Conserved Protein Domain Family
PLPDE_III_Y4yA_like

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cd06842: PLPDE_III_Y4yA_like 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA
This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic 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. 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.
Statistics
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PSSM-Id: 143509
View PSSM: cd06842
Aligned: 19 rows
Threshold Bit Score: 477.524
Threshold Setting Gi: 54024534
Created: 12-Jun-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
Conserved Features/SitesClick to see Conserved Features Help
 
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 2496780    31 LFDWAARHGSPLNLVWPDALRENLAALKGVLTERRLEHAIYYGAKANKSPGLMQAALSAGa---GLDVSSLYELRDARRL 107
gi 32471477   53 VKQLIEFHGSPVNVLSTDPMRSNIKDLQNVASQASVPLQIHFARKANKCAEFVRTGLMESi---GFDVASEFEKQQTLDE 129
gi 149178621  48 LPELAQKQGSPLNVLNTQPFERNAKALYDVAEAQGLEFDVYFARKANKCLAFVETAKNQGy---GVDTASIQELQQVLDN 124
gi 32473071  109 LFDLVETYGSPLNLVRPRTMRRNVEELNAVARERGLDFRVFFARKANKCLGFVDEAIESNf---GVDTASENELRQCLQQ 185
gi 126347857  25 LHSLVDALGSPLNVLLPETIAENAERFRAVYRRHHLTGRVYFAHKANRSSALLRRLAAEDpahvGVDVASPAELRHALGC 104
gi 54024534   25 AVAAVADGGTPAHVVFPQVLAENVGALAAVLDRSPVRSRMCYAHKVNRSPALARAAERCGi---GIDVASPGELANARAA 101
gi 150389435  22 LLNLIDGLGSPLNIIFPEEINQNIEEFKEVFNKHFVSGKVFYAHKTNKSNSIVRQASFEAv---NIDVASENELKSALKN 98
gi 83944546   35 LDALTDRFGAPLNIQSVDPFRRNIAQLTDCVTDYGLPFLPMFARKANKCLSYVQAARDMGi---GIDTASHAEVEQCLEQ 111
gi 23308900   15 CRHLIEEFGSPVNVLHSGSMPRNINELVDAGIQMGVDTRIFFARKANKGLTFVDAVKDTGh---GVDVASERELSQVLNR 91
gi 68537075   25 LPQMRELASGPFHVLYPAQLRTNLRDFATTAQDMNVDCTVFFARKANKAECWLQEIAAADq---GVDVASGPELVGALAG 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #                                                   #            
gi 2496780   108 GAd------GARLVATGPAKTsAFHQELINCNALISVDSpEELEDLIHGLpa------daGQQSILLRLRPrdq------ 169
gi 32471477  130 LYrlpqhpfDSPIVCTAAVKPvSLIRSCVLSNIVLVIDNeDELTTLRETLahlg---staPKARIAFRLQHcsakf---- 202
gi 149178621 125 QVp------PEKIICTAAVKSeALLRLCIKSGVTIAVDHlDELMQIVILAeq------lkQRADIAVRLSGfqhqg---- 188
gi 32473071  186 CVp------AKDLICTAAIKSdSLIDLCLQQQVCIAVDNdDELQVVVDRAne------lgRQARIALRLGGfqheg---- 249
gi 126347857 105 GFt------GDRIMATGPKDP-EFLWLAARVGATVNLDSlRELDQLAELVrty-----glGRADVLVRLSGfesvdghgg 172
gi 54024534  102 GFg------PARIEVTGPKGA-RFLATAVASGATINVDNlWELAALDDLArg-------tDPIPTLLRVGDlpg------ 161
gi 150389435  99 GFt------GDRIEATGPKNR-NFITLGLQHNIIFNIDNlQELDQVMELKkaid--fqntKKVKILLRFSGfksesi--- 166
gi 83944546  112 GLp------GDRIVCTAAVKDrALMTLCVGGGVTVILDNeDELELLEDVAeg------atKPVSVGLRLNGferdg---- 175
