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: 2-Oct-2020
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:
Feature 1                                       # #                    #                      #  
YP_001320186   7 NPKVTIDLaKLRHNARVMTEKCneYGIAIAGVTKVFGGRPEIAQAMIDgGIQYLADSRVENLKKMKDLSL--PKILLRLP 84  Alkaliphilus me...
ZP_02907240    1 MSKLIIDLeKIRHNLGVIKRACdrRDLKLNAVLKSCQLLPEVVNALIQcDIERMSFSGPVDFTSAGPGKLp-HTTLLKMP 79  Burkholderia am...
ZP_01719885    1 MALLTLHRtKLKENFEFLKELFdsQKISWGVVSKLLCGNRMYLQELINlGVREIHDSRISNLAMVKKIKPsvQTVYIKPV 80  Algoriphagus sp...
YP_001999917   2 YPRIVINEaKFKNNIKKAIEICkaKNIEVLAVTKGFVGQRRMAELYYEaGIRYFGDSRLDNFEVYKDIPG--HKQMLRLP 79  Mycoplasma arth...
YP_001126098   4 YPRVTWDEkKLIHNARVLNAICk-HHVEWIPVTKSVGANIEIVDSLYKqGYRKFADSRLQNLKAIKEYDSsiNTCLLRIP 82  Geobacillus the...
NP_646921      1 MAHVNINIsKIKYNAKVLQTVFqsKNMQFTPVIKCIAGDRTIVESLKAlGINHVAESRLDNIISIADQDL--TYTLLRTP 78  Staphylococcus ...
YP_252777      1 MAQININLsKIEYNADALRTLLenNDIHLTPVIKCIAGDSRIIETLIQsGFTHFAESRLENINEDFKGQC--NYLLLRPT 78  Staphylococcus ...
ZP_02861613    2 KPTLKINLnKIYDNAKIVKDTLdkYNVDITSVTKLHCCNPVIVDTLMQaGIKKFGDSRIDNLKNIKDIDA--EKWLIRLP 79  Anaerofustis st...
ZP_01734888    1 MAFLKLYKtKLQHNYSFLNTLFkeRNIEWGIVTKILCGNTIYLKELLDlGVTEMHDSRISNLKKIKKLNPevQTVYIKPP 80  Flavobacteria b...
NP_765324      1 MANVRVNLsKIKYNAKVLQSLLerRHIHFTPVIKCVAGDKRIVSSIKSlGITHFAESRLDNIEQLKDLDI--TFTLLRPT 78  Staphylococcus ...
Feature 1                                                 #      #                               
YP_001320186  85 MiSRVDDVVKYCDISLNSEVETIIALSQAAeKQHKTHKIILMVDLGDLREGIFdsqaLKLALDEIKNL--KGIKVVGIGT 162 Alkaliphilus me...
ZP_02907240   80 ApSGIDSVVRYANSSVNSELGTVKQLADAAaRDGLRHEIVVMVDLGDRREGILpn-eIKRFSEQIRNLlsDYIAFSGIGV 158 Burkholderia am...
ZP_01719885   81 SkRNVGKMVEFADVSLNSELNTIHWISEEAvLQKKKHKIIIMVETGDLREGVMge-qLVEFYSQIFQL--PNIEVIGLGT 157 Algoriphagus sp...
YP_001999917  80 MlEEIPRLVELCDSSLNGDLTIIKAISEYClKVNKVHDIVLMIDMGDRREGILpe-dTLKVVKEILEY--RGVNLIGIGC 156 Mycoplasma arth...
YP_001126098  83 GiHEIKDVITWADCSLVSEYKVIEALNQEAlSQGKIHHIILMIELGDLREGIMpe-eLMDIGKHILKF--PAIHWLGIGT 159 Geobacillus the...
NP_646921     79 AkKEISDMIEKVDMSIQTELSTIHQINEVAeVLGKKHKILLMVDWKDGREGVLty-dVLDYIKEIIHL--KNIHFVGLAF 155 Staphylococcus ...
YP_252777     79 SkNRYTQLIKSVKMSMQTEIESIREINDIAkQLNQKHQIMLMIDWKDRREGVIty-dVLNYIEEIIKM--THIQLIGIAF 155 Staphylococcus ...
ZP_02861613   80 SiSEAEEVVKYSDISLNSEYDTVKALNEEAkIQNKVHDILLMFDVGDLREGYFdkkdIVDSAKRIKNL--TNIRLRGVAT 157 Anaerofustis st...
ZP_01734888   81 SkLNIKKIVEFADVSFNTEIYTIKLLSEEAkRQEKIHKIIIMIEMGDLREGVLge-eLISFYEQVFSL--PNIEIRGIGT 157 Flavobacteria b...
NP_765324     79 VeADLEKMISRVEMSIQTELTTIKKLNTLAkSLDIKHQIMLMVDWKDGREGVLty-dVVRYVQEVLRL--SHIQLVGLAF 155 Staphylococcus ...
Feature 1        #                                      ##                  ####                 
YP_001320186 163 NLTCYGGVIPDEENLGRLIAYASEIEavlGTKLEIISGGNSSSIYMVQEGrmLEEVNLLRLGEAIVLGTEsayGNVIPGT 242 Alkaliphilus me...
ZP_02907240  159 NFGCLSSYCPSDHEFSLIDDLVWTAQkiiGYRLPRISIGGSILLDRVLSDgyLGMANELRVGEAIFLGTSpgrQGAHTDL 238 Burkholderia am...
ZP_01719885  158 NLNCLNGVMPSTDKLIQLSLYKQIIElkfNKKIPWVSAGTSVTIPLMLTHqlPLGINHFRVGETLYFGLDlfeEKLIEGM 237 Algoriphagus sp...
