Conserved Protein Domain Family
PLPDE_III_cryptic_DSD

?
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
?
PSSM-Id: 143492
View PSSM: cd06818
Aligned: 20 rows
Threshold Bit Score: 449.817
Threshold Setting Gi: 86360219
Created: 18-Jun-2008
Updated: 2-Oct-2020
Structure
?
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
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                         # #                   #                    #   
NP_792586     31 VSLPALVIHNQALEHNIRWMQQFVTDSGAELAPHGKTSMVPALFRRQLDAGAWGMTLATAIQTQTAYAHGVKRVLMANQL 110 Pseudomonas syr...
YP_001107463  50 FVGPLLVLDDDALEHNLRTMARWCAEHGLRLAPHGKTTMAPRLFERQLEHGAWGITAANVSQLRVYRAFGVRRVLLANEL 129 Saccharopolyspo...
YP_001261927  44 VLFPACILKRSAIDGNRAAMREFLRDTSLHLAPHGKTTLAPQLFALQEEDGVWGFTAATVAHVQTYRQAGIDRIFYANQL 123 Sphingomonas wi...
NP_396163     33 LALPLLTVDLAVYRGNRDRFLALVSAHGAKAAPHAKTPMCPEIAIDLIEAGAWGATVADLFQAEVLLKAGVSNILIANQI 112 Agrobacterium t...
NP_107128     43 LPLPAAIIRADALAHNSRWMQRFVSERGALIAPHVKTTMCPQIIARQIADGAWGVTVATVQQMRVCRNFGADRIILANQA 122 Mesorhizobium l...
YP_001623989  50 FSTPLLTLDGAALDANLERMAQWCQEHSVALAPHGKTTMAPQLWKRQLDRGAWGMSLANLAQLRVAKEFGFRQLMLANVL 129 Renibacterium s...
YP_702423     51 FSTPVMVLDETAIAGNLDTMAAWCEAHGVDLAPHGKTTMSPVLWDRQIRSGAWGITLANFGQLRVAVRFGARRVQIANSL 130 Rhodococcus sp....
NP_824457     45 FTTPVLALSAERLTHNLELMETYAARHGLAFAPHGKTSMAPQLFQRQLEHGAWGITLAVPHQVRVAREFGIQRVFLANEL 124 Streptomyces av...
NP_770621     42 LALPALTLDEAAFAANRDLFLTWCASAGVSVAPHAKTPMSPELARSLRAAGAWGTTVANVQQAAVLLASGERRLLLANEI 121 Bradyrhizobium ...
ZP_01155150   42 LPLPLMLLRRSHLDHNAATFGAWLAERGLSFAPHGKTTMAPQIFAEQLRDGAWALTAATVQQALVMHRFGVRRIIIANQV 121 Oceanicola gran...
Feature 1                                                            #       #                   
NP_792586    111 VGAPNMAVIASLLa-dPMFEFHCMVDHP-DNVAALGEffaa--hglRLNVMIEYGv-pGGRCGCRSEAEVLALADAVQAQ 185 Pseudomonas syr...
YP_001107463 130 VDPHGLAWLAGELaddPDFSVACWVDSV-RGVELMTEalga--prrKLDVLVELGd-pGGRTGVRTLAEAVEVADAVAAS 205 Saccharopolyspo...
YP_001261927 124 VDPTGLSYVLDELaadPAFEFFSLVDSG-RGARLLAEaalarglerPLDVLIEIGm-pGTRGGVRTEEEAIALMSAIDAL 201 Sphingomonas wi...
NP_396163    113 GGLTSARRLRMLAdafPKAEIICCVDSVqASANLVQAfqgr--vdaPFKVFIEVG---VGRTGARTLNVAKDIIDTISTS 187 Agrobacterium t...
NP_107128    123 VGRSELDAITAMVk-ePDLDFMMIVDSA-VGIEAAAEavrrnrldrPLQLLLERGy-pGGRTGCRTNDIALALARQIRAT 199 Mesorhizobium l...
YP_001623989 130 ADPEAIRWVANEVs--DGTRILSWVDSI-QTVRRIDSvlsg--tetLLEVLVELGa-pGGRTGARGIESTFEMAQAVQNS 203 Renibacterium s...
YP_702423    131 VDPTALRWLAEQMdanPELEVLMWADSP-QTVDAMTAaladvtvvrPLPVLVELGg-eGGRTGARSVAEAVKVAERIGES 208 Rhodococcus sp....