gi 23308900   92 GVp------GERIILSAAIKPdRLLALAIENGVIISVDSrDELDRISALVg--------dRVARVAPRVAPdpav----- 152
gi 68537075  102 GIr------GTKLVITGAEKAdNLLWLGIRHGCTIAADSpGELQRILDITrretsahhtdGHTRVLLRILPaeq------ 169
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                    #  #                                
gi 2496780   170 -------skSRFGMPpDAVVHCLARLAGe-----gRVRFDGLHFHLSGY----RRETRVAALREAADLIAEARRmGFFPG 233
gi 32471477  203 -----pdlpSRFGMPaNELTLLARSLCDe-----pRIQVVGIHFHVHRSdeqfSPSFTKALIDDALDVVDRVREiGHAVA 272
gi 149178621 189 -----arllSRFGFDlDEIRPLIEDLQNasphclqYLNLIGVHFHLDGY----CQAQRVSAIQQLLPLIDELRSrDFPVR 259
gi 32473071  250 -----nklpTRFGFDvDRDCDLPQRLTSl------PVMVQGIHFHLDGY----DAGQRVSALSVAMEWVERLRAvGQPVE 314
gi 126347857 173 agtrllsrrSRFGTPvREVETVLSAVERha----dAVTLTGLAYHLDTT----GLAEKGRALERCVLLMDECRArGLAPR 244
gi 54024534  162 ------tprSRFGVPlPRVDDALRLLAAsa----aRIRFLGFAFHLDSG----AVTDRVRAVQTCLALIERAHAhGLAPH 227
gi 150389435 167 ---kvlsknSKFGIPaSGIYQALEKLSQyr----eDIHFWGFSFHVDTI----DLKEKVIAIENCIDFFDIARDhDFEPR 235
gi 83944546  176 -----tklySRFGFPlTQVPTLAARIAAs-----eTLRLDGLHFHLNGY----SAEDRIAAILQTLPLIHKIKGdSTAPF 241
gi 23308900  153 ------lppTRFGERaADWGNRLTEVIP-------GVDIVGLHVHLHGY----AAKDRALALQECCQLVDSLREcGHSPQ 215
gi 68537075  170 -------teSRFGCTpQEWSACISGLPElg----kHVDIVGSCFHLNEY----SSEQRGKEAHRSLDFMRELRRkGWRAD 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1             ##                                                                         
gi 2496780   234 MIDIGGGLPIQYvd-raRYKAHLAAQAPEDYrtgk-------------------ipdSFYPYGSTL-SAADWLHRLLEAE 292
gi 32471477  273 WLDIGGGFPVNYlchqkHWQRFLKEAHTFTEssgrfeanrk-------ltwnqrplkDIDPTWQPM-NAADWLRAVLTSS 344
gi 149178621 260 FLDIGGGFPMSYlesetEWDTFWQTHRRALLgehrpltyrnhglgltlvegtligkpNCYPYYQSP-VQANWLEGILTSE 338
gi 32473071  315 FIDMGGGFPMSYleehrQWATFWKEHRRALLgerdtltyrghglglaieggrvvgqpKMYPFFQRP-VRGHWLAGVLDSR 393
gi 126347857 245 AIDIGGGFGVGYvadaeEWERWTTALSEAVLggrppltwrghgyglrneggtvrgsvALYPGHRPH-AGPGYLDELLSLP 323
gi 54024534  228 VLDIGGGLRQVFtadadRFDGYVRALRAGLAgrgpamswpgqtfgyhvaggaahgtpVFHKYGNTV-GAADMLAELLAAP 306
gi 150389435 236 VLDIGGGFKVSYiedakEWNDSISYLKESILgyqegvtwnnqtfgiqqekgvlkgtlNIYNYHDNL-TGPKYLDALLSTR 314
gi 83944546  242 FLDIGGGIPMNYlddaaEWETWLAELDRALIgdrdpitqhndg---lgrkvggegkvDSYPVAQTL-VQEDWMRRILDHM 317
gi 23308900  216 FIDLGGGVPMSYieseeDWIRYQSAKSATSAgyaesft------------wkddplsNTYPFYQTP-VRGNWLKDVLSKG 282
gi 68537075  235 TLDIGGGFSVRYsa-daDWEAFQPTLTDASAfhag------------------htpsTSYPYGGEKaTGPEMLRAILNTP 295
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                              ####                                                      
