2OO0,2PLJ,1D7K,1F3T,3BTN,1QU4,2TOD,2ON3,3BTN


Conserved Protein Domain Family
PLPDE_III_ODC

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cd00622: PLPDE_III_ODC 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase
This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily 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. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this subfamily are proteins with homology to ODC but do not possess any catalytic activity, the Antizyme inhibitor (AZI) and ODC-paralogue (ODC-p). AZI binds to the regulatory protein Antizyme with a higher affinity than ODC and prevents ODC degradation. ODC-p is a novel ODC-like protein, present only in mammals, that is specifically exressed in the brain and testes. ODC-p may function as a tissue-specific antizyme inhibitory protein.
Statistics
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PSSM-Id: 143482
View PSSM: cd00622
Aligned: 105 rows
Threshold Bit Score: 343.707
Threshold Setting Gi: 66045783
Created: 7-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 15 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.
  • Structure:1F3T_AB; Trypanosoma Brucei Ornithine decarboxylase dimer binds two cofactor-substrate (PLP-putrescine) complexes; defined at 4A contacts.
    View structure with Cn3D
  • Structure:2PLJ_AB; Vibrio vulnificus LysineOrnithine decarboxylase dimer binds two PLP-putrescine complexes; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      # #                  #                            
2OO0_A        47 KDAFYVADLGDILKKHLRWLKALPrVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVppERIIYANPCKQ 126 human
YP_190879     15 ATPCLVVDLDVVGAHYRALHDALPeAKIYYAIKANPAPAILDRLVALGSSFDVASPAEIRMCLDAGAtpDRISYGNTLKK 94  Gluconobacter o...
YP_001601608  80 ATPCLVVDVDRVEARYQSLRAALPlARIYYAVKANPAPAILRRLVSLGSAFDAASWEEIRLCLAAGAagADISFGNTVKK 159 Gluconacetobact...
YP_001235297  15 STPAILVDLDRVAANFAALRAALPdAAIYYAVKANPAAPVLDRLVGLGSRFDAASIEEIRACLAAGAapAAISFGNTVKK 94  Acidiphilium cr...
ZP_01756186   44 ARPTLVVDLDAVAAQYRALEAGLGrARIHYAVKANPEAAILKRLVALGAHFDAAGRAEIDMCLAAGAtaAQISFGNTIKR 123 Roseobacter sp....
ZP_01666158   20 GTPLLVLSRDQIRYNYNFLAEHLPgVHIYYAMKANPDPRIIDELAGLGACFDVASDGEILALAQMGIapERIVYANPVKT 99  Thermosinus car...
YP_855811     18 GSPLLLLDKAAVRKQYRALAAALPdVRLHYALKPLPHEAVVSVLKEEGACFDLATNGEVDLVRSQGVrpGRCIHTHPIKR 97  Aeromonas hydro...
O50657        19 PTPFLVASLDKVEENYQFMRRHLPrAGVFYAMKANPTPEILSLLAGLGSHFDVASAGEMEILHELGVdgSQMIYANPVKD 98  Selenomonas rum...
NP_868377     42 GTPLLVVSRSKAIETYWAMKNALPgVDLYYAAKANPDLHFLSTLNGENAFIDVCSPGELKAALAAGFtpDRMLHTHPCKT 121 Rhodopirellula ...
2PLJ_A        54 GAPLLLLDCDVIRQQYRALKNALPnVTLHYALKPLPHPVVVRTLLAEGASFDLATTGEVELVASEGVpaDLTIHTHPIKR 133 Vibrio vulnificus
Feature 1                                             #                                          
2OO0_A       127 vSQIKYAANNgVQMMTFDSEVELMKVARahpKAKLVLRIATDDSKavCRLSVKFGATLRTSRLLLERAKelNIDVVGVSF 206 human
YP_190879     95 aEWIREAHDLgISLFVFDSIEELEKLAKhapGARVFCRLAVENEGadWPLSRKFGTTLSNARALMLRARdlGLKPYGLSF 174 Gluconobacter o...
YP_001601608 160 aSAIAQAHQAgVTMFAFDSIEELEKLARhapGSRVYCRLIVENEGaeWPLSRKFGTTLDSARDLMLRARdmGLDPYGLSF 239 Gluconacetobact...