YP_001999917 157 NFGCYGARVPSKETMDKFVSLKKAIEttyNLKLKHISGGNSLSLHMVWENtmPTEVNFLRMGFAMIFGTEdmyRQTIDGM 236 Mycoplasma arth...
YP_001126098 160 NLTCFGGVLPTSDKLAQLVQLKESVEkklGYHLSVISGGNSSSLHLLMSGemPREINHLRLGESLFFGREtafSKQIPGM 239 Geobacillus the...
NP_646921    156 NFMCFKSDAPSDDDIFMINRFVSAVEreiGYRLKIISGGNSSMLPQLLYNd-LGKINELRIGETLFRGVDtttNQAIAML 234 Staphylococcus ...
YP_252777    156 NFMCFKSSAPTEEDILKINQFVDAIEynlGFRLKVVSGGNSSMIPQLMYNd-LGRINELRIGEALFRGIDtttNQSIPML 234 Staphylococcus ...
ZP_02861613  158 NLTCYGGVLPDENNLTNLVKVNELLEaelNTNLDIVSGGNSTSYTMFREDnpVKGVTNIRIGDTILFGRDctyRSHIEGM 237 Anaerofustis st...
ZP_01734888  158 NLNCLSGVMPTQDKLIQLSLYKQLIEakfNVKIPWVSGGTSVAVPLLLKNarPMAVNHFRIGEALFFGKDlftGETIEGM 237 Flavobacteria b...
NP_765324    156 NFMCFKSEAPNEKDVRMINKFIHNVEnetHFKFRIISGGNSSMLPQTLYNh-LDKINDLRIGEALLRGIDtttNHSINSL 234 Staphylococcus ...
Feature 1                                                              #                         
YP_001320186 243 HQDIFQLEAEIIEIKEKPSIPIGKIGmdafgnkps----fedkgvrkRAILAVGKQDIGTHAIrPVNVNVIILGGSSDHL 318 Alkaliphilus me...
ZP_02907240  239 FDDAFVYSGEILEIKDKPRHCDRWNTet-----------------mkRAVVNFGSLNTVPEGLhCLDHGARYVGNTSDYT 301 Burkholderia am...
ZP_01719885  238 QGDVFVLHTEIVEMQEKPMLPVGNLAnnpqgetaei-dtelygqssfRAILDIGLLDVDPKYLiPKDQGIEILGASSDMI 316 Algoriphagus sp...
YP_001999917 237 FRDTFRCEAEVVEVDYKSSLPVGKSGidafghkpv----fedigdikRLILAIGKLDTMFDAMyPYDPDLKILGGSSDHL 312 Mycoplasma arth...
YP_001126098 240 HHDIFLLEAEVIEIKDKPSYPQGIIVknafgetph----ftdkgirrRAILALGEQDVPLSELtPVKNGIEIIGGSSDHA 315 Geobacillus the...
NP_646921    235 YQDAITLEAEILEIKPRVNTQTHESFl--------------------QAIVDIGYLDTKVDNIsPMDQHINILGASSDHL 294 Staphylococcus ...
YP_252777    235 FQNAITVEAEILEIKPRLSDNNQCYL---------------------QAIVDIGYVDTDVNKIkPIKNDVSIVGASSDHL 293 Staphylococcus ...
ZP_02861613  238 NKDAFIIKAEIIEIKEKPSIPIGRRGfsalnskpe----fvdegirkRAILSVGKQDIDMDMF-PLDNDTKILGGSSDHL 312 Anaerofustis st...
ZP_01734888  238 HHDVFKLYAEIIEITEKPNNPTGELGenvagntfevdenvdlsetslRAILDFGLLDMQPQYLtPTDESITIIDSSSDMT 317 Flavobacteria b...
NP_765324    235 YQNAIVLEAEIIEIKPRLYQKNNQSYl--------------------QAIVDIGYLDTFIEGIkPLGNDIRILGASSDHL 294 Staphylococcus ...
Feature 1                                                
YP_001320186 319 IVDITDcdmqHQIGSTLTFDLTYGALLSLMTSEYIYKQMN 358 Alkaliphilus metalliredigens QYMF
ZP_02907240  302 VFDVTRcersLKAGDVLRFIPDYEALAQCLISPYNLHEIR 341 Burkholderia ambifaria MEX-5
ZP_01719885  317 IINLGKnlqnYKVGDSLTFDLKYMGALGLLNSDYVDKKVI 356 Algoriphagus sp. PR1
YP_001999917 313 IINAQDskinYKAGDIITFGLDWGSLLYLFNSKFVEKVFE 352 Mycoplasma arthritidis 158L3-1
YP_001126098 316 ILDVTEhhdqIQVGSILSFQMSYKALLHAMTSNYIYKKKI 355 Geobacillus thermodenitrificans NG80-2
NP_646921    295 MLDLNGqg-hYQVGDHISFSLNYEALSHSMYMKNLHKVYI 333 Staphylococcus aureus subsp. aureus MW2
YP_252777    294 MINLNNqd-yYKVGDIIEFAMEYEALSQVMYHNHMTKHYF 332 Staphylococcus haemolyticus JCSC1435
ZP_02861613  313 IIDITDskkdYKVGDTFELYMYYTATLRAFTSKYVVKEFI 352 Anaerofustis stercorihominis DSM 17244
ZP_01734888  318 VIDISYsknkYKVGDLVSFNLQYMGALYLLNSDYIEKIVE 357 Flavobacteria bacterium BAL38
NP_765324    295 MIDLNNqd-hYQIGDKLQFSLNYEALSQSMYMKNLTKLYS 333 Staphylococcus epidermidis ATCC 12228

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