gi 2496780   293 Mnqg--rsvAGYLAREGLTLAMEPGRALADQAAITVFRISRVKAlg---------------pDSHVIFVEGSSFSACEtw 355
gi 32471477  345 L--------AYEINRRELILKCEPGRALLDGCGLTIAEVLFVKRdq---------------nQNHLIGLMMNSSQCRT-- 399
gi 149178621 339 Ceag---tiADSLRKRQIQLRCEPGRSLLDGCGFTAARVEFRKQqp---------------tGDWLIGLSMNRTQCRT-- 398
gi 32473071  394 Iegk---tiADRLVELNVQLRCEPGRSILDGCGLTVARVEFRKQna---------------eGDWLIGLSMNRTQCRT-- 453
gi 126347857 324 Apvlg-rapGTLLLEHLHDLHIEPGRALADQCGLSLARVLDVRPtge-------------gpDQYLVRLGMNAGDVSL-- 387
gi 54024534  307 LaehegrplGTVLADNLLELWLEPGKALVDHAGLTLASVEFVKElg---------------dGTVLVTLDLSRDTVTP-- 369
gi 150389435 315 LpkfenrtiGTILSENMIDLFIEPGKALVNQLGLSAAKVNFIKQss---------------dDEILIGLDLKRTDVVM-- 377
gi 83944546  318 Adgq---tvAAHLRDAHISLRCEPGRSLLDGCGMTLARVAFCKRds---------------aGTPVIGVQMNRTQSRS-- 377
gi 23308900  283 V--------AQMLIDRGLRLHLEPGRSLLDGCGVTLAEVAFVKTrs---------------dGLPLVGLAMNRTQCRT-- 337
gi 68537075  296 TkqvdgqtlAERLRTEGVKLALEPGRALLAGCGLTVFPVQGVKSaeterkspdlnpqenshyRYQILTAAGLSMSLSEqw 375
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                              ##                             #   #    # 
gi 2496780   356 FASEFLIDPILVPatkat------vqlpPVRAYLAGHSCLDEDVISNRWLTFPTaPRAGDLLVYANTGGYQMDLLENeFH 429
gi 32471477  400 TRDDFLVDPIVISasnesakptnqtdhaEIEGYFVGGYCTESEYLMQRRFRFPRgISRGDFVLIPNTAAYQMHFAESrAH 479
gi 149178621 399 SSDDFLVDPLLIPateesl---lprtpaGISGYLVGAYCTESELLCLRKLQFPHgVGIGDLIVFPNTAGYFMHFLESrSH 475
gi 32473071  454 SSDDFLVDPILVPkqssfg---ratetkPMLGYLVGAYCTESELISLRKMQFPSgVQRGDLIAFPNTAGYFMHFLESrSH 530
gi 126347857 388 EEHGVLVDPVLLPrggpe-----dggqgPVGVHLVGNLCLEADLITRRLVFLPAlPRAGDLLAFVNTAGYAMDFHAHrAQ 462
gi 54024534  370 ADQEVMVDPLVLPgarr-------ddgpAVGVYFAGRLCLERDLITTRQVFLPGlPAPGDVVVFPNTAAYHMDLSAStAA 442
gi 150389435 378 GDQELFIDPIIIHrskvt------dlqeDKGVYFIGNLCLESDLIFKHKIFINQlPANGDIVIFPNTAGYFMDFNATdSI 451
gi 83944546  378 GFAEFALDPLMVPapgp--------rkgPIEGYLAGTYCTESEWLTRRKMSFPQgVKAGDLMVFPNTAGYLMHFLESrSH 449
gi 23308900  338 TSDDFLIDPLHITdgd---------vgeEIEAYLVGAYCIEDELILRRRIRFPRgVKPGDIIGIPNTAGYFMHILESaSH 408
gi 68537075  376 KSSEFLPDPTLWPqre----------gtPTRACVGGSSCMEYDMLTWRTICFPRaPKRGDLLIYHNTAGYQMDKNESsFH 445
                        490
                 ....*....|
Feature 1                  
gi 2496780   430 RHPMPARFCV 439
gi 32471477  480 QMPLAENVFL 489
gi 149178621 476 QFPLAQNVVY 485
gi 32473071  531 QFPLAKNLIV 540
gi 126347857 463 RQPLARTVAV 472
gi 54024534  443 RWAPPRRWVV 452
gi 150389435 452 MQPIAKKVAV 461
gi 83944546  450 QFPLARNVFV 459
gi 23308900  409 QIPLAKNVVW 418
gi 68537075  446 QLPLPSRFVW 455

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