Conserved Protein Domain Family
PLPDE_III_DSD

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cd06817: PLPDE_III_DSD 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase
This subfamily is composed of chicken D-serine dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic proteins. Chicken DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. It is a fold type III PLP-dependent enzyme 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. Experimental data suggest that chicken DSD also exists as dimers. Sequence comparison and biochemical experiments show that chicken DSD is distinct from the ubiquitous bacterial DSDs coded by dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes.
Statistics
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PSSM-Id: 143491
View PSSM: cd06817
Aligned: 15 rows
Threshold Bit Score: 493.389
Threshold Setting Gi: 83767293
Created: 19-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                                                  # #                                   
BAF95910       7 LDTLPTPALTIDRTTARRNAERMRER------CRALGVRLRPHVKTHK-------------------------------- 48  chicken
AAI22307      37 IKDLCTPALVVDLDKVKRNAEGMKER------CQKLQVQLRPHMKTHK-------------------------------- 78  zebrafish
XP_002127262   4 MNDLRTPALVVYKHKVEANCERMLKL------AKDHGVTLKPHFKTTK-------------------------------- 45  Ciona intestinalis
XP_001544668  24 LRDVDGPAAIIDVAVARKNCQLMLDA------AEALGVLFRSHVKTHK-------------------------------- 65  Ajellomyces cap...
BAE57432      25 LTEIPKPAAVLDLAIIKRHCNSMLQT------IQTLGVGFRAHVKSHKvssisisqtsrnqatlfpkkkkkrthrrnphp 98  Aspergillus oryzae
XP_572767     27 LSALRTPALIVDRKKFKDNCERVASN------AKERGMKFRAHVKTHK-------------------------------- 68  Cryptococcus ne...
EDP47329      16 ATDLPTPAVVLSKPILERNIKQLLQD------VKDLEISFRPHVKTLK-------------------------------- 57  Aspergillus fum...
P53095        13 VRDLPTPNFVINEEKFDKNCTTMLNNveklsqECGVPIKFRAHVKTHK-------------------------------- 60  baker's yeast
XP_382632     16 ISDLPTPALVVNLPVLKKNIDTLHQD------VERLGIGFRPHVKTLK-------------------------------- 57  Gibberella zeae...
XP_445494     13 ISTLPTPCMVIDEKKFNSNCENMLKHvgelgsLTEHPILFRAHVKTHK-------------------------------- 60  Candida glabrat...
Feature 1                                           #                            #               
BAF95910      49 ------------TLEGGLLATGGTR-------RGIAVSTLAEARFFADGGf--------DDILLAYPVPt-ARLEECAGL 100 chicken
AAI22307      79 ------------TLECADIMTGGSR-------RCIVVSTLAEASFYADNGy--------DDILYAYPLPf-DKVERCAEL 130 zebrafish
XP_002127262  46 ------------CLEVAIMQTGGTK-------CGMEVSTLVEADLLAENGf--------ENVIYAYPISp-HKTPKCAEL 97  Ciona intestinalis
XP_001544668  66 ------------TTELTKFQVGEQSn-----pVRLVVSTLAEAEQLQPYLeeckangrsIDLIYGLPVQp-SSFKRLTAL 127 Ajellomyces cap...
BAE57432      99 ksplptndnnekTTELSRLQVGTSSp-----eINYVASTVLEIESLVPLLrefqskgrkVNILYGIPLVp-SQVSRLALA 172 Aspergillus oryzae
XP_572767     69 ------------TTEGTRMQVEAAGg-----vKATIASTMVEVWQIVEAGlvne--glvNDILYSMPISa-DKLEDINSV 128 Cryptococcus ne...
EDP47329      58 ------------SIEVTRMMLGNGTh------RRIVASTLCEIRGALPLAeeg----ilDEALYGIPFYp-SALPQLAAL 114 Aspergillus fum...
P53095        61 ------------TAKGTLKQLGHGLplakrttRAILVSTLKEAEELLNYQdrqc-sdyiDDITYSLPCCvpEFIPLLSNL 127 baker's yeast
XP_382632     58 ------------TLELTRMMIAEGKy------KGMIASTIPEIKGALPLVeeg----lvEECLYGIPVYp-GVLPRLIEL 114 Gibberella zeae...
XP_445494     61 ------------TTEGTLRQLGFEGtsapfrsKAILVSTIKEAEGLLEYQdsin-gvfvDDIAFSLPACvpEVLERLSSI 127 Candida glabrat...
