Conserved Protein Domain Family
PLPDE_III_AR_like_1

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cd06815: PLPDE_III_AR_like_1 
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.
Statistics
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PSSM-Id: 143490
View PSSM: cd06815
Aligned: 39 rows
Threshold Bit Score: 410.397
Threshold Setting Gi: 171318070
Created: 12-Jun-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the binding of the PLP cofactor and substrate analogs to other members of the superfamily.
  • Comment:The active site is composed of residues from both subunits of the dimer. There are two active sites in the functional dimer.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       # #                    #                      #  
gi 150390137   7 NPKVTIDLaKLRHNARVMTEKCneYGIAIAGVTKVFGGRPEIAQAMIDgGIQYLADSRVENLKKMKDLSL--PKILLRLP 84
gi 171318070   1 MSKLIIDLeKIRHNLGVIKRACdrRDLKLNAVLKSCQLLPEVVNALIQcDIERMSFSGPVDFTSAGPGKLp-HTTLLKMP 79
gi 126647380   1 MALLTLHRtKLKENFEFLKELFdsQKISWGVVSKLLCGNRMYLQELINlGVREIHDSRISNLAMVKKIKPsvQTVYIKPV 80
gi 193216675   2 YPRIVINEaKFKNNIKKAIEICkaKNIEVLAVTKGFVGQRRMAELYYEaGIRYFGDSRLDNFEVYKDIPG--HKQMLRLP 79
gi 138895645   4 YPRVTWDEkKLIHNARVLNAICk-HHVEWIPVTKSVGANIEIVDSLYKqGYRKFADSRLQNLKAIKEYDSsiNTCLLRIP 82
gi 21283833    1 MAHVNINIsKIKYNAKVLQTVFqsKNMQFTPVIKCIAGDRTIVESLKAlGINHVAESRLDNIISIADQDL--TYTLLRTP 78
gi 70725863    1 MAQININLsKIEYNADALRTLLenNDIHLTPVIKCIAGDSRIIETLIQsGFTHFAESRLENINEDFKGQC--NYLLLRPT 78
gi 169334420   2 KPTLKINLnKIYDNAKIVKDTLdkYNVDITSVTKLHCCNPVIVDTLMQaGIKKFGDSRIDNLKNIKDIDA--EKWLIRLP 79
gi 126663893   1 MAFLKLYKtKLQHNYSFLNTLFkeRNIEWGIVTKILCGNTIYLKELLDlGVTEMHDSRISNLKKIKKLNPevQTVYIKPP 80
gi 27468687    1 MANVRVNLsKIKYNAKVLQSLLerRHIHFTPVIKCVAGDKRIVSSIKSlGITHFAESRLDNIEQLKDLDI--TFTLLRPT 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                 #      #                               
gi 150390137  85 MiSRVDDVVKYCDISLNSEVETIIALSQAAeKQHKTHKIILMVDLGDLREGIFdsqaLKLALDEIKNL--KGIKVVGIGT 162
gi 171318070  80 ApSGIDSVVRYANSSVNSELGTVKQLADAAaRDGLRHEIVVMVDLGDRREGILpn-eIKRFSEQIRNLlsDYIAFSGIGV 158
gi 126647380  81 SkRNVGKMVEFADVSLNSELNTIHWISEEAvLQKKKHKIIIMVETGDLREGVMge-qLVEFYSQIFQL--PNIEVIGLGT 157
gi 193216675  80 MlEEIPRLVELCDSSLNGDLTIIKAISEYClKVNKVHDIVLMIDMGDRREGILpe-dTLKVVKEILEY--RGVNLIGIGC 156
gi 138895645  83 GiHEIKDVITWADCSLVSEYKVIEALNQEAlSQGKIHHIILMIELGDLREGIMpe-eLMDIGKHILKF--PAIHWLGIGT 159
gi 21283833   79 AkKEISDMIEKVDMSIQTELSTIHQINEVAeVLGKKHKILLMVDWKDGREGVLty-dVLDYIKEIIHL--KNIHFVGLAF 155
gi 70725863   79 SkNRYTQLIKSVKMSMQTEIESIREINDIAkQLNQKHQIMLMIDWKDRREGVIty-dVLNYIEEIIKM--THIQLIGIAF 155
gi 169334420  80 SiSEAEEVVKYSDISLNSEYDTVKALNEEAkIQNKVHDILLMFDVGDLREGYFdkkdIVDSAKRIKNL--TNIRLRGVAT 157
gi 126663893  81 SkLNIKKIVEFADVSFNTEIYTIKLLSEEAkRQEKIHKIIIMIEMGDLREGVLge-eLISFYEQVFSL--PNIEIRGIGT 157
gi 27468687   79 VeADLEKMISRVEMSIQTELTTIKKLNTLAkSLDIKHQIMLMVDWKDGREGVLty-dVVRYVQEVLRL--SHIQLVGLAF 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        #                                      ##                  ####                 
