1B54,1W8G


Conserved Protein Domain Family
PLPDE_III_YBL036c_like

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cd00635: PLPDE_III_YBL036c_like 
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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.
Statistics
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PSSM-Id: 143483
View PSSM: cd00635
Aligned: 128 rows
Threshold Bit Score: 201.929
Threshold Setting Gi: 152967138
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
pyridoxalcatalytic
Conserved site includes 9 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
  • Structure:1W8G_A; Escherichia coli Yggs protein binds PLP; defined at 4A contacts.
    View structure with Cn3D
  • Citation:PMID 8864839

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                        # #                     #                       
1B54_A        15 LIAQYESVREVVNaeaknvhvnenaskILLLVVSKLKPASDIQILYd-hGVREFGENYVQELIEKAKLLpd-----dIKW 88  baker's yeast
YP_001940760  10 IQERLEKLQYKIEtasrks--grnpkdITLVAVTKGFGPEVVETLLr-mGIVHIGENRVQEARLKKEQIge-----kGIW 81  Methylokorus in...
ZP_01872723  239 VPQRYDNVLNDIAesakkh--qrdmtdIQLLTVTKNHPADKIFALYk-hGQNEFAENRVQELLTKAESLpq-----dIHW 310 Lentisphaera ar...
YP_001875681   7 VIEKYNKVITRIRnsaevr--nrnfkrIKPILVIKYAKDLDVLELLgflGAASAAESKLQDAQKRWNKDefkalrnkTAL 84  Elusimicrobium ...
ACI18703       7 IAENWKKVQERIIkkaeec--grdpseINVVAVSKGVPPEGIREAVk-vGIKAIGENRVQEAEKKISLLsd----lsCEW 79  Dictyoglomus th...
CAO80073       3 IAENIKHLQDNIAdilsrl---nrkdeITLVAVTKTHPVEIIETALq-sGIEHIGENRVQEARRKIPFLkv----pyKGF 74  Candidatus Cloa...
YP_001356166   6 LRDNFDEIVQRVEkarmer---sehhiVQIVAVTKYVGAEEIEALYe-lGQRAFGESRVQDLKTKSEALgd----lpIEW 77  Nitratiruptor s...
EAY57389       8 FRDRFDRLKRDIAvkarsn---gfsheIRIVGVTKGRSDEDALALFt-aGVDHLAENRWEFLSGRADLClsg---rsPLW 80  Leptospirillum ...
O25156         4 YRQKIDALITKIEkartay---srhhiVKIVAVSKNASPEAIQHYYn-cSQRAFGENKVQDLKTKMHSLeh----lpLEW 75  Helicobacter py...
NP_711661      3 VLESYQKIYEELQqlrs-------enpPTLIAVSKFQPIEKIKEAIg-cGVVHFGENRIQEGIEKFSQWlkdk-ntsLVL 73  Leptospira inte...
Feature 1          #                                                                             
1B54_A        89 HFIGGLQTNKCKDLAKvpnlYSVETIDSLKKAKKLNESRakfqpdcnPILCNVQINTShedQKSGLnn---eaEIFEVID 165 baker's yeast
YP_001940760  82 HFIGHLQKNKIKLTSHl--fDWIDSVDDLEDATLLSHFAqnm---gkTLKILVQVNVSgesTKFGTtp----eLAQSLCL 152 Methylokorus in...
ZP_01872723  311 HLIGPLQSNKVRQAVKv--aKTIHSVDNTSLAKRIDRIAeee---gkQIDIFIQLNLTgeiQKSGIst----lSLEKLLI 381 Lentisphaera ar...
YP_001875681  85 HFIGALQKNKIAKIVNl--fDYIDSVDTIEHAEFINAKAkeq---gkKVNCLLQIKLTksaTQSGAnp----qDVHTLVE 155 Elusimicrobium ...
