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Conserved domains on  [gi|6005842|ref|NP_009129|]
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pyridoxal phosphate homeostasis protein isoform 2 [Homo sapiens]

Protein Classification

YggS family pyridoxal phosphate enzyme( domain architecture ID 10160097)

YggS family pyridoxal phosphate enzyme is a pyridoxal 5-phosphate (PLP)-dependent enzyme; similar to human pyridoxal phosphate homeostasis protein, which may be involved in intracellular homeostatic regulation of pyridoxal 5'-phosphate (PLP), the active form of vitamin B6

Gene Ontology:  GO:0030170

Graphical summary

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List of domain hits

 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, ...
 17-248 1.05e-150

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: 420.07  E-value: 1.05e-150
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQRKGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLE 176
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6005842  177 FVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKLNIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 248
Cdd:cd06822 156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
 
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, ...
 17-248 1.05e-150

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: 420.07  E-value: 1.05e-150
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQRKGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLE 176
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6005842  177 FVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKLNIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 248
Cdd:cd06822 156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-251 2.77e-87

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


Pssm-ID: 440094  Cd Length: 227  Bit Score: 259.20  E-value: 2.77e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKILslcpEIKWHFIGH 96
Cdd:COG0325   8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIEALADL----DIEWHFIGH 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNL 175
Cdd:COG0325  82 LQS---NKVKYVAELFdLIHSVDRLKLAEELNKRAAKAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAI-AALPNL 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6005842  176 EFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKKLNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGERD 251
Cdd:COG0325 156 RLRGLMTIAPLTEDPEE-VRPAFARLRELFDRL-RAQGPGLD--ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-250 1.11e-55

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: 178.88  E-value: 1.11e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842     41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGHLQKqNVNKLMaVPNLFMLETVDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842    121 KLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNpDFQL 200
Cdd:TIGR00044 105 KIATKLNEQREALLPP--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQ 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 6005842    201 LLSLREELckKLNIPADQV-ELSMGMSADFQHAVEVGSTNVRIGSTIFGER 250
Cdd:TIGR00044 181 MKVLFAQI--KQRSPHGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-251 1.58e-17

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 78.81  E-value: 1.58e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842     41 RLVAVSKtkpADmvieAYGHG------------QRTFGENYVQELLEKASN---PKILSLcpeikwhfiGHLQKQNVnKL 105
Cdd:pfam01168  22 KLMAVVK---AN----AYGHGavevaralleggADGFAVATLDEALELREAgitAPILVL---------GGFPPEEL-AL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842    106 MAVPNLFMleTVDSVKLADKVNSSWQRKGSPerLKVMVQINTSGeeSKHGLPPSETIAIVEHINAkCPNLEFVGLMTIGS 185
Cdd:pfam01168  85 AAEYDLTP--TVDSLEQLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFA 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6005842    186 FGHDLSQGPNP-DFQLLLSLREELcKKLNIPadQVELSMGMSAD-FQHAVEvgSTNVRIGSTIFGERD 251
Cdd:pfam01168 158 CADEPDDPYTNaQLARFREAAAAL-EAAGLR--PPVVHLANSAAiLLHPLH--FDMVRPGIALYGLSP 220
 
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, ...
 17-248 1.05e-150

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: 420.07  E-value: 1.05e-150
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGH 96
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQRKGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLE 176
Cdd:cd06822  76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6005842  177 FVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKLNIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 248
Cdd:cd06822 156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-251 2.77e-87

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


Pssm-ID: 440094  Cd Length: 227  Bit Score: 259.20  E-value: 2.77e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASNPKILslcpEIKWHFIGH 96
Cdd:COG0325   8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIEALADL----DIEWHFIGH 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNL 175
Cdd:COG0325  82 LQS---NKVKYVAELFdLIHSVDRLKLAEELNKRAAKAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAI-AALPNL 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6005842  176 EFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKKLNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGERD 251
Cdd:COG0325 156 RLRGLMTIAPLTEDPEE-VRPAFARLRELFDRL-RAQGPGLD--ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
PLPDE_III_YBL036c_like cd00635
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family ...
 17-248 4.48e-86

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: 256.24  E-value: 4.48e-86
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnPKILSlcPEIKWHFIGH 96
Cdd:cd00635   5 LEEVRERIAAAAERAGRDPDEV--TLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKA--EELPD--PDIEWHFIGH 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNL 175
Cdd:cd00635  79 LQT---NKVKYAVRLFdLIHSVDSLKLAEELNKRAEKEGRV--LDVLVQVNIGGEESKSGVAPEELEELLEEI-AALPNL 152

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6005842  176 EFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELCKKLNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFG 248
Cdd:cd00635 153 RIRGLMTIAPLTEDPEE-VRPYFRELRELRDELGAKGGVNLK--ELSMGMSGDFEIAIEEGATLVRIGTAIFG 222
PLPDE_III_Yggs_like cd06824
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-249 2.18e-64

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: 200.88  E-value: 2.18e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   17 LRAVNERVQQAVARRPRDLPAIQprLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGH 96
Cdd:cd06824   6 LAQVKQRIAQAAKQAGRDPSSVQ--LLAVSKTKPADAIREAYAAGQRHFGENYVQEALEKI---EALRDLQDIEWHFIGP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   97 LQKqNVNKLMAvPNLFMLETVDSVKLADKVNSswQRKGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLE 176
Cdd:cd06824  81 IQS-NKTKLIA-ENFDWVHSVDRLKIAKRLND--QRPAGLPPLNVCIQVNISGEDSKSGVAPEDAAELAEAI-SQLPNLR 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6005842  177 FVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKKLNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGE 249
Cdd:cd06824 156 LRGLMAIPAPTDDEAA-QRAAFKRLRQLFDQL-KKQYPDLD--TLSMGMSGDLEAAIAAGSTMVRIGTAIFGA 224
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-250 1.11e-55

