Conserved Protein Domain Family
PLPDE_III_DSD_D-TA_like_1

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cd06812: PLPDE_III_DSD_D-TA_like_1 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1
This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains 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. Based on their similarity to AR, it is possible members of this family also form dimers in solution.
Statistics
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PSSM-Id: 143487
View PSSM: cd06812
Aligned: 12 rows
Threshold Bit Score: 572.369
Threshold Setting Gi: 163797790
Created: 18-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                                            # #                    #                    
CAJ48274       9 LDSLDTPCLLLDEaRMEANIEYMKARMRrLGVTLRPHLKTPKSVEVARRAMQTpq-gPAAVSTLQEAEQFARAGVRDILY 87  Bordetella aviu...
EDQ38870      19 LDALQTPCLLLDEvRLRANVERMRAHLTrLGVAFRPHLKTAKSLDVARIAMTApe-gPAMVSTLREAEYFARGGVRDMIY 97  Methylobacteriu...
YP_551592      6 FEPLETPALLLDTaRMDRNIERMRGRMTrHGVHFRPHVKTNKCMDVTQRLLDAga-rGITVSTLREAEYFSERGITDILY 84  Polaromonas sp....
EAY65560       3 LHTLNTPAALIDVaRMQRNIARMQTHLDaLGVRFRPHVKTTKCRQVVDVQIAAga-qGITVSTLKEAEQFFAHGIRDIVY 81  Burkholderia ce...
NP_793416      5 LPSLDTPVALLDMpRMQRNIQRMQQRMNeLGVRLRPHVKTSKSLPVIQAQMAAga-rGVTVSTLKEAEHCFAEGISDVFY 83  Pseudomonas syr...
YP_050133      7 LNALETPFLLIDEfRFQRNIDRLYQRTKnLGSQVRPHLKTLRSIEAGRYLLKDsa-sPATVSTLAEAEAFAGAGYTNLLY 85  Erwinia carotov...
ZP_01898222   25 LAKIDTPFLLVDKaKFDTNVAFLRAKLApHNVILRPHLKTVKSIAGAKHVLEGfd-sPATVSTVKEAEAFADAGYTNLTY 103 Moritella sp. PE36
YP_001501469  15 YQSLDTPFLSVDKqIVLKNLARLRNKIDgLGAELRPHFKTVRAIEAVEHLLPQki-sPITVSTVKEAEALVEEGYSNIVY 93  Shewanella peal...
ZP_01042500    3 WDALETPYLRVDRpRFDANIKRLNCHLSaLKTPLRPHVKTLKSLPAVKAIFNGgt-gPITVSTLKEADFFAEHGFLDQIY 81  Idiomarina balt...
ZP_02191736    3 IRDLPTPHLVLDRrKLEHNLARMRGRASeLGVRLRPHGKTAKSAEVVRRAVGDgp-vMVTVSTLREAGYFAENGIRDIVH 81  alpha proteobac...
YP_156143      8 IAHPDTPYLLIDEaKLKSNINYLKQRVEsLGSHLRPHLKTLRTLEAAGYLLDSks-aPATVSTLAEAEAYAKAGYTDLLY 86  Idiomarina loih...
YP_002203427   4 LADPDTPFAVVDVhKVRRNVERLATRAErLGVTLRPHVKTAKSLDVAALLHAGdrpcPVTVSTLAEAEAFADGGYRDITY 83  Streptomyces sv...
Feature 1        #                                                  #      #                     
CAJ48274      88 AVGLSPAKIDRVLALRAQGVNLTVVVDSV-EAAQALASRSRaagapIPALIEIDADGHRAGVRPeQQALLCAIGRAlheG 166 Bordetella aviu...
EDQ38870      98 GVGIAPAKLARVSAIRAGGADLTVILDSL-EQAEAVADHSSsssdpLPVLIEVDADGHRSGVAPgDADTLLAIGRLllaG 176 Methylobacteriu...
YP_551592     85 AVCLSPNKLAHALRLRRQGIRLTVIVDSV-EMALQLNPERIqgddrLDVLIEIDCDGHRSGVQP-DSPALLAIAQAlqsQ 162 Polaromonas sp....
EAY65560      82 AVDMVPAKLGQALALRRQGCDLKIVADSL-PAAHAIAAFGRehgerFDVWIEVDVDGHRSGIPP-DADLLIDVGRAltdG 159 Burkholderia ce...
NP_793416     84 AVAIAPGKLDQALKLRRIGCRLSILTDSV-VAAQAIVAFGQqhdeqFQVWIEIDCDGHRSGLTV-EDNALIEVARTlveG 161 Pseudomonas syr...
YP_050133     86 AVGIAPHKLPRIANLIHKGVNLHILLDSV-EQARAVTDYALannvtFSVFIEIDCDGHRGGIPP-ESDALLELAQQidgN 163 Erwinia carotov...