Feature 1                                                #      #                                
BAF95910     101 ARRLDa---FHVLLDRpEALASLRQr--PLGHGKRWLVWLKLDCGNGRAGVRpTDPAALELAQAIand---apEEVTLVG 172 chicken
AAI22307     131 SERLSl---FHVLLDNtLALQELKKr--PLKQGKVWSVWMKLDCDNGRAGVPhYEPAALQLAQEIwq-----tEGVELTG 200 zebrafish
XP_002127262  98 SEKMKs---FVVFVDNvAALKALEQw--KLKDNKNWQVLVEVDTGAGRSGVQiESLDAVSLIKEVvk-----cGNVTFSG 167 Ciona intestinalis
XP_001544668 128 GKSLGta-sISVLVDNpDIIPFLSQy--RETTSDTLGVFIKLDTGNNRAGILpESQQFKDLVAAVhaaehddsIGISLRG 204 Ajellomyces cap...
BAE57432     173 AAELGpd-sVSVMIDHpDQIKFLDTf--SRIAGFAAGVFLKVDCGYHRAGLPpRAMDKGGLFSKLeel--ektGAGRLVG 247 Aspergillus oryzae
XP_572767    129 QEIVGaqatIRLMVDHaEQIRILQSfsqKIQRPARWSVFVKVDGGGKRAGAPaESEQMKELIQALve----sqDYVEIFG 204 Cryptococcus ne...
EDP47329     115 SSKLK----IVLMVDNeAQIDALESfaqSTGRTAPWPVFIKVDVGSHRAGLEsSSSAMRLLVEKVes-----sHAAEVYG 185 Aspergillus fum...
P53095       128 SRRVNn---FQVFVDNiEHLENLKNf-gRPASGKKWSVFIKVDMGTKRAGLAfDSPEFLSLLKKLtss--eikEVIEPYG 201 baker's yeast
XP_382632    115 RKSLR----LQLMVDNeQQVSFLEE---SASSQEPWDIFIKLDVGSHRAGVEaNSDALHRLVKRAek-----sSAVNIYG 182 Gibberella zeae...
XP_445494    128 STRVSn---LRVFVDNiDHLENLKQf-gRPKSGKKWSIFLKIDMGTSRAGLEvRSEEFKELVEKLcde--svkEVTQIFG 201 Candida glabrat...
Feature 1           #                                                ##                          
BAF95910     173 VYAHCGNTYGCSGaDTIQAIARTTTNAVLSFVAALrq----aGVPCPQASIGSTPSCSH--------------------- 227 chicken
AAI22307     201 VYAHCGNTYSCQGeEQIKAVAQQTTTVTLQFMDKLka----aGIHSPKSSIGSTPSCSH--------------------- 255 zebrafish
XP_002127262 168 LYSHCGHSYKCKNaEEIKEVGKMATNKMLTLVDELkk----qGITCPSYGIGSTPSCSK--------------------- 222 Ciona intestinalis
XP_001544668 205 FYSHLGHSYSSDStNEAMDYLAQEVERCGIAAAYAstv-gkySGSRFLISVGATPTTTAaqnltspdtvd---ptikrvk 280 Ajellomyces cap...
BAE57432     248 IYSHSSLSYGGRNrGDALRHLRGEVEACLLALDSYagv--lpVDRELVVSVGATPQVVAaeavaegddaeleelrkflke 325 Aspergillus oryzae
XP_572767    205 FYSHFGQSYASDSlSAGSSYFAGEINCVQTAAKIArn---lgAKGKWTLSVGATPTAHAavqe----------------- 264 Cryptococcus ne...
EDP47329     186 FYCHAGHSYACRTeEAAAAVLKSELEGVVRAAGYLdr----kEGRKVVVSFGSTPTAHVvns------------------ 243 Aspergillus fum...
P53095       202 FYAHAGHSYSSTSiNDTQNLLMEEVKAVNSAAKVLcsvdpqfDPSKLTLSVGATPTSNSlkldnk------------stl 269 baker's yeast
XP_382632    183 FYCHAGHSYGGRSrKEAEETLNIEVSSVLAAAKLLp------SDRRLIISVGSTPTAHVves------------------ 238 Gibberella zeae...
XP_445494    202 LYAHAGHSYSSHDiNEANGYLIDEITAVNEAAKLVgsv-teiEPRLLTLSVGATPTANSlstken------------kkl 268 Candida glabrat...
Feature 1                      ####                                                    #         
BAF95910     228 ---PIPEMSQLTELHPGNYIFYDLQQTQLGSC------QPQDVAIRVLTRVIGHYAHR----GQLLVDCGWAALSLHGAG 294 chicken
AAI22307     256 ---PVPDMAKLSEVHPGNCVFYDVQQSLIGSC------RLEDVAVRVLTRVIGHYPRR----NQLLVDCGWTALSHDGGG 322 zebrafish
XP_002127262 223 ---PAPEMSKLTEWHPGNYVLYDLMQVKIGSC------EIDDIASFVLTRVIGHYTKGe--dVFLIIDCGWTAISLHGVK 291 Ciona intestinalis
XP_001544668 281 elfDRSKESYDIELHAGAYVTLDMQQLAAHARptsshlSFNDIALTVLAEVGSLYPHRe--kPEALAACGSLCLGREACR 358 Ajellomyces cap...
