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: 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_001160832  36 RLDRATAHLDPPYAVVDLRAFDANAAALAERA-RGKPIRLASKSVRCRTLISRALAa-----PGWAGVLAFTLAEALWLV 109 Salinispora tro...
YP_250550      4 ETRLAVAHLDAPFAVLDLDAARANARDMTHRS-RGTPIRVASKSLRIRSLISEVLTl-----PGYRGVLAYNLNEALWLC 77  Corynebacterium...
YP_373761     19 TYRDALAGRRLPAAFVNLDCLDANLADLKRRA-RGLPIRLATKSVRSRELIGAVLAa----gPFMQGLLCYSAAEAAWLA 93  Burkholderia sp...
YP_705966     14 RLIASTTEVDPPLAALDLTTLRANAADLVLRA-GGTPVRVASKSVRCRAVLQVALGekltgaGGFRGIMAYSLREAIWLA 92  Rhodococcus sp....
YP_001700860   5 RLAEALRGAPAPLAAVDIDAARSNAATLVDAA-SGLPIRVASKSIRSTALIRKFLEi-----PGFHGVLAFTPAEAVHLG 78  Mycobacterium a...
ZP_01695007   22 YYCEIFKNTPKPFAFTDLDLLNENIRQILKRTgSAKKIRVASKSVRCRAVLEHVLAa----sDQFQGIMSFHPQEAVWLS 97  Microscilla mar...
NP_843206      1 MDRGIFKEVPLPCAFLDEVALDRNIQSIIELS-GNKKIRIASKSLRSVPVMQRILAa----sDRFQGIMCFSPREALFLI 75  Bacillus anthra...
ZP_01725504    4 RWDQPFGHLERPFAWLDFDALDKNIQIVQGAC-GGKPIRLATKSIRSVEVLRYIQHq----lVNVVGFMTFTAAETIFLL 78  Bacillus sp. B1...
ZP_01911850    6 RYRRALAGYRMPCAFVDLDRFDANAESMARRA-GGRPIRVVSGSLRCVNLLERVLEv-----PGFQGVLAGSAGEAAYLH 79  Plesiocystis pa...
ZP_00994031   13 ALESATAGLPAPLVTVDQDAFDANADDLVRRA-AGRPIRVASKSVRCRSLLRRVLDr-----PGFAGVMAYAVPEAVWLV 86  Janibacter sp. ...
Feature 1                  #                                                           #         
YP_001160832 110 RCGvtDDAVVAYPStdRAALAELAGDptl-aaaVTLMIDDpAQLDLVDAVrapg-------hrpeLRVCLDLDASwrpl- 180 Salinispora tro...
YP_250550     78 REQvsDDILVAYPSahREGLHRLIHDara-mdcVTLMVDSvAHLDFIDAVvppr-------ergeIRVCIDIDAAlra-- 147 Corynebacterium...
YP_373761     94 DGGf-DDIVVAYPTvePDDLRAVAAQlrr-grsITLMVDDaAQVDAIDRVahde--------rvtIPLAIDLDMSsay-- 161 Burkholderia sp...
YP_705966     93 RRGa-DDILMGYPTvdRGALAELAADpel-lnrITLMVDSdDHLDFVLAAagts--------slrARLCIDVDASlrl-- 160 Rhodococcus sp....
YP_001700860  79 DAGv-DDVLIAYPSvdRGALATAARHrs----vIRPLIDSaDHVRLLAEIsret--------napIPVCLDIDAGwrpl- 144 Mycobacterium a...
ZP_01695007   98 QQGf-DDILMGYPIwhETDLRAVAEEvkq-gkmLVLMIDSpAHVQRINAIgqam--------qvaLPVCIDIDMSskf-- 165 Microscilla mar...
NP_843206     76 EQGf-NDLLLGYPAydERALHEISLLtkq-gliITCMVDCeDHIVYLEKIaeks--------kgcFRVCLDIDMSsrf-- 143 Bacillus anthra...
ZP_01725504   79 QQQf-DDVLLGYPVmeETAIRQLLHFvqe-gktVTFMVDRqEHIQLLAKLgnem--------gvrVPICIDINVSndf-- 146 Bacillus sp. B1...
ZP_01911850   80 YMGi-DDILVAYPSveRNDLEVVCRRilkngatIRLTVDDpEQVLLLGQVaasvrvdlaggedfeLQLLLDLDMLdlrha 158 Plesiocystis pa...