ZP_01898222  104 AVGITPQKLPRIQALLNKGINISILLDSV-AQAQAVTAFCQaqnikIPTLLEIDCDGHRGGIQP-DDTRLVEIGKIlhqG 181 Moritella sp. PE36
YP_001501469  94 AVGISEGKLPRISQLIAKGAKVRVLLDTL-EQAQFVSQYSEqhccvIPAMIEVDCDGHRGGIHP-DDPLLIEIANIlhqG 171 Shewanella peal...
ZP_01042500   82 AVGIVQNKLPHVKRLIEQGVDLKIILESE-TQALQVVEFCRmhdivIPVLIEIDCDGSRAGLTA-ESPTLMDVSKIl-aQ 158 Idiomarina balt...
ZP_02191736   82 ANCIAPNRLPEAAALLRDGVNLAITTDSPaVAAEIVRAGREfg-vrFAVMIEVDVGEHRGGVAA-ESDALLATARTlhdG 159 alpha proteobac...
YP_156143     87 AVGIAPAKLKRVAALRQQGINLHILLDNI-TQAQAVVDYAAefgqdFSVFIEIDSDDHRGGIKP-SDSKLLTIAKT---L 161 Idiomarina loih...
YP_002203427  84 AVGIDPHKLPRVVALLRRGVTLRVLLDSA-EQAEAVAEASRraglrVPTQIEIDCDGHRGGLEP-DAPGLPEIGGIl-hE 160 Streptomyces sv...
Feature 1                 #                                            ##               ####     
CAJ48274     167 GAELRGVMTHAGESYSSpDVVAIRDMAERERSAAVRAAAVLREQGLPCPVVSVGSTPTAMFAENLEGVTEVRAGVYVFFD 246 Bordetella aviu...
EDQ38870     177 GVSLRGVLLHAGDSYALsDPEALAAAAEAERRAAVTAAETLRAAGLPCPMVSVGSTPTARYARNLVGVTEVRAGVFMFGD 256 Methylobacteriu...
YP_551592    163 GLAVGGVMTHAGDSYICrSTEAIVAMAEQERAGAVQAARRLRAAGHACPVVSVGSTPTALFAENLDGVTEVRAGVFVFFD 242 Polaromonas sp....
EAY65560     160 GMLLGGVLAHAGSSYEYdTPEALAAIAEQERSRTVRAAERLRAAGLPCPVVSIGSTPTALAAERLDGVTEVRAGVYVLFD 239 Burkholderia ce...
NP_793416    162 GMQLRGVMTHAGSSYDLdTPEALQALAEQERLLCVSAAERIRQAGLPCPEVSIGSTPTALSAQGLAGVTEVRAGVYVFFD 241 Pseudomonas syr...
YP_050133    164 GATLTGLLAHAGESYACrTDEAIRAAARAECAAINIAGRRVRALGIACPVLSVGATPTAHFAEDLTGITEVRAGVFTTFD 243 Erwinia carotov...
ZP_01898222  182 GAELRGVLTHAGESYDCfNKAALVAAAEGERHAAVIAATQLIASGLPCPVVSVGSTPTAHFAENLDGVTEVRAGVYTFFD 261 Moritella sp. PE36
YP_001501469 172 VASFHGVLAHAGESYLCfDPKSLAEAANNEVNMTLKAANNLRAAGIPCDIVSIGSTPTAHSYQDLNGITEVRAGVYGFFD 251 Shewanella peal...
ZP_01042500  159 AELFKGILLHAGGSYGCmTRSDKVAAAENERATAVYVKERLELAGIDCPMVSIGSTPTAHFAQDLTGVTEVRAGVYTFFD 238 Idiomarina balt...
ZP_02191736  160 GMEVRGVLAHAGHTYGCtDAAAVAVIAEAERAGAVRAAQRVREAGIPCREVSVGSTPGALFAKHLNGVTEFRPGVYMFMD 239 alpha proteobac...
YP_156143    162 GEHFTGLMTHAGGSYACnTEQGLKNFAKQECDAVRIARNNLETAGIHCAITSVGSTPTAHFGEDFSDISEVRAGVYTTFD 241 Idiomarina loih...
YP_002203427 161 AGCLDGVLTHAGESYFArTAAEQRLAAENERDSAVAAAERLRAAGLTVSTVSVGSTPTAHAAEDLTGVTELRAGNYVFFD 240 Streptomyces sv...
Feature 1                                             #                                          
CAJ48274     247 LFMAGLGVCKQDDIALSVLTTVIGHQPEKAWILVDAGWMAMSRDRGTANQAvDQYYGLVCDVAGRPLPGLVLKQTNQEQG 326 Bordetella aviu...
EDQ38870     257 LFQAGVGAVAMEDIALSVLATVIGHQRAKGWIITDAGWMALSRDRGTARQKvDQGYGVVCNLAGQPYPDLIVADTNQEHG 336 Methylobacteriu...
