Conserved Protein Domain Family
PLPDE_III_ODC_DapDC_like_1

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cd06836: PLPDE_III_ODC_DapDC_like_1 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases
This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Statistics
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PSSM-Id: 143505
View PSSM: cd06836
Aligned: 8 rows
Threshold Bit Score: 589.749
Threshold Setting Gi: 162455320
Created: 16-Jun-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the structures of PLP and substrate bound to ornithine and diaminopimelate decarboxylases.
  • 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 21218863   29 RTPLVGLLDVDGVLAAVDALNEAFEgp----apVQHTFAAKACGLVPVLRLLAEAGMGCEVASPGELEQALAAGFTYDRL 104
gi 62424373   57 GTPVIGLIDLDHIAETYALLTSAFSga----adVLHAVACKAVPLQPLLRSYAEAGAGCEVASPGELELALSAGFSPEAI 132
gi 71280920   20 NLTAIGVMDLDGLKKTVNDAYAAFPa------nFFHTFAVKANALVKVLEPLREYGMGAEVASPGELLIAVTAGFTAENI 93
gi 29830040   60 DAPIVALLDVAGIRGSAAALRAAFDavvapgtpVLHAFAVKATPLVPVLRLLGEAGIGAEVASPGELALAQAAGVAPERT 139
gi 118472318  38 LHPLCGVIDLDTLDELMASLHAAYPad----lpALHTIAAKAISLRPVLARFAAAGFGCEVASPGELELALAAGFPAERI 113
gi 66819325   31 EHDYVMLYNLDEFRALAKEACDNLK--------GLQTMAVKCNPVMSLMKEAIKAGLGAEVASFGELRIAEIAGFEPSKI 102
gi 156371417  32 KQPVGLFYDLDEFEANVDRVTEAFGq------gCLHAIAVKANPVPALLDLVNKKGQGAECASIGEVLNALKVGFPAERI 105
gi 162455320  26 VEPAVLFHDLGRMRARIGRIGAAFPp------gALHTVAIKANPLVEVLRAAVDCGAGLEAASLEEVKLSLAAGCPPDRI 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #                                                 #                           
gi 21218863  105 VFDSPAKTvEELEFALAHGIAINLDNFQEMARVDGLLag----reAAGPIGLRVNPQVGAGAIgAMSTATATSKFGVALr 180
gi 62424373  133 VFDSPAKTwTELRRAVDLGVSMNIDNFDELERLDVLLtg----htTSARVGIRINPQSGTGTIgALSTATQTSKFGIGLa 208
gi 71280920   94 IFDSPAKTlQDLRTCIKKGIALNIDNLQELERIDALMlef---peSTSIIGFRVNPQIGGGKIgSTSTATATSKFGYALv 170
gi 29830040  140 VLDSPAKTpAELREALALGIAVNADNPQELDRIDALVrs----apSGSPVGIRVNPQVGGGSIdALSTATATSKFGVALr 215
gi 118472318 114 VFDSPAKTpTEIARALELGVSFNVDNFEELARIDAAVarn---grPRSVIGVRVNPQTGAGTIdAMSTATSTSKFGIGLa 190
gi 66819325  103 IFDSPIKTkKELEYALNLGVVINIDNFEELETIESIVskfskekyESLSLGIRVNPQVGAGKLtDLSTGVPTSKFGIGIe 182
gi 156371417 106 VYDSPVKTrPELKFLMEQGVHLNVDNFQELQVITELMkel---knVKSTIGLRINPVMDAGDIkALSVSCTDSKFAVALt 182
gi 162455320 100 VYDSPAKSrADIAEALRLGVRINADNLDELGRIDELVgh----ggAASRIGLRINPQVGASSIaLTSVADRRSKFGVPLe 175
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                               #  #                                          ##         
gi 21218863  181 degAVDAVIEAFARRPWLNRLHAHVGSQGCPLPLIAQGVRTAYELAERInrel-----graQITGLDIGGGLPVNFDGED 255
gi 62424373  209 dpgARDELIEAYLSRPWLNQIHVHSGSQGISLDQAAAGIETVVDLAKEVnelaaqkhgrdrQITRIDIGGGLPVNFSGEE 288
