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: 2-Oct-2020
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:
Feature 1                                           # #                  #                       
1KNW_A        24 FGCPVWVYDAqIIRRQIAALKQF-------DVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGynpqthpdD 96  Escherichia coli
YP_001540358  19 YDTPLIVYDLnLIEGNYRSIKDSl-----nAKVLYSIKANPNLAILAFLRRLGSGADAASPGEVFLALKAGfk----psE 89  Caldivirga maqu...
YP_022794     26 FGTPLIVLSEkRINNNYLKIKSAfskhfrhFKVHYALKANSNPAVISILRRLGAGADAANPNEAEIAMYSGis----pdN 101 Picrophilus tor...
NP_111325     28 FGTPVIIYSApRIVKNVSSLFGAmp---kvTKCFYSVKANSNPNLVRLIGRQGCGSEVTSLGEIQIAMISSid----pdD 100 Thermoplasma vo...
CAC11919      61 YGTPVIIYSRaRIVSNIRRIREAye---nrVRMLYSVKANDNPRIIEIMHQESIGSDSASPMEIMMSIFSGip----peD 133 Thermoplasma ac...
YP_001616199  20 YGTPLYAYDAeRIRENFRRLTRAlrgnypeVSVFYAIKACNNLEIAKLLVDEGSGVDAASPNEIRLAQALGls----geR 95  Sorangium cellu...
YP_001530016  22 YGTPFHIYDEaGIRGTGKALLDAfss-vpgFREYYAVKALPNPRILDIMRSMGFGFDCSSIPELVLARRAGai----geE 96  Desulfococcus o...
NP_868750     20 HPTPFVLYHEdGIRARARELTDAfaw-negFQQYFAVKATPNPHIVAMMAEEGGGADCSSVAELITCERLGit----gqD 94  Rhodopirellula ...
P31851        22 YPTPFHIYDErAIVQTHRNVAQAfad--saFRQYFAVKALPTPAILSLLLKEGSGLDCSSPVELMLAERLGar----gdD 95  Pseudomonas syr...
AAN31485      20 YGTPLQIYDEqLIRDNARRLLTAfrahfpdFQQFYAVKALPNPAILKLLHQEGCGMDCSSSAELHIVKELGvp----gdQ 95  potato late bli...
Feature 1           #                                            #                               
1KNW_A        97 IVFTADVIDqATLERVSELq-IPVNAGSvDMLDQLGQVsp--gHRVWLRVNPGfghghsq--ktntggENSKHGIWytDL 171 Escherichia coli
YP_001540358  90 VLYTGAYLSnNDIKYGIDSr-VVLNFDSvRAFERAMALgy-rpRLVFFRIDLGygegftp--gvtlagEESKFGMFlnDA 165 Caldivirga maqu...
YP_022794    102 IIMTGNNLSyNDLKRALEMn-IKINFDDvNQMNILKNEl---pDIISFRINPGygngeft--giktagPSSKFGIPvnEA 175 Picrophilus tor...
NP_111325    101 ILFTPNNVSkEEMDFALDRg-IKITFNSpGQFELVSNRv----EEATFRINPGighgehp--gtttggHGSKFGIDpeTA 173 Thermoplasma vo...
CAC11919     134 ILYSPNNASeYDLNFALDRg-IAINFNTfTQYRKMREKp----ERISFRINPGfgmgefa--gtttggARTKFGIDpdAA 206 Thermoplasma ac...
YP_001616199  96 IIYTGNSLSdEDLAAGLRAg-VNFNVDDhGILKRLFSIgk--pRCMSFRINPSgediatp-dlkpfagPSAKFGIHprHV 171 Sorangium cellu...
YP_001530016  97 IMFTSNNTSaEEFEAALADsgCILNLDDiSLIYKVPKLp----DLVCFRYNPGerrtgn---aiignpVEAKYGVAhdQI 169 Desulfococcus o...
NP_868750     95 VMFTSNNTTmEEFEIANKLg-AIINLDTpHHIDQIAQLsp-lpEMVSFRFNPGperqgn---viigdpKEAKFGSTreQL 169 Rhodopirellula ...
P31851        96 IVFTSNNTSlSEYQMALQAg-ALVTFDDrSMLEQVIALp----DIVAFRVSPHgviars---sqmgnaQQSKFGIPeaEL 167 Pseudomonas syr...
AAN31485      96 VIFTSNFTAkNDLGTAFDQg-VIMNLDDvSLVDSLVAVrgkcpELMSFRLNPGigrtdsetksnvlggPDAKFGVPpfQI 174 potato late bli...
Feature 1                         # #  #                                    ##                   
1KNW_A       172 PAALDVIQrhHLQLVGIHMHIGSGv-DYAHLEQVCGAMVRQVief----gqDLQAISAGGGLSVPYqqgeeavDTEHYYG 246 Escherichia coli
YP_001540358 166 IKAYRLAKsnGVKEFGIHAMMGSNvlNPDYFLKIAELLKEQAkviegevgiKISYFDMGGGFGIPYkp----gEKPLDLN 241 Caldivirga maqu...
YP_022794    176 LNGYRTALnaGVKKFGIHMMAGSNnlDPGYFYELSGIFAGIIktinnelgiSFDFIDIGGGFGVPYkne-aalDINETAR 254 Picrophilus tor...
NP_111325    174 LKLYTRAKelGIRKFGIHMMVGSNntDADLMLTFYKKFFDMAseiektahlQFSYIDIGGGFGVPYndeqrslDIKKLGS 253 Thermoplasma vo...
