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Conserved domains on  [gi|1159261258|ref|NP_001336277|]
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pyridoxal phosphate homeostasis protein isoform 4 [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, ...
 1-196 7.45e-128

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: 359.98  E-value: 7.45e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGHLQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQR 80
Cdd:cd06822    37 LIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGHLQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEK 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  81 KGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLEFVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKL 160
Cdd:cd06822   112 LGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLKFSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKL 191

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1159261258 161 NIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 196
Cdd:cd06822   192 GINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 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, ...
 1-196 7.45e-128

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: 359.98  E-value: 7.45e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGHLQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQR 80
Cdd:cd06822    37 LIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGHLQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEK 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  81 KGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLEFVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKL 160
Cdd:cd06822   112 LGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLKFSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKL 191

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1159261258 161 NIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 196
Cdd:cd06822   192 GINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 1-199 1.00e-73

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


Pssm-ID: 440094  Cd Length: 227  Bit Score: 222.61  E-value: 1.00e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKASNPKILslcpEIKWHFIGHLQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQ 79
Cdd:COG0325    42 AIREAYAAGQRDFGENRVQEALEKIEALADL----DIEWHFIGHLQS---NKVKYVAELFdLIHSVDRLKLAEELNKRAA 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  80 RKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKK 159
Cdd:COG0325   115 KAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAI-AALPNLRLRGLMTIAPLTEDPEE-VRPAFARLRELFDRL-RA 189

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1159261258 160 LNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGERD 199
Cdd:COG0325   190 QGPGLD--ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 4-198 2.67e-48

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: 158.08  E-value: 2.67e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   4 EAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGHLQKqNVNKLMaVPNLFMLETVDSVKLADKVNSSWQRKGS 83
Cdd:TIGR00044  45 EAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSLKIATKLNEQREALLP 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  84 PerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNpDFQLLLSLREELckKLNIP 163
Cdd:TIGR00044 120 P--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQMKVLFAQI--KQRSP 193

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1159261258 164 ADQV-ELSMGMSADFQHAVEVGSTNVRIGSTIFGER 198
Cdd:TIGR00044 194 HGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
5-199 1.21e-16

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 75.34  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   5 AYGHG------------QRTFGENYVQELLEKASN---PKILSLcpeikwhfiGHLQKQNVnKLMAVPNLFMleTVDSVK 69
Cdd:pfam01168  31 AYGHGavevaralleggADGFAVATLDEALELREAgitAPILVL---------GGFPPEEL-ALAAEYDLTP--TVDSLE 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  70 LADKVNSSWQRKGSPerLKVMVQINTSGeeSKHGLPPSETIAIVEHINAkCPNLEFVGLMTIGSFGHDLSQGPNP-DFQL 148
Cdd:pfam01168  99 QLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFACADEPDDPYTNaQLAR 173

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1159261258 149 LLSLREELcKKLNIPadQVELSMGMSAD-FQHAVEvgSTNVRIGSTIFGERD 199
Cdd:pfam01168 174 FREAAAAL-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, ...
 1-196 7.45e-128

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: 359.98  E-value: 7.45e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKASNPKIlslcpEIKWHFIGHLQKQNVNKLMAVPNLFMLETVDSVKLADKVNSSWQR 80
Cdd:cd06822    37 LIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGHLQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEK 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  81 KGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLEFVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKL 160
Cdd:cd06822   112 LGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLKFSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKL 191

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1159261258 161 NIPADQVELSMGMSADFQHAVEVGSTNVRIGSTIFG 196
Cdd:cd06822   192 GINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 1-199 1.00e-73

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


Pssm-ID: 440094  Cd Length: 227  Bit Score: 222.61  E-value: 1.00e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKASNPKILslcpEIKWHFIGHLQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQ 79
Cdd:COG0325    42 AIREAYAAGQRDFGENRVQEALEKIEALADL----DIEWHFIGHLQS---NKVKYVAELFdLIHSVDRLKLAEELNKRAA 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  80 RKGSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKK 159
Cdd:COG0325   115 KAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAI-AALPNLRLRGLMTIAPLTEDPEE-VRPAFARLRELFDRL-RA 189

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1159261258 160 LNIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGERD 199
Cdd:COG0325   190 QGPGLD--ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
PLPDE_III_YBL036c_like cd00635
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family ...
 4-196 1.21e-72

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: 220.03  E-value: 1.21e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   4 EAYGHGQRTFGENYVQELLEKAsnPKILSlcPEIKWHFIGHLQKqnvNKLMAVPNLF-MLETVDSVKLADKVNSSWQRKG 82
Cdd:cd00635    42 EAIEAGQRDFGENRVQEALDKA--EELPD--PDIEWHFIGHLQT---NKVKYAVRLFdLIHSVDSLKLAEELNKRAEKEG 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  83 SPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELCKKLNI 162
Cdd:cd00635   115 RV--LDVLVQVNIGGEESKSGVAPEELEELLEEI-AALPNLRIRGLMTIAPLTEDPEE-VRPYFRELRELRDELGAKGGV 190

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1159261258 163 PADqvELSMGMSADFQHAVEVGSTNVRIGSTIFG 196
Cdd:cd00635   191 NLK--ELSMGMSGDFEIAIEEGATLVRIGTAIFG 222
PLPDE_III_Yggs_like cd06824
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 1-197 4.19e-52

