Conserved Protein Domain Family
PLPDE_III_cryptic_DSD

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cd06818: PLPDE_III_cryptic_DSD 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase
This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity 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 dimers 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 similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties of cryptic DSDs are still poorly understood. Typically, DSDs catalyze the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia.
Statistics
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PSSM-Id: 143492
View PSSM: cd06818
Aligned: 20 rows
Threshold Bit Score: 449.817
Threshold Setting Gi: 86360219
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 28869967   31 VSLPALVIHNQALEHNIRWMQQFVTDSGAELAPHGKTSMVPALFRRQLDAGAWGMTLATAIQTQTAYAHGVKRVLMANQL 110
gi 134101802  50 FVGPLLVLDDDALEHNLRTMARWCAEHGLRLAPHGKTTMAPRLFERQLEHGAWGITAANVSQLRVYRAFGVRRVLLANEL 129
gi 148554345  44 VLFPACILKRSAIDGNRAAMREFLRDTSLHLAPHGKTTLAPQLFALQEEDGVWGFTAATVAHVQTYRQAGIDRIFYANQL 123
gi 16119457   33 LALPLLTVDLAVYRGNRDRFLALVSAHGAKAAPHAKTPMCPEIAIDLIEAGAWGATVADLFQAEVLLKAGVSNILIANQI 112
gi 13475564   43 LPLPAAIIRADALAHNSRWMQRFVSERGALIAPHVKTTMCPQIIARQIADGAWGVTVATVQQMRVCRNFGADRIILANQA 122
gi 163839584  50 FSTPLLTLDGAALDANLERMAQWCQEHSVALAPHGKTTMAPQLWKRQLDRGAWGMSLANLAQLRVAKEFGFRQLMLANVL 129
gi 111019451  51 FSTPVMVLDETAIAGNLDTMAAWCEAHGVDLAPHGKTTMSPVLWDRQIRSGAWGITLANFGQLRVAVRFGARRVQIANSL 130
gi 29829823   45 FTTPVLALSAERLTHNLELMETYAARHGLAFAPHGKTSMAPQLFQRQLEHGAWGITLAVPHQVRVAREFGIQRVFLANEL 124
gi 27379092   42 LALPALTLDEAAFAANRDLFLTWCASAGVSVAPHAKTPMSPELARSLRAAGAWGTTVANVQQAAVLLASGERRLLLANEI 121
gi 89067696   42 LPLPLMLLRRSHLDHNAATFGAWLAERGLSFAPHGKTTMAPQIFAEQLRDGAWALTAATVQQALVMHRFGVRRIIIANQV 121
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                            #       #                   
gi 28869967  111 VGAPNMAVIASLLa-dPMFEFHCMVDHP-DNVAALGEffaa--hglRLNVMIEYGv-pGGRCGCRSEAEVLALADAVQAQ 185
gi 134101802 130 VDPHGLAWLAGELaddPDFSVACWVDSV-RGVELMTEalga--prrKLDVLVELGd-pGGRTGVRTLAEAVEVADAVAAS 205
gi 148554345 124 VDPTGLSYVLDELaadPAFEFFSLVDSG-RGARLLAEaalarglerPLDVLIEIGm-pGTRGGVRTEEEAIALMSAIDAL 201
gi 16119457  113 GGLTSARRLRMLAdafPKAEIICCVDSVqASANLVQAfqgr--vdaPFKVFIEVG---VGRTGARTLNVAKDIIDTISTS 187
gi 13475564  123 VGRSELDAITAMVk-ePDLDFMMIVDSA-VGIEAAAEavrrnrldrPLQLLLERGy-pGGRTGCRTNDIALALARQIRAT 199
gi 163839584 130 ADPEAIRWVANEVs--DGTRILSWVDSI-QTVRRIDSvlsg--tetLLEVLVELGa-pGGRTGARGIESTFEMAQAVQNS 203
gi 111019451 131 VDPTALRWLAEQMdanPELEVLMWADSP-QTVDAMTAaladvtvvrPLPVLVELGg-eGGRTGARSVAEAVKVAERIGES 208
gi 29829823  125 VDAAALRHIAADLaadPGYRFICYVDSV-RGVELMDAalrg--tprPVDVVVELAageGARTGVRTEEECAAVADAVAAT 201
gi 27379092  122 GGLAAGRRLGALLgayPDAEFHAFADSP-AAVAALAEaari-asrrELSVLVELG---AGRAGARDRAAIEATIAAVLAA 196
gi 89067696  122 VGRANVAAVAAMLeadAALELFCFVDSPaHLANFVGHlaaa-gaprPVGLLLEVGv-vGGRTGVRTRDAALTLADAIAQA 199
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #                                                         ##        
gi 28869967  186 --PALALSGIEGYEGvi------------hgDQAIAGIKAFAAslvslavnl--qdkgafaldRPIVTASGSAWYDLIAE 249
gi 134101802 206 --PALRLVGVAGYEAtaah---------dltEHDLSIVDTHMTrlrevvsela-grgrfghldEVVVTAGGSAYFDQVAA 273
gi 148554345 202 --PQLRLRGVEAFEGvvsld-------ragaERVRRQLDLVRRtaahist-------glpgdmRLIFSAGGSAFLEQVAE 265