CAC11919     207 ILAYRKARedGIREFGIHMMIGSNnrDHVKIAEAYSNFFRIAdrigreagvSFQFADVGGGLGIPYvqgenelDIAALGS 286 Thermoplasma ac...
YP_001616199 172 EEAYRTALenGVERLGVHMMPHSQahKPENFAHVTGKLLDLIgpvarklgfDLAFVDIGGGLGIPYrreqpplDVEAVAR 251 Sorangium cellu...
YP_001530016 170 LEAYRKVRdmGARRFGLHAMLASNerNHTYMVTTAEMLLDLVrdisdtldiQFEFVNIGGGLGISYrpgepplDLPAMGA 249 Desulfococcus o...
NP_868750    170 MDGYRRCAelGISRFGLHAMVVSNelNIEALLQTAEMLFELAaeihretgiSVECINLGGGIGVPYqpgqepvDLPAFGD 249 Rhodopirellula ...
P31851       168 VQSYREAWdrGARRFGIHGMMCANelSLEAAVQAGVQVIEVGarvareagiELEYINIGGGLGIPYriddqalDLTAYAD 247 Pseudomonas syr...
AAN31485     175 VEAYRKAQqaGAKGFGIHMMTGSCvmNQEYWRETVTVLFNTIvqlkkelgiEFEFMNIGGGLGIPYredqepvNVEAIAK 254 potato late bli...
Feature 1                               ####                                   #   #             
1KNW_A       247 LWNAAReqiarh--lghpvKLEIEPGRFLVAQSGVLITQVRSVKQmgsrHFVLVDAGFNDLMRpamYGSYHHISALaadg 324 Escherichia coli
YP_001540358 242 RLSALRgff--------pgELWVEPGRFIVGNAGYLLTRVTEVKKkgnrTYIGVDVGMNVLIRpmlYNAYHHIITCnege 313 Caldivirga maqu...
YP_022794    255 LIAMALdgimd---snpdaEIIIEPGRYLVADAGIALATVTDLKNyg-rSIAGTDLGMNILIRpalYGAVHEIICInknd 330 Picrophilus tor...
NP_111325    254 GLKELVdqy-------gieRLFIEPGRYIVADAGILVGKVYDVYN----GFVGTDIGMNINIRhalYGAEHRFYALtgrs 322 Thermoplasma vo...
CAC11919     287 AVLKEFdry-------hfgDLVLEPGRYLVGDAGIIVGTVNDVHN----GFAGTDIGMNLNIRpalYGARHTIIPVgerv 355 Thermoplasma ac...
YP_001616199 252 GIAAMVrkkcae-hglkepRLVMEPGRYFVGDAGYVLGRVISIKQgy-kTIIGTDISMNTMARpvmYGAYHEVRINgrgg 329 Sorangium cellu...
YP_001530016 250 QISDVFerfgre--rrympRLYIESGRYMTGPHGALVTRVINRKHiy-rTYVGVDACMSALMRpaiYGAYHHISLPtksg 326 Desulfococcus o...
NP_868750    250 GVRKLYesilvp-agiapvRILMENGRAMTGPFGYLITKVINQKSsy-kDYVGVDACMSNLMRpgmYGAYHHITVMgked 327 Rhodopirellula ...
P31851       248 ALKRALkqafp----hntpKLLMELGRYISGPHGVLVSRVINRCSkg-rEIVGLDASMSALMRpglYGAYHHLTLPfadq 322 Pseudomonas syr...
AAN31485     255 MLREVFdeavkehglqtlpRLCMENGRFMTGPFGWLVTRCEAIKEty-gRYYGVDACMAHLMRpgmYGAFHHISIParan 333 potato late bli...
Feature 1                         #                                   #   #   #           
1KNW_A       325 rslehaptvETVVAGPLCESgDVFTQqeggnvetralpevkaGDYLVLHDTGAYGASMSsNYNSRPLLPEVLF 397 Escherichia coli
YP_001540358 314 ------gseIVDVVGPICENtDKLAInrelp-------rvkeGDLLVILNAGAYVYSMSsNYNGRLRPAEVVV 373 Caldivirga maquilingen...
YP_022794    331 -----dklfNYDITGQICENtDFTGLnvklp-------glepGDILGIMNAGAYVSSMSsNYNSLSRAAEVLI 391 Picrophilus torridus D...
NP_111325    323 ------deaEYIVTGQICENtDVTGRltgk---------vqiGDLVAMYDAGAYIYSMSsNYNGRFRPTEVIV 380 Thermoplasma volcanium...
CAC11919     356 ------egeKITVTGQICENtDRIGDtawr---------lseGDRIMVLDAGAYVYSMSsRYNGRPRPPEIMI 413 Thermoplasma acidophilum
YP_001616199 330 ------qtaPMAMTGQVCENtDMWIPerefp------advaeGDVVVLMDAGAYGHVMSyDYNGRLRPAEVLI 390 Sorangium cellulosum '...
YP_001530016 327 -----gpveTVDVVGALCENnDKFAVqrelp-------vaaeGDLMVIHDTGAHGIAMGfNYNGRMRPMELLL 387 Desulfococcus oleovora...
NP_868750    328 q----padrTVDIVGSLCENnDKFAIdrkmp-------atevGDIAVIHDAGAHGHSMGfQYNGRLRSAEIVF 389 Rhodopirellula baltica...
P31851       323 -----rpegVFDVVGALCENfDKFAVdrllp-------spliGDLALIHDTGAHGHAMGfTYNGRLRPAELML 383 Pseudomonas syringae p...
AAN31485     334 -----eevsPSHVVGTLCENnDWFAKdrplp-------kaqvGDLFVIHDTGAHSHSMGfQYNGKLRAPEVLL 394 potato late blight agent

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