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: 167.75  E-value: 4.19e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   1 MVIEAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGHLQKqNVNKLMAvPNLFMLETVDSVKLADKVNSswQR 80
Cdd:cd06824    40 AIREAYAAGQRHFGENYVQEALEKI---EALRDLQDIEWHFIGPIQS-NKTKLIA-ENFDWVHSVDRLKIAKRLND--QR 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  81 KGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQgPNPDFQLLLSLREELcKKL 160
Cdd:cd06824   113 PAGLPPLNVCIQVNISGEDSKSGVAPEDAAELAEAI-SQLPNLRLRGLMAIPAPTDDEAA-QRAAFKRLRQLFDQL-KKQ 189

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1159261258 161 NIPADqvELSMGMSADFQHAVEVGSTNVRIGSTIFGE 197
Cdd:cd06824   190 YPDLD--TLSMGMSGDLEAAIAAGSTMVRIGTAIFGA 224
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 4-198 2.67e-48

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: 158.08  E-value: 2.67e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   4 EAYGHGQRTFGENYVQELLEKAsnpKILSLCPEIKWHFIGHLQKqNVNKLMaVPNLFMLETVDSVKLADKVNSSWQRKGS 83
Cdd:TIGR00044  45 EAYDAGQRAFGENYVQELVEKI---RHLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSLKIATKLNEQREALLP 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  84 PerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNpDFQLLLSLREELckKLNIP 163
Cdd:TIGR00044 120 P--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQMKVLFAQI--KQRSP 193

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1159261258 164 ADQV-ELSMGMSADFQHAVEVGSTNVRIGSTIFGER 198
Cdd:TIGR00044 194 HGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
5-199 1.21e-16

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 75.34  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   5 AYGHG------------QRTFGENYVQELLEKASN---PKILSLcpeikwhfiGHLQKQNVnKLMAVPNLFMleTVDSVK 69
Cdd:pfam01168  31 AYGHGavevaralleggADGFAVATLDEALELREAgitAPILVL---------GGFPPEEL-ALAAEYDLTP--TVDSLE 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  70 LADKVNSSWQRKGSPerLKVMVQINTSGeeSKHGLPPSETIAIVEHINAkCPNLEFVGLMTIGSFGHDLSQGPNP-DFQL 148
Cdd:pfam01168  99 QLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFACADEPDDPYTNaQLAR 173

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1159261258 149 LLSLREELcKKLNIPadQVELSMGMSAD-FQHAVEvgSTNVRIGSTIFGERD 199
Cdd:pfam01168 174 FREAAAAL-EAAGLR--PPVVHLANSAAiLLHPLH--FDMVRPGIALYGLSP 220
PLPDE_III cd06808
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
 2-191 4.00e-16

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: 73.89  E-value: 4.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258   2 VIEAYGHGQRTFGENYVQELLEKASnpkilSLCPEIKWHFIGHLQKQNVNKLMAVPNLFMLeTVDSVKLADKVNSSWQRK 81
Cdd:cd06808    30 VARTLAALGTGFDVASLGEALLLRA-----AGIPPEPILFLGPCKQVSELEDAAEQGVIVV-TVDSLEELEKLEEAALKA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  82 GSPerLKVMVQINTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGSFGHDLSQGPNPDFQLLLSLREELCKKLN 161
Cdd:cd06808   104 GPP--ARVLLRIDTGDENGKFGVRPEELKALLERA-KELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALDQLGELGI 180

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1159261258 162 IPAdqvELSMGMSAD---FQHAVEVGSTNVRIG 191
Cdd:cd06808   181 DLE---QLSIGGSFAilyLQELPLGTFIIVEPG 210
PLPDE_III_LS_D-TA_like cd06820
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine ...
 64-215 2.26e-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: 2.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258  64 TVDSVKLADKVNSSWQRKGSPerLKVMVQINtSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMTIGsfGHDLSQGPN 143
Cdd:cd06820   101 GVDSAEVARGLAEVAEGAGRP--LEVLVEVD-SGMNRCGVQTPEDAVALARAI-ASAPGLRFRGIFTYP--GHSYAPGAL 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258 144 P-----DFQLLLSLREELcKKLNIPADQVelSMGMSADFQHAVEV-GSTNVRIGSTIFGERDYSKK--PTPDKCAADVKA 215
Cdd:cd06820   175 EeaaadEAEALLAAAGIL-EEAGLEPPVV--SGGSTPTLWRSHEVpGITEIRPGTYIFNDASQVALgaCTLDDCALTVLA 251
LysA COG0019
Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Diaminopimelate ...
 93-133 4.74e-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: 4.74e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1159261258  93 INTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGLMT-IGS 133
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 ...
 106-195 9.73e-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: 39.45  E-value: 9.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159261258 106 PSETIAIVEHInAKCPNLEFVGLMT-IGSFGhdlSQGPNPD-FQLLLSLREELCKKLNIPADQVelSMGMSADFqHAVEV 183
Cdd:cd06815   134 PEDLLDFVEEI-LKLPGIELVGIGTnLGCYG---GVLPTEEnMGKLVELKEEIEKEFGIKLPII--SGGNSASL-PLLLK 206

                          90
                  ....*....|....*..
gi 1159261258 184 GS-----TNVRIGSTIF 195
Cdd:cd06815   207 GElpggiNQLRIGEAIL 223
PLPDE_III_DapDC cd06828
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; ...
 93-133 1.66e-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: 1.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1159261258  93 INTSGEESKHGLPPSETIAIVEHInAKCPNLEFVGL-MTIGS 133
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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