BAE57432     326 pdtGAFKGRVRVELHAGNYPLLDMQQMSTNAGgvr-erFFDEVGAYVVAETCSVYNDGereyPEALVAVGTLGMGREPCP 404 Aspergillus oryzae
XP_572767    265 avkEHGPLEGELELHAGCYCMCDLQQCATSLV------SYSDVAISVLGRVVSVYPLR----KEAMCDVGALSVSKDTGR 334 Cryptococcus ne...
EDP47329     244 -lrRALPEGMEVELHAGNFPANDLQQVCTGLV------AEEQQAVRVLVEVCSVYPER----NEALINAGTVALTKETSD 312 Aspergillus fum...
P53095       270 vkfITTQLVSTLEIHCGNYCMYDLQQVATGCV------QDHELSGFVLGTVLSSYPSR----GELLSNTGVMCLTREASS 339 baker's yeast
XP_382632    239 -lkASMPENVILELHAGNFPCNDLQQVSTGLV------TESQQAVSVAAEVCSVYPER----NEALVNAGVIALSREASA 307 Gibberella zeae...
XP_445494    269 idiIRNDLVAPLEIHCGNYPCYDLQQYSTKCI------KLNKISAFVLASIVSKYEKR----NEALINAGVLALARENSS 338 Candida glabrat...
Feature 1                                                                                        
BAF95910     295 AgqGPQGCAA-------------------IDGHPELRLVGLTQEHGLLehaggq--mdfgrFPVGSVLALIPYHACATAA 353 chicken
AAI22307     323 R--LPTGYAI-------------------IEGHPELKLLSMTQEHGRVepvsgk--ldfkqFPLGSLLTLMPYHACATAM 379 zebrafish
XP_002127262 292 DseETSGYGL-------------------IVDHPELKLAHMSQEHGIVkskdstkpldlsrYPVDSFLRIYPYHSCATCA 352 Ciona intestinalis
XP_001544668 359 Ny-PGWGVVTpwleggegirtaetgwydpEGDRRGWIMDRISQEHGILawhgpr--dkvrlLKIGEKIRIWPNHCCICIA 435 Ajellomyces cap...
BAE57432     405 Sy-KGWGVVGpwg-------------lptTPQRDRLYIDRISQEHSILrwesed-vakkipLSVGQTVKIYPNHACITGA 469 Aspergillus oryzae
XP_572767    335 F--TGFGRVVk------------------PDYATGWDLGRISQEHGTLvhrqgedikegneLKIGNSVQIIPQHACLVCA 394 Cryptococcus ne...
EDP47329     313 V--VGFGRVTdrpg------------wavVRMAQEHGILGLANASGVQrve--------etFRVGQKVMLYIQHACITAA 370 Aspergillus fum...
P53095       340 I--KGFGICAdleh-----------vlksESFSREWYVARVSQEHGILrpirnw--nettpLKLGSKIAVLPQHACITMG 404 baker's yeast
XP_382632    308 F--SGFGRVVgspa------------wglVRLSQEHGIMGTSEGRKVDd-----------dFKVGQRVEIWCNHSCIAAA 362 Gibberella zeae...
XP_445494    339 I--PGMGLCIntdky----------lhapRDFEVSSFVNRVSQEHGILqpynr---dkcedWKLGEKLLVIPQHACITMA 403 Candida glabrat...
Feature 1                                        
BAF95910     354 MHPVYYVHEEGKvv---------aLWHPVRGW 376 chicken
AAI22307     380 MHPVYFVHSKGKiv---------dTWKPTRGW 402 zebrafish
XP_002127262 353 MHPVFYVADQNDni--------idHWRPVKGW 376 Ciona intestinalis
XP_001544668 436 GFSYVLVVDSSLegaer--drvqdVWFSWRGW 465 Ajellomyces capsulatus NAm1
BAE57432     470 MYGWYLVVDSSSdpdat---kvvdVWVRWLGW 498 Aspergillus oryzae
XP_572767    395 CFPWLYVVDDGGnev-------vdVWVPWKGW 419 Cryptococcus neoformans var. neoformans JEC21
EDP47329     371 QHHVYHVVDEEDiv--------reTWVPWKGW 394 Aspergillus fumigatus A1163
P53095       405 QFPYYFVVNSEGiv--------ndVWLPFQKW 428 baker's yeast
XP_382632    363 AFHVYYVVDEGGivvdlephtssaNCGSFKKD 394 Gibberella zeae PH-1
XP_445494    404 QFPYYFVFNDSGkv--------idVWKPHQKW 427 Candida glabrata CBS 138

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