1B54


Conserved Protein Domain Family
PLPDE_III_YBL036c_euk

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cd06822: PLPDE_III_YBL036c_euk 
Click on image for an interactive view with Cn3D
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).
Statistics
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PSSM-Id: 143496
View PSSM: cd06822
Aligned: 36 rows
Threshold Bit Score: 287.173
Threshold Setting Gi: 124506942
Created: 21-Mar-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
pyridoxalcatalytic
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:pyridoxal 5'-phosphate (PLP) binding site [chemical binding site]
Evidence:
  • Structure:1B54_A; Saccharomyces cerevisiae Hypothetical Protein-A binds PLP; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                        # #                     #                       
1B54_A        15 LIAQYESVREVVNAeaknvhvnenasKILLLVVSKLKPASDIQILYDh-GVREFGENY---VQELIEKAKLLPdDIKWHF 90  baker's yeast
XP_001021721   5 IAKSLKQVIDKVNSaikns---tktsRCTIVGASKTKPLELLQQAYDa-GLRHFGENY---VDEIVTKAPKLPqDIKWHY 77  Tetrahymena the...
XP_001439744   5 LQQNLQKVLQTIVKaset-----tnkQVTLVAVSKTKPVELIKEAYEg-GQKHFGENY---VNELIEKAPLLPnDISWHF 75  Paramecium tetr...
ABK22393      15 LRTVLRRVQQAAEKsgr------qasQVRVVAVSKTKPVSLIREVYEa-GHRYFGENY---VQEILDKAPELPtDIQWHF 84  Sitka spruce
XP_001315632   6 VAENYKHINEIVKNls---------sTAHLVCVSKTKPIEDLKQVFEa-GGRIFGENY---VDEIITKGPQLP-DAQFHM 71  Trichomonas vag...
T46722       159 LALNYKAVCDTVAQesg-------nrRVTLIAVSKTKSPACLLNLYNl-GQRVFGENY---VQELGEKAKELPeDTVWHF 227 Leishmania major
EAK88262      13 VIDNYMKIKNQIKElcsg-----fesFPELLVVSKYQSEENIKLLHEktDQKIFGENY---VQELMEKSRNLPkSIKWHF 84  Cryptosporidium...
EDQ69823      13 LRNVMQRVSQASERanr------pasQVRLVAVSKTKPVELVQEVYDa-GHRHFGENY---VQELIDKAPQLPqDIKWHF 82  Physcomitrella ...
XP_001689869  10 LQDVLSRMKQATERanr-------thPVRLVAVSKTKPAEALQEAYDa-GQRVFGENYvqaRCEMLDKAPALPgDVQWHF 81  Chlamydomonas r...
NP_567760     14 LRSVILRARKAAEQvgr------daeRVRVLPVSKTKPVSLIRQIYDa-GHRCFGENY---VQEIIDKAPQLPeDIEWHF 83  thale cress
Feature 1        #                                                                               
1B54_A        91 IGGLQTNKCKDLAKv-PNLYSVETIDSLKKAKKLNESRAKfqpdcNPILCNVQINTSHEDQKSGLnneaEIFEVIDFFLs 169 baker's yeast
XP_001021721  78 IGHLQTNKIKQVLV--PNLYMLETIDSIKLATKVNKECQKl---sKKLKVLIQVKTSTEDRVSTE----DAPALVEFIMt 148 Tetrahymena the...
XP_001439744  76 IGHLQTNKVSTIMKi-QNLEFIQSVDSLKLAQKIEKHCEKl---gRNINIFVQIKLSEEESKTGAei-dEAKLIIQEIIt 150 Paramecium tetr...
ABK22393      85 IGHLQSNKAKAVIAgvPNLYMVESVDSSKVANHLDRAVSSig--rKPLKVLVQVNTSGEESKYGVep-sECVELAKHVKf 161 Sitka spruce