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: 178.88  E-value: 1.11e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842     41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGHLQKqNVNKLMaVPNLFMLETVDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842    121 KLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNpDFQL 200
Cdd:TIGR00044 105 KIATKLNEQREALLPP--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQ 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 6005842    201 LLSLREELckKLNIPADQV-ELSMGMSADFQHAVEVGSTNVRIGSTIFGER 250
Cdd:TIGR00044 181 MKVLFAQI--KQRSPHGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
PLPDE_III cd06808
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
 41-243 4.16e-18

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: 80.44  E-value: 4.16e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842   41 RLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLEKASnpkilSLCPEIKWHFIGHLQKQNVNKLMAVPNLFMLeTVDSV 120
Cdd:cd06808  17 TLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRA-----AGIPPEPILFLGPCKQVSELEDAAEQGVIVV-TVDSL 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842  121 KLADKVNSSWQRKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNPDFQL 200
Cdd:cd06808  91 EELEKLEEAALKAGPP--ARVLLRIDTGDENGKFGVRPEELKALLERA-KELPHLRLVGLHTHFGSADEDYSPFVEALSR 167

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 6005842  201 LLSLREELCKKLNIPAdqvELSMGMSAD---FQHAVEVGSTNVRIG 243
Cdd:cd06808 168 FVAALDQLGELGIDLE---QLSIGGSFAilyLQELPLGTFIIVEPG 210
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-251 1.58e-17

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 78.81  E-value: 1.58e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842     41 RLVAVSKtkpADmvieAYGHG------------QRTFGENYVQELLEKASN---PKILSLcpeikwhfiGHLQKQNVnKL 105
Cdd:pfam01168  22 KLMAVVK---AN----AYGHGavevaralleggADGFAVATLDEALELREAgitAPILVL---------GGFPPEEL-AL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842    106 MAVPNLFMleTVDSVKLADKVNSSWQRKGSPerLKVMVQINTSGeeSKHGLPPSETIAIVEHINAkCPNLEFVGLMTIGS 185
Cdd:pfam01168  85 AAEYDLTP--TVDSLEQLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFA 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6005842    186 FGHDLSQGPNP-DFQLLLSLREELcKKLNIPadQVELSMGMSAD-FQHAVEvgSTNVRIGSTIFGERD 251
Cdd:pfam01168 158 CADEPDDPYTNaQLARFREAAAAL-EAAGLR--PPVVHLANSAAiLLHPLH--FDMVRPGIALYGLSP 220
PLPDE_III_LS_D-TA_like cd06820
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine ...
 116-267 4.90e-05

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like; This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists 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. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity.


Pssm-ID: 143494 [Multi-domain]  Cd Length: 353  Bit Score: 44.23  E-value: 4.90e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842  116 TVDSVKLADKVNSSWQRKGSPerLKVMVQINtSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGsfGHDLSQGPN 195
Cdd:cd06820 101 GVDSAEVARGLAEVAEGAGRP--LEVLVEVD-SGMNRCGVQTPEDAVALARAI-ASAPGLRFRGIFTYP--GHSYAPGAL 174

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842  196 P-----DFQLLLSLREELcKKLNIPADQVelSMGMSADFQHAVEV-GSTNVRIGSTIFGERDYSKK--PTPDKCAADVKA 267
Cdd:cd06820 175 EeaaadEAEALLAAAGIL-EEAGLEPPVV--SGGSTPTLWRSHEVpGITEIRPGTYIFNDASQVALgaCTLDDCALTVLA 251
LysA COG0019
Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Diaminopimelate ...
 145-185 7.67e-04

Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Diaminopimelate decarboxylase is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 439790 [Multi-domain]  Cd Length: 417  Bit Score: 40.52  E-value: 7.67e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 6005842  145 INTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMT-IGS 185
Cdd:COG0019 161 ISTGGKDSKFGIPLEDALEAYRRA-AALPGLRLVGLHFhIGS 201
PLPDE_III_AR_like_1 cd06815
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily ...
 158-247 9.00e-04

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists 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. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.


Pssm-ID: 143490 [Multi-domain]  Cd Length: 353  Bit Score: 40.22  E-value: 9.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6005842  158 PSETIAIVEHInAKCPNLEFVGLMT-IGSFGhdlSQGPNPD-FQLLLSLREELCKKLNIPADQVelSMGMSADFqHAVEV 235
Cdd:cd06815 134 PEDLLDFVEEI-LKLPGIELVGIGTnLGCYG---GVLPTEEnMGKLVELKEEIEKEFGIKLPII--SGGNSASL-PLLLK 206

                        90
                ....*....|....*..
gi 6005842  236 GS-----TNVRIGSTIF 247
Cdd:cd06815 207 GElpggiNQLRIGEAIL 223
PLPDE_III_DapDC cd06828
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; ...
 145-185 2.59e-03

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists 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. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.


Pssm-ID: 143501 [Multi-domain]  Cd Length: 373  Bit Score: 38.62  E-value: 2.59e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 6005842  145 INTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGL-MTIGS 185
Cdd:cd06828 138 ISTGGKDSKFGIPLEQALEAYRRA-KELPGLKLVGLhCHIGS 178
 
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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