gi 150390137 163 NLTCYGGVIPDEENLGRLIAYASEIEavlGTKLEIISGGNSSSIYMVQEGrmLEEVNLLRLGEAIVLGTEsayGNVIPGT 242
gi 171318070 159 NFGCLSSYCPSDHEFSLIDDLVWTAQkiiGYRLPRISIGGSILLDRVLSDgyLGMANELRVGEAIFLGTSpgrQGAHTDL 238
gi 126647380 158 NLNCLNGVMPSTDKLIQLSLYKQIIElkfNKKIPWVSAGTSVTIPLMLTHqlPLGINHFRVGETLYFGLDlfeEKLIEGM 237
gi 193216675 157 NFGCYGARVPSKETMDKFVSLKKAIEttyNLKLKHISGGNSLSLHMVWENtmPTEVNFLRMGFAMIFGTEdmyRQTIDGM 236
gi 138895645 160 NLTCFGGVLPTSDKLAQLVQLKESVEkklGYHLSVISGGNSSSLHLLMSGemPREINHLRLGESLFFGREtafSKQIPGM 239
gi 21283833  156 NFMCFKSDAPSDDDIFMINRFVSAVEreiGYRLKIISGGNSSMLPQLLYNd-LGKINELRIGETLFRGVDtttNQAIAML 234
gi 70725863  156 NFMCFKSSAPTEEDILKINQFVDAIEynlGFRLKVVSGGNSSMIPQLMYNd-LGRINELRIGEALFRGIDtttNQSIPML 234
gi 169334420 158 NLTCYGGVLPDENNLTNLVKVNELLEaelNTNLDIVSGGNSTSYTMFREDnpVKGVTNIRIGDTILFGRDctyRSHIEGM 237
gi 126663893 158 NLNCLSGVMPTQDKLIQLSLYKQLIEakfNVKIPWVSGGTSVAVPLLLKNarPMAVNHFRIGEALFFGKDlftGETIEGM 237
gi 27468687  156 NFMCFKSEAPNEKDVRMINKFIHNVEnetHFKFRIISGGNSSMLPQTLYNh-LDKINDLRIGEALLRGIDtttNHSINSL 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                              #                         
gi 150390137 243 HQDIFQLEAEIIEIKEKPSIPIGKIGmdafgnkps----fedkgvrkRAILAVGKQDIGTHAIrPVNVNVIILGGSSDHL 318
gi 171318070 239 FDDAFVYSGEILEIKDKPRHCDRWNTet-----------------mkRAVVNFGSLNTVPEGLhCLDHGARYVGNTSDYT 301
gi 126647380 238 QGDVFVLHTEIVEMQEKPMLPVGNLAnnpqgetaei-dtelygqssfRAILDIGLLDVDPKYLiPKDQGIEILGASSDMI 316
gi 193216675 237 FRDTFRCEAEVVEVDYKSSLPVGKSGidafghkpv----fedigdikRLILAIGKLDTMFDAMyPYDPDLKILGGSSDHL 312
gi 138895645 240 HHDIFLLEAEVIEIKDKPSYPQGIIVknafgetph----ftdkgirrRAILALGEQDVPLSELtPVKNGIEIIGGSSDHA 315
gi 21283833  235 YQDAITLEAEILEIKPRVNTQTHESFl--------------------QAIVDIGYLDTKVDNIsPMDQHINILGASSDHL 294
gi 70725863  235 FQNAITVEAEILEIKPRLSDNNQCYL---------------------QAIVDIGYVDTDVNKIkPIKNDVSIVGASSDHL 293
gi 169334420 238 NKDAFIIKAEIIEIKEKPSIPIGRRGfsalnskpe----fvdegirkRAILSVGKQDIDMDMF-PLDNDTKILGGSSDHL 312
gi 126663893 238 HHDVFKLYAEIIEITEKPNNPTGELGenvagntfevdenvdlsetslRAILDFGLLDMQPQYLtPTDESITIIDSSSDMT 317
gi 27468687  235 YQNAIVLEAEIIEIKPRLYQKNNQSYl--------------------QAIVDIGYLDTFIEGIkPLGNDIRILGASSDHL 294
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
Feature 1                                                
gi 150390137 319 IVDITDcdmqHQIGSTLTFDLTYGALLSLMTSEYIYKQMN 358
gi 171318070 302 VFDVTRcersLKAGDVLRFIPDYEALAQCLISPYNLHEIR 341
gi 126647380 317 IINLGKnlqnYKVGDSLTFDLKYMGALGLLNSDYVDKKVI 356
gi 193216675 313 IINAQDskinYKAGDIITFGLDWGSLLYLFNSKFVEKVFE 352
gi 138895645 316 ILDVTEhhdqIQVGSILSFQMSYKALLHAMTSNYIYKKKI 355
gi 21283833  295 MLDLNGqg-hYQVGDHISFSLNYEALSHSMYMKNLHKVYI 333
gi 70725863  294 MINLNNqd-yYKVGDIIEFAMEYEALSQVMYHNHMTKHYF 332
gi 169334420 313 IIDITDskkdYKVGDTFELYMYYTATLRAFTSKYVVKEFI 352
gi 126663893 318 VIDISYsknkYKVGDLVSFNLQYMGALYLLNSDYIEKIVE 357
gi 27468687  295 MIDLNNqd-hYQIGDKLQFSLNYEALSQSMYMKNLTKLYS 333

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