ZP_00994031   87 RQGf-TDVFVAYPSvdREWLQTVVADehl-rdeISVAIDSvEQVRFLADLlgp---------hsgLRVALDVDCSlri-- 153 Janibacter sp. ...
Feature 1                        #                                     #                         
YP_001160832 181 ------------ggrLHLGVRRSPVh---DPRAAGALAAtvaarSGFRLVGLMAYEAQIAGMGDAPPgral-lgaaIRLV 244 Salinispora tro...
YP_250550    148 -------------gpVHIGALRSPLh---TAEEVRNIARevrqrEGFRLVGLMAYEGQVAGTTDTSPa--------IAAM 203 Corynebacterium...
YP_373761    162 -------------pgLYFGMYRSPVr---DAAGVLALAHrigerPHVRLDGLMGYEGQIAGVADTEPgnga-rnalVRHL 224 Burkholderia sp...
YP_705966    161 -------------gpLHIGVRRSPLr---EPSTVAAFAKra-agRGFAVVGVMFYEAQIAGLPDSSPp--------IGWM 215 Rhodococcus sp....
YP_001700860 145 ------------ggpVHLGPKRSPVr---TPEQAAALTDlvcatPGLRLAAVMAYDGQIAGVGDIVPgnpw-yqlaVRGM 208 Mycobacterium a...
ZP_01695007  166 -------------pgIHFGVFRSSVh---NATEALEVYEaieaaDFVTLDGIMGYEAQIAGLGDKIPgqav-knamIKLL 228 Microscilla mar...
NP_843206    144 -------------fkFHFGVKRSPVk---DGQGALKIVKrlkesSFLILDGVMGYEAQIAGVGDHIPnqrv-kskvISYL 206 Bacillus anthra...
ZP_01725504  147 -------------klLYFGTKRSSLysleMLTPFLQAIKn---nPSIEVVGAMGYEAQIAGVGNRPAnvlk--grvIEAM 208 Bacillus sp. B1...
ZP_01911850  159 wrqrvpgmgpgerfgTSSVPHRTAIh---TVEDALDVADmiaelDGLRLVGVIGYAASFAIERPSETvsgrlrerfTEPL 235 Plesiocystis pa...
ZP_00994031  154 -------------grVHLGVRRSPLr---TPADALAVTRaa-ldAGLRVVGIMFYDAQVAGLPDRGPh--------LKTL 208 Janibacter sp. ...
Feature 1                                                 ##               ####                  
YP_001160832 245 QRGSYRELLARR----SAAVAAVREHAe------LEFVNGGGTGSLAATSADpaVTEVAAGSGLYGPTLFDTYRAWRPTP 314 Salinispora tro...
YP_250550    204 KALSVRELASRR----AKIVEAVAEELrvaglppLEFVNGGGTGSIETTSAEaaVTEIGAGSGIIGPALFDHYRQFQPTP 279 Corynebacterium...
YP_373761    225 KRRSAREINARR----QAAVQALAAAGh-----rLRFVNGGGTGSIESTLGDasVTELAAGSGLYAPALFDHYAAFHAQP 295 Burkholderia sp...
YP_705966    216 KRASANELATRR----DAVVNAVQSEVg-----vLEIVNSGGTGSLEVSSADpvVTEVTAGSGLYVPTLFDRYRAFRPHP 286 Rhodococcus sp....
YP_001700860 209 QASSLRELGERLprvlDAVTARLRAAGap----pLELVNSGGTGSLARIAGLgfATELAAGSGFFAPALFDHYRSLHLEP 284 Mycobacterium a...
ZP_01695007  229 KKRSIKEIARRR----ASVVHALAAQGa-----kLRVVNGGGTGSLESTIQEevVTEVTVGSGFYTPGLFDNYSQFSHLP 299 Microscilla mar...
NP_843206    207 KKKSVLEVKERR----GHIVKEIQNLGi-----eLRFVNGGGTGSIKTTEQDhsVSEITIGSAFYAPKLFDYYKEVQFHP 277 Bacillus anthra...
ZP_01725504  209 QAQAKKQVTQFR----RLAIAHIKAYFp-----nLRFVNGGGSGSMTYTTQQkeVTEITVGSAFYAPALFDQFTHLQLEK 279 Bacillus sp. B1...