NP_824457    125 VDAAALRHIAADLaadPGYRFICYVDSV-RGVELMDAalrg--tprPVDVVVELAageGARTGVRTEEECAAVADAVAAT 201 Streptomyces av...
NP_770621    122 GGLAAGRRLGALLgayPDAEFHAFADSP-AAVAALAEaari-asrrELSVLVELG---AGRAGARDRAAIEATIAAVLAA 196 Bradyrhizobium ...
ZP_01155150  122 VGRANVAAVAAMLeadAALELFCFVDSPaHLANFVGHlaaa-gaprPVGLLLEVGv-vGGRTGVRTRDAALTLADAIAQA 199 Oceanicola gran...
Feature 1                    #                                                         ##        
NP_792586    186 --PALALSGIEGYEGvi------------hgDQAIAGIKAFAAslvslavnl--qdkgafaldRPIVTASGSAWYDLIAE 249 Pseudomonas syr...
YP_001107463 206 --PALRLVGVAGYEAtaah---------dltEHDLSIVDTHMTrlrevvsela-grgrfghldEVVVTAGGSAYFDQVAA 273 Saccharopolyspo...
YP_001261927 202 --PQLRLRGVEAFEGvvsld-------ragaERVRRQLDLVRRtaahist-------glpgdmRLIFSAGGSAFLEQVAE 265 Sphingomonas wi...
NP_396163    188 --AEIVLAGVSTYEGsv-------------sGETSEALDANMAalfdlltdslasirekdpgrPLTVSAGGSIHFDRVLA 252 Agrobacterium t...
NP_107128    200 --PELRLVGIEAFEGliqtengspeqavglfMDEIAALFGLCAddgl------------fesdAPLVTAGGSSHYDIVID 265 Mesorhizobium l...
YP_001623989 204 --RHLRLVGVAGYEGslah---------dasASGLRVVRAYLAdlkilherll-aaklyapdtRVILSAGGSAYFDLVVE 271 Renibacterium s...
YP_702423    209 --PALRLAGVSGYEGalah---------dasEESLARVRTYLRsmaelhrrle-aegrypegrDVYVTAGGSAYFDVVAE 276 Rhodococcus sp....
NP_824457    202 --PTLRLVGVAGYEGevpr---------adsERVHAWLRRLVAlavdldra-----grfkdagEIVVSAGGSAWFDAVAD 265 Streptomyces av...
NP_770621    197 --DRLVLGGVATYEGaaat---------pdaDETMRAIAALMErtietfal----vraaapqrPLIISAGGSAYFDIVAR 261 Bradyrhizobium ...
ZP_01155150  200 dpALVRFAGVSAFEGvvp-----------glAESDAPVRAFAQtvvdiaaal--ppallagldEVILTGGGSAHFDLIAE 266 Oceanicola gran...
Feature 1                        ####                                                           #
NP_792586    250 AFDaqav-rdrFLSVLRPGSYVVHDHGIYKdAQCCVLDRra--------elSEALRPALEVWAHVQSMPEPGFAVIAMGK 320 Pseudomonas syr...
YP_001107463 274 ALAapw--pvpVVPVLRSGGYLTHDDGLYRkMSPFGRQHrla-------gdEAPFRPAMRIWSQVVSCPEPGLALLTMGR 344 Saccharopolyspo...
YP_001261927 266 EMAkwp---fpADYVLRSGCYITNDHGMYArAQRDPDLRgai-------gfRRPFQPAIEVWGHVLSRPEPNRVIVGIGK 335 Sphingomonas wi...
NP_396163    253 ALVpvceadgnATLLLRSGAIFFSDHGVYQrGFQAVDARnllasgkvvfkaSEAFQPSMRIWAEVISVPEPGLAIVGMGM 332 Agrobacterium t...
NP_107128    266 RLAhc-----tARVVTRSGCYVTHDSGLYRiAHQRLQAKig---------eQDGLRRALEIWTYVQSIPEPGLALLTAGR 331 Mesorhizobium l...
YP_001623989 272 VLGnkq--laeVELILRSGAYLVHDDGFYRaISPFSRAAd-----------GQALLAGMHGWARVASQPEPRLAILDAGK 338 Renibacterium s...