YP_001235297  95 rAAIAEAHARgVDLFAFDSDEELDKLAEaapGAKVYCRLAVSQDGadWPLSRKFGTSGTHARDLLVRAAerGLIPWGVSF 174 Acidiphilium cr...
ZP_01756186  124 pADIAYAHACgITHFAFDASEELEKIAThapGAEVCLRIIVENCEadWPLSRKFGCAPEDALRLMDQARglGLVVNGLSF 203 Roseobacter sp....
ZP_01666158  100 aSGLAAARQTgVRKFTFDSESEIYKMAKavpGGTVLLRVRVDNPHalVDLNKKFGAHPDEALRLLTIAReqGLDVAGLCF 179 Thermosinus car...
YP_855811     98 dSDIRYALEYgCTVFVYDNPLELEKFIPykdEVKLLLRVSFPNPEtkVDLSKKFGCTPEQALPLLQLAHakGIKVMGLSF 177 Aeromonas hydro...
O50657        99 aRGLKAAADYnVRRFTFDDPSEIDKMAKavpGADVLVRIAVRNNKalVDLNTKFGAPVEEALDLLKAAQdaGLHAMGICF 178 Selenomonas rum...
NP_868377    122 dANLWECYEAgVNWFVFDNPIEAEKIRRltpDVNLLLRLATTGASsrINLSAKFGCPMHEALELLATAKakGLKVRGFSF 201 Rhodopirellula ...
2PLJ_A       134 dADIRDALAYgCNVFVVDNLNELEKFKAyrdDVELLVRLSFRNSEafADLSKKFGCSPEQALVIIETAKewNIRIKGLSF 213 Vibrio vulnificus
Feature 1        #  #                                    ##                                      
2OO0_A       207 HVGSGCtDPETFVQAISDARCVFDMGae-vGFSMYLLDIGGGFPGsed--vklKFEEITGVINPALDKYFPsdsgVRIIA 283 human
YP_190879    175 HVGSQQtGVAAYDHAIAKAAGLYHDLra-qGVDLQMLNLGGGFPThyre-nvpSVQDFADTIHASLRTHFPdg-aPEILL 251 Gluconobacter o...
YP_001601608 240 HVGSQQtSTDAYEAAIARVGMLFTDLaa-aGLNLRMVNLGGGFPIryre-dvpEIDRFAVAISHAMTEHFGnd-lPEMIV 316 Gluconacetobact...
YP_001235297 175 HVGSQQtGVGAWRTAIGQAAAVFTDLra-rGIDLRLLNLGGGFPTryrd-dipPLGDFGAAIMDTVRQAFGnn-vPDLLI 251 Acidiphilium cr...
ZP_01756186  204 HVGSQTrEPDMWVPVLDQAAAIWRQAre-aGHALRLVNIGGGFPAsydq-qmqGAEAYAREVMKQVEARFGe--aAEIMA 279 Roseobacter sp....
ZP_01666158  180 HVGSQStDAGAYVDALAACRRIFDAAak-eGFNLRILDIGGGFPIpaig-mkvDAAAMMGQIRTALAQYFPn---TEIWA 254 Thermosinus car...
YP_855811    178 HVGSQVpHARRHVQAIDACREIMEQAwe-lGLKPWVLDIGGGFPVdyeg-gefDIDGFCAPIREALAKLPAt---VQKIA 252 Aeromonas hydro...
O50657       179 HVGSQSlSTAAYEEALLVARRLFDEAee-mGMHLTDLDIGGGFPVpdakglnvDLAAMMEAINKQIDRLFPd---TAVWT 254 Selenomonas rum...
NP_868377    202 HVGSQClNPQDYVEVLRSVREVWDEAtk-aGHHLEVLDIGGGFPApyre-dapSIEAFGEVITNGLREIFGdl-pIRLIA 278 Rhodopirellula ...