ZP_01911850  236 RLPLREELRSRR----EKIVASLRAEGv-----dLQIVTGGSTVTLEKTREDtvMTEVCAGSGLFAPARLDEIPGAVYHP 306 Plesiocystis pa...
ZP_00994031  209 KKRSLDDLAERR----GPLVEAVRALTe------LDFVNGGGTGSLGRLAAAdsLTEFAAGSGLYAPTLFDAYDDFAPRP 278 Janibacter sp. ...
Feature 1                              #                                                         
YP_001160832 315 AAFFACAVARRPAPGYATVLGGGWIASGPAERSrLPRPVLPADLRLVGAEGAGEVQTPLTGRATdtLQIGDRVWFRHAKA 394 Salinispora tro...
YP_250550    280 AEWFVVPVVRRPAQDTVTVAGGGRIASGPAGKDrLPVVDWPRDLKMAPLEGPGEVQTPLTGPAArnLRLGDHVWMRHAKA 359 Corynebacterium...
YP_373761    296 AAGFALPVVRIPQPGIVTCSGGGYIASGPAGKSrLPRPWLPAGCTLIDNEGAGEVQTPLRVPHGvaPAIGDPILFRHAKA 375 Burkholderia sp...
YP_705966    287 SLYFALSAVRRPTPGIATLFGGGYIASGPAGGSrVPRPVWPPRLKLLRNEGAGEVQSPVTGKAAadLGIGDRVWFRHAKA 366 Rhodococcus sp....
YP_001700860 285 AAAFALPVVRKPAPGLATVLGGGYIASGPAGASrVPVPSWPPGLSFEASEGAGEVQTPLRGARA--LRIGDAVWFRHAKA 362 Mycobacterium a...
ZP_01695007  300 AAAYAIEVVRQPLPGMYTCLGGGYVASGAIAKDkQPVPYLPQGFRLTDNEGTGEVQTPITYQGSetLTYGSPIFLRHSKA 379 Microscilla mar...
NP_843206    278 AVGFALPVVRKPAPTIYTCLGGGYIASGAIGKDkEPEIWRPGGAKLLALEGAGEVQTPIFYNGEerVEIGDSILFRHSKA 357 Bacillus anthra...
ZP_01725504  280 AAGFALRVTRQPEKNIVVCHGGGYTASGAIGSDrLPVFYEPTNFAYLSLEGAGEVQTPIKVKGKn-IEIGDTIYFRHAKA 358 Bacillus sp. B1...
ZP_01911850  307 AAGYALPVIRRPSANLLTCAGGGYLASGVADGAaLPKPWLPQGGRLVPMIGAGGSATPVEYEELprVGIGDPLFFRHARA 386 Plesiocystis pa...
ZP_00994031  279 AMTYALPVVRRPAKGIVTAYSGGYVASGEPGWT-RVPSPIGAALKLIRSEAAGEVQTPLRGPAAdgLALGDRVWMRGAKA 357 Janibacter sp. ...
Feature 1                                        
YP_001160832 395 GELAEHVNELHLVEAETVGTAAATYRGEGWAF 426 Salinispora tropica CNB-440
YP_250550    360 GEATEYINTVLVVSAGEIIAEWPTYRGEGKSF 391 Corynebacterium jeikeium K411
YP_373761    376 GELCERFNTLLLIRGGRVVGEAPTYRGEGKSF 407 Burkholderia sp. 383
YP_705966    367 GELCERFTEVHLVESDGSRTVVPTYRGEGQCF 398 Rhodococcus sp. RHA1
YP_001700860 363 GELCEHFTELQLVEGGQHAGSVSTYRGEGMMF 394 Mycobacterium abscessus
ZP_01695007  380 GELCERFNEMHLVSEGKIAGKEPTFRGEGKCF 411 Microscilla marina ATCC 23134
NP_843206    358 GELCERFPFLYRVKEGEIVGEYSTYRGDGQCF 389 Bacillus anthracis str. Ames
ZP_01725504  359 GELCERFQLLHGVRGDKYVGSYTTYRGDGQCF 390 Bacillus sp. B14905
ZP_01911850  387 GELCEHFDALALIRDGEVVELAPTYRGAGQRW 418 Plesiocystis pacifica SIR-1
ZP_00994031  358 GELLERFDHVHLVQQGRLVETVPSYRGEGQNF 389 Janibacter sp. HTCC2649

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