YP_551592    243 LVMAGLGVCRTDEIALSVLTTVIGHQKDKGWTVTDAGWMAMSRDRGTSRQSlDQGYGVVCGVDGAPLEDLIMVDANQEHG 322 Polaromonas sp....
EAY65560     240 LVMHNVGVCELSDIALSVLTTVIGHQEEKGWAIVDAGWMAMSRDRGTQRQArDFGYGQICTEAGDVLGDYLLSAANQEHG 319 Burkholderia ce...
NP_793416    242 LVMHNIGVCGADELALSVLTTVIGHQQDKGWVIVDAGWMAMSRDRGTQRQRqDFGYGQVCTETGEWIDGARVTGANQEHG 321 Pseudomonas syr...
YP_050133    244 LVMKNVGVCSLDDIALSVVSTVIGHNREKGWVFIDAGWMALSRDRGTASQAkDYGYGLVCDLHGSPYHDLCVTVTNQEHG 323 Erwinia carotov...
ZP_01898222  262 LVMAGIGVCKPDDIALSVVTSVIGHNEEKDWLFIDAGWMSLSQDRGTQSQRqDCGYGLVCDSEGNIIPGLQVIGANQEHG 341 Moritella sp. PE36
YP_001501469 252 LVMAGIGVCQLKDIAASVVTTVIGHNREKGWIFIDAGWMALSLDRGTAGQPkDCGYGLVTDCNGAVLDGLQVISVNQEHG 331 Shewanella peal...
ZP_01042500  239 LVMANINVCSLDDIALSVVTTVIGVKPEKGWILIDAGWMALSRDRGTASQAvDYGYGMVLDGAGRPLTDWIVESTSQEHG 318 Idiomarina balt...
ZP_02191736  240 LFQVGVGCCGIGEIALTVLGTVINHRPDEGTAHIDAGALALSKDRSTSAQPvDRGFGLVTDVFGLPLPGLSVEAVHQEHG 319 alpha proteobac...
YP_156143    242 LVMKNIGVCDFSHIAMSVVTTVIGHNKEKNWLLTDSGWMALSRDSGTAGQNrDFGYGQVCKIDGSVLDGLCVNSTSQEHG 321 Idiomarina loih...
YP_002203427 241 LVMAGLGVCRVEDLALSVVVTVIGHRPEYGWILTDGGWMAMSRDRGTAAQAqDQGYGLVTDLAGNPIPGLVMTAASQEHG 320 Streptomyces sv...
Feature 1                                                                                  
CAJ48274     327 IITLRPGATgt----------lPDLPIGTRLRILPNHACATGAQHDAYQVL-------RGADVA-AVWPRFRGW 382 Bordetella avium 197N
EDQ38870     337 IVALRRGSDaa----------lPDLPVGARVRILPNHACATGAQHDCYYVL-------DGSGRVgAVWPRINGW 393 Methylobacterium nodu...
YP_551592    323 IIARRPGSTag---------psPFLPIGSQLRILPNHACATAAQFPCYQAL-------DGEQRLaGTWQRFYGW 380 Polaromonas sp. JS666
EAY65560     320 IVSRVGTPDtg---------iaQRFPIGTRLRILPNHACATGAQHPDYQAI-------GDDGAA-QTWPRFYGW 376 Burkholderia cenocepa...
NP_793416    322 IITLATGDStd---------itGRFPIGSRLRILPNHACATGAQFPDYHAC-------DAEGAV-HIWSRLHGW 378 Pseudomonas syringae ...
YP_050133    324 IIALPTDSGfs----------vDNFPVGTRLRILPNHACATAAMHQHYQVL-------KSHRHEqETWQRITGW 380 Erwinia carotovora su...
ZP_01898222  342 IIAAVGSDIdritdgmndglrlSDIAVGTQLRILPNHACATAAMHAGYYVA-------DPVQIElDYWARIQGW 408 Moritella sp. PE36
YP_001501469 332 IIGAVDNSDls----------lDNFPVGSRLHILPNHGCATASMHQHYHVF-------DTANETyEIWNRIQGW 388 Shewanella pealeana A...
ZP_01042500  319 VIKQRAGSSei----------pSDVQIGDKLRILPNHACATASQFDKYYVA-------DAEGQLsEQWSRFNFW 375 Idiomarina baltica OS145
ZP_02191736  320 RLAGAGGVPf------------EILPIGSRVRVLPNHVCMTAAMYDRYAVVdgt--ekGDEQPVeAFWDRVNGW 379 alpha proteobacterium...
YP_156143    322 VIELSDAYQl------------EDFPVGHQLRIMPNHACATAAMHPVYHVL-------MSDGSH-NTWQRITGW 375 Idiomarina loihiensis...
YP_002203427 321 TLTARDGTRl------------PELPLGTRLRILPNHACATAAQHHGYHVVdgtrtttAGAQVVqAFWSRVSGW 382 Streptomyces sviceus ...

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