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: 2-Oct-2020
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:
Feature 1                                              # #                  #                    
NP_624642     29 RTPLVGLLDVDGVLAAVDALNEAFEgp----apVQHTFAAKACGLVPVLRLLAEAGMGCEVASPGELEQALAAGFTYDRL 104 Streptomyces co...
ZP_00379520   57 GTPVIGLIDLDHIAETYALLTSAFSga----adVLHAVACKAVPLQPLLRSYAEAGAGCEVASPGELELALSAGFSPEAI 132 Brevibacterium ...
YP_269410     20 NLTAIGVMDLDGLKKTVNDAYAAFPa------nFFHTFAVKANALVKVLEPLREYGMGAEVASPGELLIAVTAGFTAENI 93  Colwellia psych...
NP_824674     60 DAPIVALLDVAGIRGSAAALRAAFDavvapgtpVLHAFAVKATPLVPVLRLLGEAGIGAEVASPGELALAQAAGVAPERT 139 Streptomyces av...
YP_890417     38 LHPLCGVIDLDTLDELMASLHAAYPad----lpALHTIAAKAISLRPVLARFAAAGFGCEVASPGELELALAAGFPAERI 113 Mycobacterium s...
XP_643322     31 EHDYVMLYNLDEFRALAKEACDNLK--------GLQTMAVKCNPVMSLMKEAIKAGLGAEVASFGELRIAEIAGFEPSKI 102 Dictyostelium d...
XP_001628760  32 KQPVGLFYDLDEFEANVDRVTEAFGq------gCLHAIAVKANPVPALLDLVNKKGQGAECASIGEVLNALKVGFPAERI 105 starlet sea ane...
YP_001617687  26 VEPAVLFHDLGRMRARIGRIGAAFPp------gALHTVAIKANPLVEVLRAAVDCGAGLEAASLEEVKLSLAAGCPPDRI 99  Sorangium cellu...
Feature 1          #                                                 #                           
NP_624642    105 VFDSPAKTvEELEFALAHGIAINLDNFQEMARVDGLLag----reAAGPIGLRVNPQVGAGAIgAMSTATATSKFGVALr 180 Streptomyces co...
ZP_00379520  133 VFDSPAKTwTELRRAVDLGVSMNIDNFDELERLDVLLtg----htTSARVGIRINPQSGTGTIgALSTATQTSKFGIGLa 208 Brevibacterium ...
YP_269410     94 IFDSPAKTlQDLRTCIKKGIALNIDNLQELERIDALMlef---peSTSIIGFRVNPQIGGGKIgSTSTATATSKFGYALv 170 Colwellia psych...
NP_824674    140 VLDSPAKTpAELREALALGIAVNADNPQELDRIDALVrs----apSGSPVGIRVNPQVGGGSIdALSTATATSKFGVALr 215 Streptomyces av...
YP_890417    114 VFDSPAKTpTEIARALELGVSFNVDNFEELARIDAAVarn---grPRSVIGVRVNPQTGAGTIdAMSTATSTSKFGIGLa 190 Mycobacterium s...
XP_643322    103 IFDSPIKTkKELEYALNLGVVINIDNFEELETIESIVskfskekyESLSLGIRVNPQVGAGKLtDLSTGVPTSKFGIGIe 182 Dictyostelium d...
XP_001628760 106 VYDSPVKTrPELKFLMEQGVHLNVDNFQELQVITELMkel---knVKSTIGLRINPVMDAGDIkALSVSCTDSKFAVALt 182 starlet sea ane...
YP_001617687 100 VYDSPAKSrADIAEALRLGVRINADNLDELGRIDELVgh----ggAASRIGLRINPQVGASSIaLTSVADRRSKFGVPLe 175 Sorangium cellu...
Feature 1                               #  #                                          ##         
NP_624642    181 degAVDAVIEAFARRPWLNRLHAHVGSQGCPLPLIAQGVRTAYELAERInrel-----graQITGLDIGGGLPVNFDGED 255 Streptomyces co...
ZP_00379520  209 dpgARDELIEAYLSRPWLNQIHVHSGSQGISLDQAAAGIETVVDLAKEVnelaaqkhgrdrQITRIDIGGGLPVNFSGEE 288 Brevibacterium ...
YP_269410    171 dgdNRNELISIYKKRPWLKSIHTHSGSQGCELSLMAKGIKIITELAEEInslv-----glqQITRLDIGGGLPVNFSSEI 245 Colwellia psych...
NP_824674    216 degAREWILRAYADRPWLTRLHAHSGSQGMPLSLMARGIAETYALAEEInrhv-----grrQIDTIDIGGGLPVNFGSDA 290 Streptomyces av...
YP_890417    191 --dHRDEIIDAFATRPWLTQLHVHSGSQGMSLEHAAEGVRLTTDLAADIdara-----gsrQIQRIDVGGGLPVNFRSDD 263 Mycobacterium s...
XP_643322    183 ---HKDKIIDAYVRNKFLKGVHIHVGSQGFEISNISESAVKVMNLVKEInard----dtksQITFFNMGGGLSVNFESEE 255 Dictyostelium d...