ACI18703      80 HMVGHLQKNKVKKAINl--fSLIHSVDTFELAEELNKYAeke---ekEVDVLIQLNLSeepTKYGFke----eEFWKVYE 150 Dictyoglomus th...
CAO80073      75 HFIGHLQSNKINQVLElk-pFLIQSVHSLELAKKLHLALgrt---nrTQDILIQINSSqefSKSGFsl----aEAKNAIC 146 Candidatus Cloa...
YP_001356166  78 HFIGRLQKNKINHLIDld-pWLMQSLDSLELAIEIDKRLerk---gkKMDCLLQINSAkeeSKAGVlpevaydEYLKIIE 153 Nitratiruptor s...
EAY57389      81 HFIGALQRRSLRQNYRp--vYSVDTVDRPSVLPVLARLAeqa---kvRQNILVELDLTglpGRSGVre----dNLDSLLK 151 Leptospirillum ...
O25156        76 HMIGSLQENKINALLSlk-pALLHSLDSLKLALKIEKRCeil---gvNLNALLQVNSAyeeSKSGVvp----eEALEIYS 147 Helicobacter py...
NP_711661     74 HHIGPVQSGTLRKLFLg--ySYAHGVGSVGIVNELLTRAlre---ekKILYFLQANLTgenTKHGFer----kELIEILK 144 Leptospira inte...
Feature 1                         #                                          #               # ##
1B54_A       166 FFLseeckyIKLNGLMTIGSwnvshedskeNRDFATLVEWKKKIDakf---gtsLKLSMGMSADFREAIRQGTAEVRIGT 242 baker's yeast
YP_001940760 153 AINal--prLEILGLMTIAPaspd--pekvRPVFSRLRMLRDKIEsqsg--iplPVLSMGMSQDFEVAIEEGATMIRIGH 226 Methylokorus in...
ZP_01872723  382 SCSel--knINLIGLMTMGPlsas--keenLKVFKELKEQSVEHSkyf---endVKLSMGMSGDFDEAIECGSHILRIGS 454 Lentisphaera ar...
YP_001875681 156 HIKtl--ehINLKGFMAIAPqven--iedlRHLFKEIKILNDKELgp------eAELSLGMSNDFETAVEEGSTMPRIGS 225 Elusimicrobium ...
ACI18703     151 KIFel--knLNVKGLMTIGPltgd--knevRKVFRKLYTIWEKLKentk--lslPYLSMGMSEDFEIAIEEGANLLRLGR 224 Dictyoglomus th...
CAO80073     147 QISty--snLHIKGLMTIGMlaep---evsRPLFARMKSLFEEIKalaipnvdmQYLSMGMSNDYVQALEEGSNMLRIGT 221 Candidatus Cloa...
YP_001356166 154 ETKh-----INLCGVMTIGAhtdd--ttliQKSFETTYKIFESLQph-----gaKICSMGMSNDFELAIRCGSNMVRIGS 221 Nitratiruptor s...
EAY57389     152 ECSgw--peLEVKGFLVMGPpped--rafsRQVFRRGRALFERFFsg-----ndHVLSMGMSEDYSEAVAEGSTEVRIGR 222 Leptospirillum ...
O25156       148 QISetc-khLKLKGLMCIGAhtdd--ekeiEKSFITTKKLFDQIKn-------aSVLSMGMSDDFELAIACGANLLRIGS 217 Helicobacter py...
NP_711661    145 QKEklsntyCKLEGLMVMGPsdgd--ltktREVFRELSKFKKDYIp-------eAKLSMGMSGDYKIAIEEGSDFVRIGS 215 Leptospira inte...
Feature 1            
1B54_A       243 DIFG 246 baker's yeast
YP_001940760 227 FLLG 230 Methylokorus infernorum V4
ZP_01872723  455 AIMG 458 Lentisphaera araneosa HTCC2155
YP_001875681 226 AIFG 229 Elusimicrobium minutum Pei191
ACI18703     225 IIFQ 228 Dictyoglomus thermophilum H-6-12
CAO80073     222 AIFG 225 Candidatus Cloacamonas acidaminovorans
YP_001356166 222 LFFK 225 Nitratiruptor sp. SB155-2
EAY57389     223 YFFG 226 Leptospirillum sp. Group II UBA
O25156       218 FLFK 221 Helicobacter pylori
NP_711661    216 AIFG 219 Leptospira interrogans serovar Lai str. 56601

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