Conserved Protein Domain Family
PLPDE_III_DSD_D-TA_like_2

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cd06813: PLPDE_III_DSD_D-TA_like_2 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2
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: 143488
View PSSM: cd06813
Aligned: 17 rows
Threshold Bit Score: 515.293
Threshold Setting Gi: 149923446
Created: 18-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 145596535  36 RLDRATAHLDPPYAVVDLRAFDANAAALAERA-RGKPIRLASKSVRCRTLISRALAa-----PGWAGVLAFTLAEALWLV 109
gi 68535845    4 ETRLAVAHLDAPFAVLDLDAARANARDMTHRS-RGTPIRVASKSLRIRSLISEVLTl-----PGYRGVLAYNLNEALWLC 77
gi 78063853   19 TYRDALAGRRLPAAFVNLDCLDANLADLKRRA-RGLPIRLATKSVRSRELIGAVLAa----gPFMQGLLCYSAAEAAWLA 93
gi 111022994  14 RLIASTTEVDPPLAALDLTTLRANAADLVLRA-GGTPVRVASKSVRCRAVLQVALGekltgaGGFRGIMAYSLREAIWLA 92
gi 169627211   5 RLAEALRGAPAPLAAVDIDAARSNAATLVDAA-SGLPIRVASKSIRSTALIRKFLEi-----PGFHGVLAFTPAEAVHLG 78
gi 124010360  22 YYCEIFKNTPKPFAFTDLDLLNENIRQILKRTgSAKKIRVASKSVRCRAVLEHVLAa----sDQFQGIMSFHPQEAVWLS 97
gi 30260829    1 MDRGIFKEVPLPCAFLDEVALDRNIQSIIELS-GNKKIRIASKSLRSVPVMQRILAa----sDRFQGIMCFSPREALFLI 75
gi 126653403   4 RWDQPFGHLERPFAWLDFDALDKNIQIVQGAC-GGKPIRLATKSIRSVEVLRYIQHq----lVNVVGFMTFTAAETIFLL 78
gi 149923446   6 RYRRALAGYRMPCAFVDLDRFDANAESMARRA-GGRPIRVVSGSLRCVNLLERVLEv-----PGFQGVLAGSAGEAAYLH 79
gi 84494912   13 ALESATAGLPAPLVTVDQDAFDANADDLVRRA-AGRPIRVASKSVRCRSLLRRVLDr-----PGFAGVMAYAVPEAVWLV 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  #                                                           #         
gi 145596535 110 RCGvtDDAVVAYPStdRAALAELAGDptl-aaaVTLMIDDpAQLDLVDAVrapg-------hrpeLRVCLDLDASwrpl- 180
gi 68535845   78 REQvsDDILVAYPSahREGLHRLIHDara-mdcVTLMVDSvAHLDFIDAVvppr-------ergeIRVCIDIDAAlra-- 147
gi 78063853   94 DGGf-DDIVVAYPTvePDDLRAVAAQlrr-grsITLMVDDaAQVDAIDRVahde--------rvtIPLAIDLDMSsay-- 161
gi 111022994  93 RRGa-DDILMGYPTvdRGALAELAADpel-lnrITLMVDSdDHLDFVLAAagts--------slrARLCIDVDASlrl-- 160
gi 169627211  79 DAGv-DDVLIAYPSvdRGALATAARHrs----vIRPLIDSaDHVRLLAEIsret--------napIPVCLDIDAGwrpl- 144
gi 124010360  98 QQGf-DDILMGYPIwhETDLRAVAEEvkq-gkmLVLMIDSpAHVQRINAIgqam--------qvaLPVCIDIDMSskf-- 165
gi 30260829   76 EQGf-NDLLLGYPAydERALHEISLLtkq-gliITCMVDCeDHIVYLEKIaeks--------kgcFRVCLDIDMSsrf-- 143