XP_001628760 183 e-sTRDEIIGWFVDRPWMNCVHVHVGSQSYGVEGLSEGARRAVDLALAVnkkv-----grnQVEIIDIGGGMGVNREDDS 256 starlet sea ane...
YP_001617687 176 ---QADAVRAAFARYAWLAGLHVHVGSQGCALSQLIDGIGRVEALRQELrram-----gplAAGTMDIGGGLPVAYRSTD 247 Sorangium cellu...
Feature 1                                       ####                                             
NP_624642    256 DRPTYADHVAELRSAAPGLFdg---rYALITEFGRSLLAKSGTIASVVEYTKSA--GGRRIAVTHAGAQVATRTVFMPDA 330 Streptomyces co...
ZP_00379520  289 ITPTFAEYRAVLEARVPELFd-----FDLVTEFGRALLAKAGTTLTHVEYAKTT--GGRRIAMTHAGVQVATRTAYAPAD 361 Brevibacterium ...
YP_269410    246 IKPSFKDYADILKAEVPLLFtd---kYQVKTEFGRAIVAKNGVIITRVEYTKNS--GGRHIATTHAGAQIITRTAFLPKS 320 Colwellia psych...
NP_824674    291 TTPTYARYARLLAESVPGLFdg---rYGLVTEFGRSLLAKHGTVVARVEYAKSA--GGRAVAVTHAGVQVATRTVYAPAS 365 Streptomyces av...
YP_890417    264 VTPTFADHRAALQAAAPRLFdg---tYTVVTEFGRALTAKAGTVVARVEYTKVT--GGRPIAITHAGVQVATRSIFAPEA 338 Mycobacterium s...
XP_643322    256 TSPTFTQYANHMKQLLPELFng---eFLLITEFGRSYWAKCGVVVSTVEYTKSS--GDREIAICHAGANMYIRTVYQFPL 330 Dictyostelium d...
XP_001628760 257 ISPTYQDYVNALKKAVPQLFpdqgvfKQLVTEFGQSLNAKTGFIVSRVEYTKKVpeSDHTIALIHAGADMCLRSCYCPQV 336 starlet sea ane...
YP_001617687 248 RPPALEDYAAALRREVPTLFee---gTTLITEFGRWIQAGCGFAVSRVEYVKKD--SAGRTAILHLGADFLLRRAYHPDD 322 Sorangium cellu...
Feature 1                                         ##                           #   #   #         
NP_624642    331 --WPLRVGVFDAAGRPKQGPa---eVVDIAGPCCFAGDLTATGRELPaVEPGDVVALYDTGAYYFSSHFSYNSLPRPAVY 405 Streptomyces co...
ZP_00379520  362 --WPLRILPFTPEGNPKTAEv---vPTDVAGPACFAGDLLVRDRMLPrLDAGDIVAVPDTGAYYFSNPFSYNLLPRVPVY 436 Brevibacterium ...
YP_269410    321 --WPIRVTGYTTKGEERTAQtsevvTTDVAGPCCFAGDLICSNQPLPkLESNDYVMVHDTGGYYFTNHFDYNSLPRVAIY 398 Colwellia psych...
NP_824674    366 --WPLRITAYDAKGHPKAGPe---vVQDVAGPACFAGDLLAVGRALPlLEQGDHVAALDTGAYYFAHHYAYNSLARPGIY 440 Streptomyces av...
YP_890417    339 --WPLRVEVYDAHGRRRDDPp---rVQDVAGPACFTGDMLAVGRELPpVHAGDLVAVPDTGGYYFSTHFSYNALPRPAVY 413 Mycobacterium s...
XP_643322    331 --WRIRVTIFDSNGEYKTGNe---kITDIAGPCCFAADVLVKERLLPpIKKDDFIMAHDSGAYMLSSYSHYNLRLAPPIF 405 Dictyostelium d...
XP_001628760 337 akYKRRVQVFDSNGKPKTGQe---kLHNIAGPLCFAGDVVRKEVMLPqIERGDYVILHDCGANSLATFSRHCSRFAPSVF 413 starlet sea ane...
YP_001617687 323 --WHHDFMALDPEAEPKGGPl---sPCTLGGPLCFGGDVLARELAFPeLSPGDLVLIRDTGAYTLSMWSRHCSRGIPAVL 397 Sorangium cellu...
Feature 1            
NP_624642    406 GYRT 409 Streptomyces coelicolor A3(2)
ZP_00379520  437 GYRV 440 Brevibacterium linens BL2
YP_269410    399 TVAG 402 Colwellia psychrerythraea 34H
NP_824674    441 GFAT 444 Streptomyces avermitilis MA-4680
YP_890417    414 TVGT 417 Mycobacterium smegmatis str. MC2 155
XP_643322    406 SFNT 409 Dictyostelium discoideum AX4
XP_001628760 414 GYRV 417 starlet sea anemone
YP_001617687 398 GVDA 401 Sorangium cellulosum 'So ce 56'

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