gi 16119457  188 --AEIVLAGVSTYEGsv-------------sGETSEALDANMAalfdlltdslasirekdpgrPLTVSAGGSIHFDRVLA 252
gi 13475564  200 --PELRLVGIEAFEGliqtengspeqavglfMDEIAALFGLCAddgl------------fesdAPLVTAGGSSHYDIVID 265
gi 163839584 204 --RHLRLVGVAGYEGslah---------dasASGLRVVRAYLAdlkilherll-aaklyapdtRVILSAGGSAYFDLVVE 271
gi 111019451 209 --PALRLAGVSGYEGalah---------dasEESLARVRTYLRsmaelhrrle-aegrypegrDVYVTAGGSAYFDVVAE 276
gi 29829823  202 --PTLRLVGVAGYEGevpr---------adsERVHAWLRRLVAlavdldra-----grfkdagEIVVSAGGSAWFDAVAD 265
gi 27379092  197 --DRLVLGGVATYEGaaat---------pdaDETMRAIAALMErtietfal----vraaapqrPLIISAGGSAYFDIVAR 261
gi 89067696  200 dpALVRFAGVSAFEGvvp-----------glAESDAPVRAFAQtvvdiaaal--ppallagldEVILTGGGSAHFDLIAE 266
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        ####                                                           #
gi 28869967  250 AFDaqav-rdrFLSVLRPGSYVVHDHGIYKdAQCCVLDRra--------elSEALRPALEVWAHVQSMPEPGFAVIAMGK 320
gi 134101802 274 ALAapw--pvpVVPVLRSGGYLTHDDGLYRkMSPFGRQHrla-------gdEAPFRPAMRIWSQVVSCPEPGLALLTMGR 344
gi 148554345 266 EMAkwp---fpADYVLRSGCYITNDHGMYArAQRDPDLRgai-------gfRRPFQPAIEVWGHVLSRPEPNRVIVGIGK 335
gi 16119457  253 ALVpvceadgnATLLLRSGAIFFSDHGVYQrGFQAVDARnllasgkvvfkaSEAFQPSMRIWAEVISVPEPGLAIVGMGM 332
gi 13475564  266 RLAhc-----tARVVTRSGCYVTHDSGLYRiAHQRLQAKig---------eQDGLRRALEIWTYVQSIPEPGLALLTAGR 331
gi 163839584 272 VLGnkq--laeVELILRSGAYLVHDDGFYRaISPFSRAAd-----------GQALLAGMHGWARVASQPEPRLAILDAGK 338
gi 111019451 277 VLAela--ggrTKVVVRAGAYIIHDDGFYTgISPFGRGEdr---------qARRLTSAMHTWARVVSRPEPGLALLDAGK 345
gi 29829823  266 VFAgipglslpVLKLLRSGAYVSHDDGHYRrLTPFTRVPe-----------EGALHPAFRLWTQIVSRPSPGQAFANAGK 334
gi 27379092  262 ALApgaqadgnASVILRSGALFFADHGIYArAFAEIDRRggllidglhhsaVEGFRPALTLWAEVLSRPETGLAIAGFGM 341
gi 89067696  267 RFAtlkl-plpVRVVLRSGCYVTNDSGAYVaAQEAARRDpar-------awSGQLKPALEVWSYVQSRPEPGLALLTMGK 338
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 28869967  321 RDVAYDAGLPNPLLRYTPgvssapgddvSACKVTAVMDQHAFMTVAADCELKv---GDIISFGTSHPCLTFDKWRSGCLV 397
gi 134101802 345 RDVSFDQHLPEPQVVRGEdgsvr-dlapGSCRVTSLADQHAFLALEPGTEVRv---GDWLGFGLSHPCTVFDKWPLIPVV 420
gi 148554345 336 RDISYDIEPPRPVGWARRgsmma-ealsDGLAVSGLNDQHAWITLPVDHPIDv---GDLMALGCSHPCTTFDKWKYLLMV 411
gi 16119457  333 RDVSFDQDLPVALRLHRDghlve-adlsSSAKVGKLNDQHAFLSFGNGSSLAi---GDVIEFGISHPCTCFDRWRVFHGI 408
gi 13475564  332 RDCGTDSGFPVPLLLSSAgayp--rdlpPGCEVINLNDQHAYMRFPPDLPLAv---GDRVGLGISHPCTTFDKWQIIYLV 406
gi 163839584 339 RDLPFDEGLPQPLGIAEElgqe--vrplVAASISAVNDQHSYLRYNPELAEIr--iGQVIKLGLSHPCTAFDKWTLIPVL 414
gi 111019451 346 RDVPFDEGLPTAQAVAGQlgat--prplDGAEVTAVNDQHAFLRLDPARPEHdlrvGDVVRLGLSHPCTAFDKWRWIPVV 423
gi 29829823  335 RDAAYDLDLPLAQVVRDAgsge--irdaAGIEVTALSDQHAWLRTAPEAELEv---GDWVGLGLSHPCTSFDKWQLIPLV 409
gi 27379092  342 RDASFDQGLPVPLRVFRDgveq--qgldAALAVTRLNDQHAFLSVAPEGALAv---GDIIAFGISHPCTCLDRWRVILGL 416
gi 89067696  339 RDVPHDAGLPVPLARFRPgagw---rdvGEAEIFATNDQHAFVRLPESSNWQv---GDMIASGISHPCTAFDKWRFLPVV 412
                        410
                 ....*....|..
Feature 1                    
gi 28869967  398 DDDLRVIEPFHT 409
gi 134101802 421 DGDEVVDLVRTF 432
gi 148554345 412 DDDYRILDAVVT 423
gi 16119457  409 DGSGRIQRIYTT 420
gi 13475564  407 DSDYRVIEAMKT 418
gi 163839584 415 DEGIVVDLVHTF 426
gi 111019451 424 GDDSDDPVVVDL 435
gi 29829823  410 EADGTVVDYIRT 421
gi 27379092  417 DADGVVTRALPT 428
gi 89067696  413 DDAYDVVDGVLT 424

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