gi 126653403  79 QQQf-DDVLLGYPVmeETAIRQLLHFvqe-gktVTFMVDRqEHIQLLAKLgnem--------gvrVPICIDINVSndf-- 146
gi 149923446  80 YMGi-DDILVAYPSveRNDLEVVCRRilkngatIRLTVDDpEQVLLLGQVaasvrvdlaggedfeLQLLLDLDMLdlrha 158
gi 84494912   87 RQGf-TDVFVAYPSvdREWLQTVVADehl-rdeISVAIDSvEQVRFLADLlgp---------hsgLRVALDVDCSlri-- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        #                                     #                         
gi 145596535 181 ------------ggrLHLGVRRSPVh---DPRAAGALAAtvaarSGFRLVGLMAYEAQIAGMGDAPPgral-lgaaIRLV 244
gi 68535845  148 -------------gpVHIGALRSPLh---TAEEVRNIARevrqrEGFRLVGLMAYEGQVAGTTDTSPa--------IAAM 203
gi 78063853  162 -------------pgLYFGMYRSPVr---DAAGVLALAHrigerPHVRLDGLMGYEGQIAGVADTEPgnga-rnalVRHL 224
gi 111022994 161 -------------gpLHIGVRRSPLr---EPSTVAAFAKra-agRGFAVVGVMFYEAQIAGLPDSSPp--------IGWM 215
gi 169627211 145 ------------ggpVHLGPKRSPVr---TPEQAAALTDlvcatPGLRLAAVMAYDGQIAGVGDIVPgnpw-yqlaVRGM 208
gi 124010360 166 -------------pgIHFGVFRSSVh---NATEALEVYEaieaaDFVTLDGIMGYEAQIAGLGDKIPgqav-knamIKLL 228
gi 30260829  144 -------------fkFHFGVKRSPVk---DGQGALKIVKrlkesSFLILDGVMGYEAQIAGVGDHIPnqrv-kskvISYL 206
gi 126653403 147 -------------klLYFGTKRSSLysleMLTPFLQAIKn---nPSIEVVGAMGYEAQIAGVGNRPAnvlk--grvIEAM 208
gi 149923446 159 wrqrvpgmgpgerfgTSSVPHRTAIh---TVEDALDVADmiaelDGLRLVGVIGYAASFAIERPSETvsgrlrerfTEPL 235
gi 84494912  154 -------------grVHLGVRRSPLr---TPADALAVTRaa-ldAGLRVVGIMFYDAQVAGLPDRGPh--------LKTL 208
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                 ##               ####                  
gi 145596535 245 QRGSYRELLARR----SAAVAAVREHAe------LEFVNGGGTGSLAATSADpaVTEVAAGSGLYGPTLFDTYRAWRPTP 314
gi 68535845  204 KALSVRELASRR----AKIVEAVAEELrvaglppLEFVNGGGTGSIETTSAEaaVTEIGAGSGIIGPALFDHYRQFQPTP 279
gi 78063853  225 KRRSAREINARR----QAAVQALAAAGh-----rLRFVNGGGTGSIESTLGDasVTELAAGSGLYAPALFDHYAAFHAQP 295
gi 111022994 216 KRASANELATRR----DAVVNAVQSEVg-----vLEIVNSGGTGSLEVSSADpvVTEVTAGSGLYVPTLFDRYRAFRPHP 286
gi 169627211 209 QASSLRELGERLprvlDAVTARLRAAGap----pLELVNSGGTGSLARIAGLgfATELAAGSGFFAPALFDHYRSLHLEP 284
gi 124010360 229 KKRSIKEIARRR----ASVVHALAAQGa-----kLRVVNGGGTGSLESTIQEevVTEVTVGSGFYTPGLFDNYSQFSHLP 299
gi 30260829  207 KKKSVLEVKERR----GHIVKEIQNLGi-----eLRFVNGGGTGSIKTTEQDhsVSEITIGSAFYAPKLFDYYKEVQFHP 277