gi 71280920  171 dgdNRNELISIYKKRPWLKSIHTHSGSQGCELSLMAKGIKIITELAEEInslv-----glqQITRLDIGGGLPVNFSSEI 245
gi 29830040  216 degAREWILRAYADRPWLTRLHAHSGSQGMPLSLMARGIAETYALAEEInrhv-----grrQIDTIDIGGGLPVNFGSDA 290
gi 118472318 191 --dHRDEIIDAFATRPWLTQLHVHSGSQGMSLEHAAEGVRLTTDLAADIdara-----gsrQIQRIDVGGGLPVNFRSDD 263
gi 66819325  183 ---HKDKIIDAYVRNKFLKGVHIHVGSQGFEISNISESAVKVMNLVKEInard----dtksQITFFNMGGGLSVNFESEE 255
gi 156371417 183 e-sTRDEIIGWFVDRPWMNCVHVHVGSQSYGVEGLSEGARRAVDLALAVnkkv-----grnQVEIIDIGGGMGVNREDDS 256
gi 162455320 176 ---QADAVRAAFARYAWLAGLHVHVGSQGCALSQLIDGIGRVEALRQELrram-----gplAAGTMDIGGGLPVAYRSTD 247
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       ####                                             
gi 21218863  256 DRPTYADHVAELRSAAPGLFdg---rYALITEFGRSLLAKSGTIASVVEYTKSA--GGRRIAVTHAGAQVATRTVFMPDA 330
gi 62424373  289 ITPTFAEYRAVLEARVPELFd-----FDLVTEFGRALLAKAGTTLTHVEYAKTT--GGRRIAMTHAGVQVATRTAYAPAD 361
gi 71280920  246 IKPSFKDYADILKAEVPLLFtd---kYQVKTEFGRAIVAKNGVIITRVEYTKNS--GGRHIATTHAGAQIITRTAFLPKS 320
gi 29830040  291 TTPTYARYARLLAESVPGLFdg---rYGLVTEFGRSLLAKHGTVVARVEYAKSA--GGRAVAVTHAGVQVATRTVYAPAS 365
gi 118472318 264 VTPTFADHRAALQAAAPRLFdg---tYTVVTEFGRALTAKAGTVVARVEYTKVT--GGRPIAITHAGVQVATRSIFAPEA 338
gi 66819325  256 TSPTFTQYANHMKQLLPELFng---eFLLITEFGRSYWAKCGVVVSTVEYTKSS--GDREIAICHAGANMYIRTVYQFPL 330
gi 156371417 257 ISPTYQDYVNALKKAVPQLFpdqgvfKQLVTEFGQSLNAKTGFIVSRVEYTKKVpeSDHTIALIHAGADMCLRSCYCPQV 336
gi 162455320 248 RPPALEDYAAALRREVPTLFee---gTTLITEFGRWIQAGCGFAVSRVEYVKKD--SAGRTAILHLGADFLLRRAYHPDD 322
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                         ##                           #   #   #         
gi 21218863  331 --WPLRVGVFDAAGRPKQGPa---eVVDIAGPCCFAGDLTATGRELPaVEPGDVVALYDTGAYYFSSHFSYNSLPRPAVY 405
gi 62424373  362 --WPLRILPFTPEGNPKTAEv---vPTDVAGPACFAGDLLVRDRMLPrLDAGDIVAVPDTGAYYFSNPFSYNLLPRVPVY 436
gi 71280920  321 --WPIRVTGYTTKGEERTAQtsevvTTDVAGPCCFAGDLICSNQPLPkLESNDYVMVHDTGGYYFTNHFDYNSLPRVAIY 398
gi 29830040  366 --WPLRITAYDAKGHPKAGPe---vVQDVAGPACFAGDLLAVGRALPlLEQGDHVAALDTGAYYFAHHYAYNSLARPGIY 440
gi 118472318 339 --WPLRVEVYDAHGRRRDDPp---rVQDVAGPACFTGDMLAVGRELPpVHAGDLVAVPDTGGYYFSTHFSYNALPRPAVY 413
gi 66819325  331 --WRIRVTIFDSNGEYKTGNe---kITDIAGPCCFAADVLVKERLLPpIKKDDFIMAHDSGAYMLSSYSHYNLRLAPPIF 405
gi 156371417 337 akYKRRVQVFDSNGKPKTGQe---kLHNIAGPLCFAGDVVRKEVMLPqIERGDYVILHDCGANSLATFSRHCSRFAPSVF 413
gi 162455320 323 --WHHDFMALDPEAEPKGGPl---sPCTLGGPLCFGGDVLARELAFPeLSPGDLVLIRDTGAYTLSMWSRHCSRGIPAVL 397

                 ....
Feature 1            
gi 21218863  406 GYRT 409
gi 62424373  437 GYRV 440
gi 71280920  399 TVAG 402
gi 29830040  441 GFAT 444
gi 118472318 414 TVGT 417
gi 66819325  406 SFNT 409
gi 156371417 414 GYRV 417
gi 162455320 398 GVDA 401

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