XP_001315632  72 IGHLQSNKVAKLCKv-ENLVMIQSIDSKELATKVDKQYVNr----KPLEVLIQINTSAEPQKSGIangaEASELAKFIVe 146 Trichomonas vag...
T46722       228 IGHLQSNKVKELLEgvPNLRVVQTIDSENLASKVNEGCRKyr-ggRPLEVYIQVNTSGEETKSGTepgeATVTLAKYIAd 306 Leishmania major
EAK88262      85 IGHLQSNKVKTLLSi-DNLEVIETVDSIKLAQVLNKECQLqg--rSVLKVMIQVKTSNEVNKSGAqi-sEAINIFEYIIs 160 Cryptosporidium...
EDQ69823      83 IGHLQSNKAKALITsvPNLYMVEGVDSQKVANHLNRAVSGlg--rPPLSVLVQVNTSREESKSGVnp-sECVDLAKHLKe 159 Physcomitrella ...
XP_001689869  82 IGHLQSNKVKAVLEgvPNLAMVETVDSAKLADKLNKTLETvsgrtAPLAVMVQVNTSGEESKYGVep-tECVSLAKHIAq 160 Chlamydomonas r...
NP_567760     84 VGHLQSNKAKTLLTgvPNLAMVHGVDGEKVANHLDRAVSNlg--rHPLKVLVQVNTSGEVSKSGIep-sSVVELARHVKh 160 thale cress
Feature 1                   # #                                               ##              ###
1B54_A       170 eECKYIKLNGLMTIGSWNvshedskENRDFATLVEWKKKIDAKFGT--------SLKLSMGMSADFREAIRQGTAEVRIG 241 baker's yeast
XP_001021721 149 -QCPNLEFSGLMTIGYEG-------DENAFIQLYDLKIEICEKFKLnk-----dEIELSMGMSQDFEKAILYGSTNVRIG 215 Tetrahymena the...
XP_001439744 151 -KFKFIKLIGLMTIGPIG-------NKEIFQQLVDLAKKFENEFNLq-------PLNLSMGMSGDYLDAIKYGADYVRVG 215 Paramecium tetr...
ABK22393     162 -QCPNLEFSGLMTIGMLDys----sRPENFEALSGCRIEVCKALGIse-----dQCELSMGMSGDFEQAIEMGSTNVRIG 231 Sitka spruce
XP_001315632 147 -NCHNLKFRGVMTIGETGe------ASRDFACLVEERRRIAGELGMkp-----eDLELSMGMSADYELALKMGATFVRVG 214 Trichomonas vag...
T46722       307 -ECPLLQLKGLMTIGMPDyt----sRPENFECLTKCREDVAQPVQMap-----eDLELSMGMSGDYVNAIRMGSTAVRVG 376 Leishmania major
EAK88262     161 -ECRNLKFQGLMTMGDSDvn----lTSECFNKMVNLRNIINEKISKngnydqsiECRLSMGTTRDMEIAIKNHTNEVRIG 235 Cryptosporidium...
EDQ69823     160 -ECPNLRFSGLMTIGMLGys----sTAEFFKTLVNCREKVCKELEIpv-----eECELSMGMSGDFELAIEMGSTNVRVG 229 Physcomitrella ...
XP_001689869 161 -NCPKLRLAGLMTIGMPDys----sRPECFICLSGCRDAVATELGLrp-----eQLELSMGMSGDFEQAIEMGSTNIRVG 230 Chlamydomonas r...
NP_567760    161 -HCPNLVFSGLMTIGMPDyt----sTPENFRTLSNCRADVCKALGMae-----dQFELSMGMSGDFELAIEMGSTNVRVG 230 thale cress
Feature 1        #    
1B54_A       242 TDIFG 246 baker's yeast
XP_001021721 216 TTIFG 220 Tetrahymena thermophila SB210
XP_001439744 216 SAIFG 220 Paramecium tetraurelia strain d4-2
ABK22393     232 STIFG 236 Sitka spruce
XP_001315632 215 SSIFG 219 Trichomonas vaginalis G3
T46722       377 TSIFG 381 Leishmania major
EAK88262     236 SAIFG 240 Cryptosporidium parvum Iowa II
EDQ69823     230 STIFG 234 Physcomitrella patens subsp. patens
XP_001689869 231 STIFG 235 Chlamydomonas reinhardtii
NP_567760    231 STIFG 235 thale cress

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