gi 126653403 209 QAQAKKQVTQFR----RLAIAHIKAYFp-----nLRFVNGGGSGSMTYTTQQkeVTEITVGSAFYAPALFDQFTHLQLEK 279
gi 149923446 236 RLPLREELRSRR----EKIVASLRAEGv-----dLQIVTGGSTVTLEKTREDtvMTEVCAGSGLFAPARLDEIPGAVYHP 306
gi 84494912  209 KKRSLDDLAERR----GPLVEAVRALTe------LDFVNGGGTGSLGRLAAAdsLTEFAAGSGLYAPTLFDAYDDFAPRP 278
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                              #                                                         
gi 145596535 315 AAFFACAVARRPAPGYATVLGGGWIASGPAERSrLPRPVLPADLRLVGAEGAGEVQTPLTGRATdtLQIGDRVWFRHAKA 394
gi 68535845  280 AEWFVVPVVRRPAQDTVTVAGGGRIASGPAGKDrLPVVDWPRDLKMAPLEGPGEVQTPLTGPAArnLRLGDHVWMRHAKA 359
gi 78063853  296 AAGFALPVVRIPQPGIVTCSGGGYIASGPAGKSrLPRPWLPAGCTLIDNEGAGEVQTPLRVPHGvaPAIGDPILFRHAKA 375
gi 111022994 287 SLYFALSAVRRPTPGIATLFGGGYIASGPAGGSrVPRPVWPPRLKLLRNEGAGEVQSPVTGKAAadLGIGDRVWFRHAKA 366
gi 169627211 285 AAAFALPVVRKPAPGLATVLGGGYIASGPAGASrVPVPSWPPGLSFEASEGAGEVQTPLRGARA--LRIGDAVWFRHAKA 362
gi 124010360 300 AAAYAIEVVRQPLPGMYTCLGGGYVASGAIAKDkQPVPYLPQGFRLTDNEGTGEVQTPITYQGSetLTYGSPIFLRHSKA 379
gi 30260829  278 AVGFALPVVRKPAPTIYTCLGGGYIASGAIGKDkEPEIWRPGGAKLLALEGAGEVQTPIFYNGEerVEIGDSILFRHSKA 357
gi 126653403 280 AAGFALRVTRQPEKNIVVCHGGGYTASGAIGSDrLPVFYEPTNFAYLSLEGAGEVQTPIKVKGKn-IEIGDTIYFRHAKA 358
gi 149923446 307 AAGYALPVIRRPSANLLTCAGGGYLASGVADGAaLPKPWLPQGGRLVPMIGAGGSATPVEYEELprVGIGDPLFFRHARA 386
gi 84494912  279 AMTYALPVVRRPAKGIVTAYSGGYVASGEPGWT-RVPSPIGAALKLIRSEAAGEVQTPLRGPAAdgLALGDRVWMRGAKA 357
                        410       420       430
                 ....*....|....*....|....*....|..
Feature 1                                        
gi 145596535 395 GELAEHVNELHLVEAETVGTAAATYRGEGWAF 426
gi 68535845  360 GEATEYINTVLVVSAGEIIAEWPTYRGEGKSF 391
gi 78063853  376 GELCERFNTLLLIRGGRVVGEAPTYRGEGKSF 407
gi 111022994 367 GELCERFTEVHLVESDGSRTVVPTYRGEGQCF 398
gi 169627211 363 GELCEHFTELQLVEGGQHAGSVSTYRGEGMMF 394
gi 124010360 380 GELCERFNEMHLVSEGKIAGKEPTFRGEGKCF 411
gi 30260829  358 GELCERFPFLYRVKEGEIVGEYSTYRGDGQCF 389
gi 126653403 359 GELCERFQLLHGVRGDKYVGSYTTYRGDGQCF 390
gi 149923446 387 GELCEHFDALALIRDGEVVELAPTYRGAGQRW 418
gi 84494912  358 GELLERFDHVHLVQQGRLVETVPSYRGEGQNF 389

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