVVSNFMDFDDDgvlngfkgplihtf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747199295 232 -----------------------------------------------------VDELLEKYMDSYDIVLVQDESLEVANS 258
Cdd:pfam05822 161 nknetvldgteyfdqlhtrdniillgdslgdlgmadgvpsvehilkigflndkVEENLDKYMDAFDIVLVDDQTMDVPNA 240


                  ....*.
gi 1747199295 259 ILQKIL 264
Cdd:pfam05822 241 ILEMIL 246
HAD_Pase cd07524
phosphatase, similar to Bacillus subtilis MtnX; belongs to the haloacid dehalogenase-like ...
 158-233 5.28e-04

phosphatase, similar to Bacillus subtilis MtnX; belongs to the haloacid dehalogenase-like superfamily; Bacillus subtilis recycles two toxic byproducts of polyamine metabolism, methylthioadenosine and methylthioribose, into methionine by a salvage pathway. The sixth reaction in this pathway is catalyzed by B. subtilis MtnX: the dephosphorylation of 2- hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HKMTP- 1-P) into 1,2-dihydroxy-3-keto-5-methylthiopentene. The hydrolysis of HK-MTP-1-P is a two-step mechanism involving the formation of a transiently phosphorylated aspartyl intermediate. Members of this family belong 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: 319826 [Multi-domain]  Cd Length: 211  Bit Score: 40.01  E-value: 5.28e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1747199295 158 QALPKAKLKEI--VAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVyhPNVKVVSNFMDFD-ETVD 233
Cdd:cd07524    53 ELLPSSLKDEIieFLEKTAKIRPGFKEFVAFCQEHGIPFIIVSGGMDFFIEPLLEGLVI--EKIAIYCNGSDFSgEQIH 129
 
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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