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Conserved domains on  [gi|84872182|ref|NP_001034166|]
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pyridoxal phosphate homeostasis protein isoform b [Mus musculus]

Protein Classification

type III PLP-dependent enzyme domain-containing protein( domain architecture ID 469)

type III PLP (pyridoxal 5-phosphate)-dependent enzyme domain-containing protein, similar to alanine racemase which catalyzes the interconversion of L-alanine and D-alanine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLPDE_III super family cl00261
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
 17-153 2.03e-81

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.


The actual alignment was detected with superfamily member cd06822:

Pssm-ID: 469695  Cd Length: 227  Bit Score: 239.41  E-value: 2.03e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlsscpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKQNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 153
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132
 
Name Accession Description Interval E-value
PLPDE_III_YBL036c_euk cd06822
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-153 2.03e-81

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins; This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog).


Pssm-ID: 143496  Cd Length: 227  Bit Score: 239.41  E-value: 2.03e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlsscpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKQNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 153
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-153 3.56e-47

Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and metabolism];


Pssm-ID: 440094  Cd Length: 227  Bit Score: 152.50  E-value: 3.56e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNpkiLSSCPeIKWHFIGH 96
Cdd:COG0325   8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIEA---LADLD-IEWHFIGH 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKQNVNKlmAVPNLSMLETVDSVKLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:COG0325  82 LQSNKVKY--VAELFDLIHSVDRLKLAEELNKRAAKAGR--PLDVLLQVNISGEESK 134
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-153 3.61e-34

pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129155 [Multi-domain]  Cd Length: 229  Bit Score: 119.18  E-value: 3.61e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182    41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSSCPEIKWHFIGHLQKqNVNKLMaVPNLSMLETVDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110
                  ....*....|....*....|....*....|...
gi 84872182   121 KLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:TIGR00044 105 KIATKLNEQREALLP--PLNVLLQINISDEESK 135
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-149 1.97e-05

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 42.60  E-value: 1.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182    41 RLVAVSKtkpADmvieAYGHG------------QRTFGENYVQELLEKASNPkilsscPEIKWHFIGHLQKQNVnKLMAV 108
Cdd:pfam01168  22 KLMAVVK---AN----AYGHGavevaralleggADGFAVATLDEALELREAG------ITAPILVLGGFPPEEL-ALAAE 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 84872182   109 PNLSMleTVDSVKLADKVNSSWQKKGPtePLKVMVQINTSG 149
Cdd:pfam01168  88 YDLTP--TVDSLEQLEALAAAARRLGK--PLRVHLKIDTGM 124
 
Name Accession Description Interval E-value
PLPDE_III_YBL036c_euk cd06822
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-153 2.03e-81

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins; This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog).


Pssm-ID: 143496  Cd Length: 227  Bit Score: 239.41  E-value: 2.03e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlsscpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKQNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 153
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-153 3.56e-47

Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and metabolism];


Pssm-ID: 440094  Cd Length: 227  Bit Score: 152.50  E-value: 3.56e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNpkiLSSCPeIKWHFIGH 96
Cdd:COG0325   8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIEA---LADLD-IEWHFIGH 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKQNVNKlmAVPNLSMLETVDSVKLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:COG0325  82 LQSNKVKY--VAELFDLIHSVDRLKLAEELNKRAAKAGR--PLDVLLQVNISGEESK 134
PLPDE_III_YBL036c_like cd00635
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family ...
 17-153 2.93e-46

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity.


Pssm-ID: 143483  Cd Length: 222  Bit Score: 149.93  E-value: 2.93e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnPKILSscPEIKWHFIGH 96
Cdd:cd00635   5 LEEVRERIAAAAERAGRDPDEV--TLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKA--EELPD--PDIEWHFIGH 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 84872182  97 LQKqnvNKL-MAVPNLSMLETVDSVKLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:cd00635  79 LQT---NKVkYAVRLFDLIHSVDSLKLAEELNKRAEKEGR--VLDVLVQVNIGGEESK 131
PLPDE_III_Yggs_like cd06824
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-153 6.55e-36

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn.


Pssm-ID: 143497  Cd Length: 224  Bit Score: 123.45  E-value: 6.55e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  17 LRAVNERVQQSVARRPRDLPAIQprLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSSCPEIKWHFIGH 96
Cdd:cd06824   6 LAQVKQRIAQAAKQAGRDPSSVQ--LLAVSKTKPADAIREAYAAGQRHFGENYVQEALEKI---EALRDLQDIEWHFIGP 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84872182  97 LQKqNVNKLMAvPNLSMLETVDSVKLADKVNSswQKKGPTEPLKVMVQINTSGEDSK 153
Cdd:cd06824  81 IQS-NKTKLIA-ENFDWVHSVDRLKIAKRLND--QRPAGLPPLNVCIQVNISGEDSK 133
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-153 3.61e-34

pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129155 [Multi-domain]  Cd Length: 229  Bit Score: 119.18  E-value: 3.61e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182    41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSSCPEIKWHFIGHLQKqNVNKLMaVPNLSMLETVDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110
                  ....*....|....*....|....*....|...
gi 84872182   121 KLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:TIGR00044 105 KIATKLNEQREALLP--PLNVLLQINISDEESK 135
PLPDE_III cd06808
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
 41-153 3.19e-09

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.


Pssm-ID: 143484 [Multi-domain]  Cd Length: 211  Bit Score: 53.09  E-value: 3.19e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182  41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASnpkilSSCPEIKWHFIGHLQKQNVNKLMAVPNLSMLeTVDSV 120
Cdd:cd06808  17 TLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRA-----AGIPPEPILFLGPCKQVSELEDAAEQGVIVV-TVDSL 90

                        90       100       110
                ....*....|....*....|....*....|...
gi 84872182 121 KLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 153
Cdd:cd06808  91 EELEKLEEAALKAGP--PARVLLRIDTGDENGK 121
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-149 1.97e-05

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 42.60  E-value: 1.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872182    41 RLVAVSKtkpADmvieAYGHG------------QRTFGENYVQELLEKASNPkilsscPEIKWHFIGHLQKQNVnKLMAV 108
Cdd:pfam01168  22 KLMAVVK---AN----AYGHGavevaralleggADGFAVATLDEALELREAG------ITAPILVLGGFPPEEL-ALAAE 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 84872182   109 PNLSMleTVDSVKLADKVNSSWQKKGPtePLKVMVQINTSG 149
Cdd:pfam01168  88 YDLTP--TVDSLEQLEALAAAARRLGK--PLRVHLKIDTGM 124
 
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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