2PLJ_A       214 HVGSQTtNPNKYVEAIHTCRHVMEQVvergLPALSTLDIGGGFPVnytq-qvmPIDQFCAPINEALSLLPEt---VHVLA 289 Vibrio vulnificus
Feature 1        ####                                                      #                     
2OO0_A       284 EPGRYYVASAFTLAVNIIAKKIVlkeqtgsddedesseqtfMYYVNDGVYGSFNCilYDHAHVKPLLQKrpkpdeKYYSS 363 human
YP_190879    252 EPGRYMVGQSGVVSSEVILVSRRggav----------tdprWVYLDIGRFGGLAEteGEAIRYTFRTSRdsd-daTCSPC 320 Gluconobacter o...
YP_001601608 317 EPGRFIVGDAGVVSSEVVLVTRRgqqd-----------gprWVYLDIGRFGGLAEteGESIRYGIRTPHdg---sPAGRV 382 Gluconacetobact...
YP_001235297 252 EPGRAIVGDAGVAVSEVVLACTRhede-----------grrWVYLDLGRFGGLAEteGEAIRYRITAPGva---gADAPA 317 Acidiphilium cr...
ZP_01756186  280 EPGRGLVAEAGAIAAEVLLVSKKhend-----------lhrWVYLDVGKFSGLAEtmDEAIRYRITTDRdh---eAKGPC 345 Roseobacter sp....
ZP_01666158  255 EPGRFICGTAVNLITRVIGVQQRng--------------qqWYFLDEGLYGTFSGiiFDHWDFELETFKs----ePKIPA 316 Thermosinus car...
YP_855811    253 EPGRFISAPAMTSVSSVMGKAHRgd--------------kiWYYLDDGLYGSYNGqlYDHVTYPVSTPLar---gELHNS 315 Aeromonas hydro...
O50657       255 EPGRYMCGTAVNLVTSVIGTKTRge--------------qpWYILDEGIYGCFSGimYDHWTYPLHCFGk----gNKKPS 316 Selenomonas rum...
NP_868377    279 EPGRGLCTESVTLITRVIGKSRRwe--------------lpWFFLDDGIYGSFSGkiFDHTDFPLLVENdg--srETVPC 342 Rhodopirellula ...
2PLJ_A       290 EPGRFICAPAVTSVASVMGQAEReg--------------qiWYYLDDGIYGSFSGlmFDDARYPLTTIKqg---gELIPS 352 Vibrio vulnificus
Feature 1              #                               #                    
2OO0_A       364 SIWGPTCDGLDRIVEr--CDLPE-MHVGDWMLFENMGAYTVAAASt-FNGFQRPTIYYV 418 human
YP_190879    321 VLAGPSCDGVDIMYEknrIPLPDsLECGDRVEILATGAYVSTYASvgFNGFPPLTEYYI 379 Gluconobacter oxydans 621H
YP_001601608 383 AIAGPTCDGADIMYEkapYALPLdLACGDRIELLSTGAYVSTYCStsFNGFAPLTEHYI 441 Gluconacetobacter diazotrophicus PAl 5
YP_001235297 318 VLAGPSCDGVDVMYRetpCPLPAsLAAGDRVLIHDTGAYVTSYASqgFNGFLPPEEHYL 376 Acidiphilium cryptum JF-5
ZP_01756186  346 VVAGPSCDSVDVLYEkqpYQLPTgLKAGDRVVIHSCGAYTSTYASigFNGFPPLDVIVI 404 Roseobacter sp. SK209-2-6
ZP_01666158  317 TFAGPSCDSLDVLFRd--KLTPP-LAMDDLILVPSCGSYTSASATv-FNGFAKAPIIVW 371 Thermosinus carboxydivorans Nor1
YP_855811    316 VLSGPTCDSVDVIRDg--IMLPD-LAIGELVVGRVMGAYTWASASt-FNFFPKASILIL 370 Aeromonas hydrophila subsp. hydrophi...
O50657       317 TFGGPSCDGIDVLYRd--FMAPE-LKIGDKVLVTEMGSYTSVSATr-FNGFYLAPTIIF 371 Selenomonas ruminantium
NP_868377    343 VVAGPTCDSTDIVSRd--QWLPD-LEVGELVLVPSMGAYAAASASp-FNGLPMANSVAI 397 Rhodopirellula baltica SH 1
2PLJ_A       353 VLSGPTCDSVDVIAEn--ILLPK-LNNGDLVIGRTMGAYTSATATd-FNFFKRAQTIAL 407 Vibrio vulnificus

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