YP_702423    277 VLAela--ggrTKVVVRAGAYIIHDDGFYTgISPFGRGEdr---------qARRLTSAMHTWARVVSRPEPGLALLDAGK 345 Rhodococcus sp....
NP_824457    266 VFAgipglslpVLKLLRSGAYVSHDDGHYRrLTPFTRVPe-----------EGALHPAFRLWTQIVSRPSPGQAFANAGK 334 Streptomyces av...
NP_770621    262 ALApgaqadgnASVILRSGALFFADHGIYArAFAEIDRRggllidglhhsaVEGFRPALTLWAEVLSRPETGLAIAGFGM 341 Bradyrhizobium ...
ZP_01155150  267 RFAtlkl-plpVRVVLRSGCYVTNDSGAYVaAQEAARRDpar-------awSGQLKPALEVWSYVQSRPEPGLALLTMGK 338 Oceanicola gran...
Feature 1                                                                                        
NP_792586    321 RDVAYDAGLPNPLLRYTPgvssapgddvSACKVTAVMDQHAFMTVAADCELKv---GDIISFGTSHPCLTFDKWRSGCLV 397 Pseudomonas syr...
YP_001107463 345 RDVSFDQHLPEPQVVRGEdgsvr-dlapGSCRVTSLADQHAFLALEPGTEVRv---GDWLGFGLSHPCTVFDKWPLIPVV 420 Saccharopolyspo...
YP_001261927 336 RDISYDIEPPRPVGWARRgsmma-ealsDGLAVSGLNDQHAWITLPVDHPIDv---GDLMALGCSHPCTTFDKWKYLLMV 411 Sphingomonas wi...
NP_396163    333 RDVSFDQDLPVALRLHRDghlve-adlsSSAKVGKLNDQHAFLSFGNGSSLAi---GDVIEFGISHPCTCFDRWRVFHGI 408 Agrobacterium t...
NP_107128    332 RDCGTDSGFPVPLLLSSAgayp--rdlpPGCEVINLNDQHAYMRFPPDLPLAv---GDRVGLGISHPCTTFDKWQIIYLV 406 Mesorhizobium l...
YP_001623989 339 RDLPFDEGLPQPLGIAEElgqe--vrplVAASISAVNDQHSYLRYNPELAEIr--iGQVIKLGLSHPCTAFDKWTLIPVL 414 Renibacterium s...
YP_702423    346 RDVPFDEGLPTAQAVAGQlgat--prplDGAEVTAVNDQHAFLRLDPARPEHdlrvGDVVRLGLSHPCTAFDKWRWIPVV 423 Rhodococcus sp....
NP_824457    335 RDAAYDLDLPLAQVVRDAgsge--irdaAGIEVTALSDQHAWLRTAPEAELEv---GDWVGLGLSHPCTSFDKWQLIPLV 409 Streptomyces av...
NP_770621    342 RDASFDQGLPVPLRVFRDgveq--qgldAALAVTRLNDQHAFLSVAPEGALAv---GDIIAFGISHPCTCLDRWRVILGL 416 Bradyrhizobium ...
ZP_01155150  339 RDVPHDAGLPVPLARFRPgagw---rdvGEAEIFATNDQHAFVRLPESSNWQv---GDMIASGISHPCTAFDKWRFLPVV 412 Oceanicola gran...
Feature 1                    
NP_792586    398 DDDLRVIEPFHT 409 Pseudomonas syringae pv. tomato str. DC3000
YP_001107463 421 DGDEVVDLVRTF 432 Saccharopolyspora erythraea NRRL 2338
YP_001261927 412 DDDYRILDAVVT 423 Sphingomonas wittichii RW1
NP_396163    409 DGSGRIQRIYTT 420 Agrobacterium tumefaciens str. C58
NP_107128    407 DSDYRVIEAMKT 418 Mesorhizobium loti MAFF303099
YP_001623989 415 DEGIVVDLVHTF 426 Renibacterium salmoninarum ATCC 33209
YP_702423    424 GDDSDDPVVVDL 435 Rhodococcus sp. RHA1
NP_824457    410 EADGTVVDYIRT 421 Streptomyces avermitilis MA-4680
NP_770621    417 DADGVVTRALPT 428 Bradyrhizobium japonicum USDA 110
ZP_01155150  413 DDAYDVVDGVLT 424 Oceanicola granulosus HTCC2516

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap