1KNW,2P3E,1HKV,1TWI,2YXX,3C5Q


Conserved Protein Domain Family
PLPDE_III_DapDC

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cd06828: PLPDE_III_DapDC 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase
Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC 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. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Statistics
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PSSM-Id: 143501
View PSSM: cd06828
Aligned: 140 rows
Threshold Bit Score: 316.733
Threshold Setting Gi: 167564952
Created: 13-Mar-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 20 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site is composed of residues from both subunits of the dimer. There are two active sites in the functional dimer. Only one subunit is shown in the structure 1KNW_A.
  • Structure:1KNW_A; Escherichia coli Diaminopimelate decarboxylase binds PLP and MES; defined at 4A contacts.
    View structure with Cn3D
  • Structure:1TWI_AB; Methanocaldococcus jannaschii Diaminopimelate decarboxylase dimer binds two cofactors (PLP) and two substrates (L-lysine); defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                           # #                  #                       
1KNW_A        24 FGCPVWVYDAqIIRRQIAALKQF-------DVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGynpqthpdD 96
gi 159041106  19 YDTPLIVYDLnLIEGNYRSIKDSl-----nAKVLYSIKANPNLAILAFLRRLGSGADAASPGEVFLALKAGfk----psE 89
gi 48477088   26 FGTPLIVLSEkRINNNYLKIKSAfskhfrhFKVHYALKANSNPAVISILRRLGAGADAANPNEAEIAMYSGis----pdN 101
gi 13541637   28 FGTPVIIYSApRIVKNVSSLFGAmp---kvTKCFYSVKANSNPNLVRLIGRQGCGSEVTSLGEIQIAMISSid----pdD 100
gi 10640067   61 YGTPVIIYSRaRIVSNIRRIREAye---nrVRMLYSVKANDNPRIIEIMHQESIGSDSASPMEIMMSIFSGip----peD 133
gi 162453832  20 YGTPLYAYDAeRIRENFRRLTRAlrgnypeVSVFYAIKACNNLEIAKLLVDEGSGVDAASPNEIRLAQALGls----geR 95
gi 158522146  22 YGTPFHIYDEaGIRGTGKALLDAfss-vpgFREYYAVKALPNPRILDIMRSMGFGFDCSSIPELVLARRAGai----geE 96
gi 32475756   20 HPTPFVLYHEdGIRARARELTDAfaw-negFQQYFAVKATPNPHIVAMMAEEGGGADCSSVAELITCERLGit----gqD 94
gi 401153     22 YPTPFHIYDErAIVQTHRNVAQAfad--saFRQYFAVKALPTPAILSLLLKEGSGLDCSSPVELMLAERLGar----gdD 95
gi 23394392   20 YGTPLQIYDEqLIRDNARRLLTAfrahfpdFQQFYAVKALPNPAILKLLHQEGCGMDCSSSAELHIVKELGvp----gdQ 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #                                            #                               
1KNW_A        97 IVFTADVIDqATLERVSELq-IPVNAGSvDMLDQLGQVsp--gHRVWLRVNPGfghghsq--ktntggENSKHGIWytDL 171
gi 159041106  90 VLYTGAYLSnNDIKYGIDSr-VVLNFDSvRAFERAMALgy-rpRLVFFRIDLGygegftp--gvtlagEESKFGMFlnDA 165
gi 48477088  102 IIMTGNNLSyNDLKRALEMn-IKINFDDvNQMNILKNEl---pDIISFRINPGygngeft--giktagPSSKFGIPvnEA 175
gi 13541637  101 ILFTPNNVSkEEMDFALDRg-IKITFNSpGQFELVSNRv----EEATFRINPGighgehp--gtttggHGSKFGIDpeTA 173
gi 10640067  134 ILYSPNNASeYDLNFALDRg-IAINFNTfTQYRKMREKp----ERISFRINPGfgmgefa--gtttggARTKFGIDpdAA 206
gi 162453832  96 IIYTGNSLSdEDLAAGLRAg-VNFNVDDhGILKRLFSIgk--pRCMSFRINPSgediatp-dlkpfagPSAKFGIHprHV 171
gi 158522146  97 IMFTSNNTSaEEFEAALADsgCILNLDDiSLIYKVPKLp----DLVCFRYNPGerrtgn---aiignpVEAKYGVAhdQI 169
gi 32475756   95 VMFTSNNTTmEEFEIANKLg-AIINLDTpHHIDQIAQLsp-lpEMVSFRFNPGperqgn---viigdpKEAKFGSTreQL 169
gi 401153     96 IVFTSNNTSlSEYQMALQAg-ALVTFDDrSMLEQVIALp----DIVAFRVSPHgviars---sqmgnaQQSKFGIPeaEL 167
gi 23394392   96 VIFTSNFTAkNDLGTAFDQg-VIMNLDDvSLVDSLVAVrgkcpELMSFRLNPGigrtdsetksnvlggPDAKFGVPpfQI 174
