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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYI---------LSScpEIKWHFIGHLQK 87
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVqeliekapdLPI--DIKWHFIGHLQS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 84872187  88 QNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 141
Cdd:cd06822  79 NKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132

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).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYI---------LSScpEIKWHFIGHLQK 87
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVqeliekapdLPI--DIKWHFIGHLQS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 84872187  88 QNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 141
Cdd:cd06822  79 NKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187    41 RLVAVSKTKPADMVIEAYGHGQRTFGENYI---------LSSCPEIKWHFIGHLQKqNVNKLMaVPNLSMLETVDSVKLA 111
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVqelvekirhLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSLKIA 107

                          90       100       110
                  ....*....|....*....|....*....|
gi 84872187   112 DKVNSSWQKKGPtePLKVMVQINTSGEDSK 141
Cdd:TIGR00044 108 TKLNEQREALLP--PLNVLLQINISDEESK 135

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).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187  17 LRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYI---------LSScpEIKWHFIGHLQK 87
Cdd:cd06822   1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVqeliekapdLPI--DIKWHFIGHLQS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 84872187  88 QNVNKLMAVPNLSMLETVDSVKLADKVNSSWQKKGPTEPLKVMVQINTSGEDSK 141
Cdd:cd06822  79 NKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESK 132

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187  17 LRAVNERVQQSVARRPRDLPAIqpRLVAVSKTKPADMVIEAYGHGQRTFGENYI---------LSScPEIKWHFIGHLQK 87
Cdd:cd00635   5 LEEVRERIAAAAERAGRDPDEV--TLVAVSKTVPAEAIREAIEAGQRDFGENRVqealdkaeeLPD-PDIEWHFIGHLQT 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 84872187  88 qnvNKL-MAVPNLSMLETVDSVKLADKVNSSWQKKGPtePLKVMVQINTSGEDSK 141
Cdd:cd00635  82 ---NKVkYAVRLFDLIHSVDSLKLAEELNKRAEKEGR--VLDVLVQVNIGGEESK 131

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84872187  41 RLVAVSKTKPADMVIEAYGHGQRTFGENYI-------LSSCPEIKWHFIGHLQKQNVNKLMAVPNLSMLeTVDSVKLADK 113
Cdd:cd06808  17 TLFAVVKANANPEVARTLAALGTGFDVASLgealllrAAGIPPEPILFLGPCKQVSELEDAAEQGVIVV-TVDSLEELEK 95

                        90       100
                ....*....|....*....|....*...
gi 84872187 114 VNSSWQKKGPtePLKVMVQINTSGEDSK 141
Cdd:cd06808  96 LEEAALKAGP--PARVLLRIDTGDENGK 121