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         # #  #                                    ##                   
1KNW_A       172 PAALDVIQrhHLQLVGIHMHIGSGv-DYAHLEQVCGAMVRQVief----gqDLQAISAGGGLSVPYqqgeeavDTEHYYG 246
gi 159041106 166 IKAYRLAKsnGVKEFGIHAMMGSNvlNPDYFLKIAELLKEQAkviegevgiKISYFDMGGGFGIPYkp----gEKPLDLN 241
gi 48477088  176 LNGYRTALnaGVKKFGIHMMAGSNnlDPGYFYELSGIFAGIIktinnelgiSFDFIDIGGGFGVPYkne-aalDINETAR 254
gi 13541637  174 LKLYTRAKelGIRKFGIHMMVGSNntDADLMLTFYKKFFDMAseiektahlQFSYIDIGGGFGVPYndeqrslDIKKLGS 253
gi 10640067  207 ILAYRKARedGIREFGIHMMIGSNnrDHVKIAEAYSNFFRIAdrigreagvSFQFADVGGGLGIPYvqgenelDIAALGS 286
gi 162453832 172 EEAYRTALenGVERLGVHMMPHSQahKPENFAHVTGKLLDLIgpvarklgfDLAFVDIGGGLGIPYrreqpplDVEAVAR 251
gi 158522146 170 LEAYRKVRdmGARRFGLHAMLASNerNHTYMVTTAEMLLDLVrdisdtldiQFEFVNIGGGLGISYrpgepplDLPAMGA 249
gi 32475756  170 MDGYRRCAelGISRFGLHAMVVSNelNIEALLQTAEMLFELAaeihretgiSVECINLGGGIGVPYqpgqepvDLPAFGD 249
gi 401153    168 VQSYREAWdrGARRFGIHGMMCANelSLEAAVQAGVQVIEVGarvareagiELEYINIGGGLGIPYriddqalDLTAYAD 247
gi 23394392  175 VEAYRKAQqaGAKGFGIHMMTGSCvmNQEYWRETVTVLFNTIvqlkkelgiEFEFMNIGGGLGIPYredqepvNVEAIAK 254
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                               ####                                   #   #             
1KNW_A       247 LWNAAReqiarh--lghpvKLEIEPGRFLVAQSGVLITQVRSVKQmgsrHFVLVDAGFNDLMRpamYGSYHHISALaadg 324
gi 159041106 242 RLSALRgff--------pgELWVEPGRFIVGNAGYLLTRVTEVKKkgnrTYIGVDVGMNVLIRpmlYNAYHHIITCnege 313
gi 48477088  255 LIAMALdgimd---snpdaEIIIEPGRYLVADAGIALATVTDLKNyg-rSIAGTDLGMNILIRpalYGAVHEIICInknd 330
gi 13541637  254 GLKELVdqy-------gieRLFIEPGRYIVADAGILVGKVYDVYN----GFVGTDIGMNINIRhalYGAEHRFYALtgrs 322
gi 10640067  287 AVLKEFdry-------hfgDLVLEPGRYLVGDAGIIVGTVNDVHN----GFAGTDIGMNLNIRpalYGARHTIIPVgerv 355
gi 162453832 252 GIAAMVrkkcae-hglkepRLVMEPGRYFVGDAGYVLGRVISIKQgy-kTIIGTDISMNTMARpvmYGAYHEVRINgrgg 329
gi 158522146 250 QISDVFerfgre--rrympRLYIESGRYMTGPHGALVTRVINRKHiy-rTYVGVDACMSALMRpaiYGAYHHISLPtksg 326
gi 32475756  250 GVRKLYesilvp-agiapvRILMENGRAMTGPFGYLITKVINQKSsy-kDYVGVDACMSNLMRpgmYGAYHHITVMgked 327
gi 401153    248 ALKRALkqafp----hntpKLLMELGRYISGPHGVLVSRVINRCSkg-rEIVGLDASMSALMRpglYGAYHHLTLPfadq 322
gi 23394392  255 MLREVFdeavkehglqtlpRLCMENGRFMTGPFGWLVTRCEAIKEty-gRYYGVDACMAHLMRpgmYGAFHHISIParan 333
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
Feature 1                         #                                   #   #   #           
1KNW_A       325 rslehaptvETVVAGPLCESgDVFTQqeggnvetralpevkaGDYLVLHDTGAYGASMSsNYNSRPLLPEVLF 397
gi 159041106 314 ------gseIVDVVGPICENtDKLAInrelp-------rvkeGDLLVILNAGAYVYSMSsNYNGRLRPAEVVV 373
gi 48477088  331 -----dklfNYDITGQICENtDFTGLnvklp-------glepGDILGIMNAGAYVSSMSsNYNSLSRAAEVLI 391
gi 13541637  323 ------deaEYIVTGQICENtDVTGRltgk---------vqiGDLVAMYDAGAYIYSMSsNYNGRFRPTEVIV 380
gi 10640067  356 ------egeKITVTGQICENtDRIGDtawr---------lseGDRIMVLDAGAYVYSMSsRYNGRPRPPEIMI 413
gi 162453832 330 ------qtaPMAMTGQVCENtDMWIPerefp------advaeGDVVVLMDAGAYGHVMSyDYNGRLRPAEVLI 390
gi 158522146 327 -----gpveTVDVVGALCENnDKFAVqrelp-------vaaeGDLMVIHDTGAHGIAMGfNYNGRMRPMELLL 387
gi 32475756  328 q----padrTVDIVGSLCENnDKFAIdrkmp-------atevGDIAVIHDAGAHGHSMGfQYNGRLRSAEIVF 389
gi 401153    323 -----rpegVFDVVGALCENfDKFAVdrllp-------spliGDLALIHDTGAHGHAMGfTYNGRLRPAELML 383
gi 23394392  334 -----eevsPSHVVGTLCENnDWFAKdrplp-------kaqvGDLFVIHDTGAHSHSMGfQYNGKLRAPEVLL 394

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