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: 2-Oct-2020
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:
Feature 1                                                  # #                     #             
P55709        31 LFDWAARHGSPLNLVWPDALRENLAALKGVLTERRLEHAIYYGAKANKSPGLMQAALSAGa---GLDVSSLYELRDARRL 107 Rhizobium sp. N...
NP_864470     53 VKQLIEFHGSPVNVLSTDPMRSNIKDLQNVASQASVPLQIHFARKANKCAEFVRTGLMESi---GFDVASEFEKQQTLDE 129 Rhodopirellula ...
ZP_01857207   48 LPELAQKQGSPLNVLNTQPFERNAKALYDVAEAQGLEFDVYFARKANKCLAFVETAKNQGy---GVDTASIQELQQVLDN 124 Planctomyces ma...
NP_866065    109 LFDLVETYGSPLNLVRPRTMRRNVEELNAVARERGLDFRVFFARKANKCLGFVDEAIESNf---GVDTASENELRQCLQQ 185 Rhodopirellula ...
CAJ89577      25 LHSLVDALGSPLNVLLPETIAENAERFRAVYRRHHLTGRVYFAHKANRSSALLRRLAAEDpahvGVDVASPAELRHALGC 104 Streptomyces am...
YP_118776     25 AVAAVADGGTPAHVVFPQVLAENVGALAAVLDRSPVRSRMCYAHKVNRSPALARAAERCGi---GIDVASPGELANARAA 101 Nocardia farcin...
YP_001319484  22 LLNLIDGLGSPLNIIFPEEINQNIEEFKEVFNKHFVSGKVFYAHKTNKSNSIVRQASFEAv---NIDVASENELKSALKN 98  Alkaliphilus me...
ZP_00956997   35 LDALTDRFGAPLNIQSVDPFRRNIAQLTDCVTDYGLPFLPMFARKANKCLSYVQAARDMGi---GIDTASHAEVEQCLEQ 111 Sulfitobacter s...
NP_601336     15 CRHLIEEFGSPVNVLHSGSMPRNINELVDAGIQMGVDTRIFFARKANKGLTFVDAVKDTGh---GVDVASERELSQVLNR 91  Corynebacterium...
YP_251780     25 LPQMRELASGPFHVLYPAQLRTNLRDFATTAQDMNVDCTVFFARKANKAECWLQEIAAADq---GVDVASGPELVGALAG 101 Corynebacterium...
Feature 1                       #                                                   #            
P55709       108 GAd------GARLVATGPAKTsAFHQELINCNALISVDSpEELEDLIHGLpa------daGQQSILLRLRPrdq------ 169 Rhizobium sp. N...
NP_864470    130 LYrlpqhpfDSPIVCTAAVKPvSLIRSCVLSNIVLVIDNeDELTTLRETLahlg---staPKARIAFRLQHcsakf---- 202 Rhodopirellula ...
ZP_01857207  125 QVp------PEKIICTAAVKSeALLRLCIKSGVTIAVDHlDELMQIVILAeq------lkQRADIAVRLSGfqhqg---- 188 Planctomyces ma...
NP_866065    186 CVp------AKDLICTAAIKSdSLIDLCLQQQVCIAVDNdDELQVVVDRAne------lgRQARIALRLGGfqheg---- 249 Rhodopirellula ...
CAJ89577     105 GFt------GDRIMATGPKDP-EFLWLAARVGATVNLDSlRELDQLAELVrty-----glGRADVLVRLSGfesvdghgg 172 Streptomyces am...
YP_118776    102 GFg------PARIEVTGPKGA-RFLATAVASGATINVDNlWELAALDDLArg-------tDPIPTLLRVGDlpg------ 161 Nocardia farcin...
YP_001319484  99 GFt------GDRIEATGPKNR-NFITLGLQHNIIFNIDNlQELDQVMELKkaid--fqntKKVKILLRFSGfksesi--- 166 Alkaliphilus me...
ZP_00956997  112 GLp------GDRIVCTAAVKDrALMTLCVGGGVTVILDNeDELELLEDVAeg------atKPVSVGLRLNGferdg---- 175 Sulfitobacter s...
NP_601336     92 GVp------GERIILSAAIKPdRLLALAIENGVIISVDSrDELDRISALVg--------dRVARVAPRVAPdpav----- 152 Corynebacterium...
YP_251780    102 GIr------GTKLVITGAEKAdNLLWLGIRHGCTIAADSpGELQRILDITrretsahhtdGHTRVLLRILPaeq------ 169 Corynebacterium...
Feature 1                                                    #  #                                
P55709       170 -------skSRFGMPpDAVVHCLARLAGe-----gRVRFDGLHFHLSGY----RRETRVAALREAADLIAEARRmGFFPG 233 Rhizobium sp. N...
NP_864470    203 -----pdlpSRFGMPaNELTLLARSLCDe-----pRIQVVGIHFHVHRSdeqfSPSFTKALIDDALDVVDRVREiGHAVA 272 Rhodopirellula ...
ZP_01857207  189 -----arllSRFGFDlDEIRPLIEDLQNasphclqYLNLIGVHFHLDGY----CQAQRVSAIQQLLPLIDELRSrDFPVR 259 Planctomyces ma...
NP_866065    250 -----nklpTRFGFDvDRDCDLPQRLTSl------PVMVQGIHFHLDGY----DAGQRVSALSVAMEWVERLRAvGQPVE 314 Rhodopirellula ...
CAJ89577     173 agtrllsrrSRFGTPvREVETVLSAVERha----dAVTLTGLAYHLDTT----GLAEKGRALERCVLLMDECRArGLAPR 244 Streptomyces am...
YP_118776    162 ------tprSRFGVPlPRVDDALRLLAAsa----aRIRFLGFAFHLDSG----AVTDRVRAVQTCLALIERAHAhGLAPH 227 Nocardia farcin...
YP_001319484 167 ---kvlsknSKFGIPaSGIYQALEKLSQyr----eDIHFWGFSFHVDTI----DLKEKVIAIENCIDFFDIARDhDFEPR 235 Alkaliphilus me...
ZP_00956997  176 -----tklySRFGFPlTQVPTLAARIAAs-----eTLRLDGLHFHLNGY----SAEDRIAAILQTLPLIHKIKGdSTAPF 241 Sulfitobacter s...
NP_601336    153 ------lppTRFGERaADWGNRLTEVIP-------GVDIVGLHVHLHGY----AAKDRALALQECCQLVDSLREcGHSPQ 215 Corynebacterium...
YP_251780    170 -------teSRFGCTpQEWSACISGLPElg----kHVDIVGSCFHLNEY----SSEQRGKEAHRSLDFMRELRRkGWRAD 234 Corynebacterium...
Feature 1             ##                                                                         
P55709       234 MIDIGGGLPIQYvd-raRYKAHLAAQAPEDYrtgk-------------------ipdSFYPYGSTL-SAADWLHRLLEAE 292 Rhizobium sp. N...
NP_864470    273 WLDIGGGFPVNYlchqkHWQRFLKEAHTFTEssgrfeanrk-------ltwnqrplkDIDPTWQPM-NAADWLRAVLTSS 344 Rhodopirellula ...
ZP_01857207  260 FLDIGGGFPMSYlesetEWDTFWQTHRRALLgehrpltyrnhglgltlvegtligkpNCYPYYQSP-VQANWLEGILTSE 338 Planctomyces ma...
NP_866065    315 FIDMGGGFPMSYleehrQWATFWKEHRRALLgerdtltyrghglglaieggrvvgqpKMYPFFQRP-VRGHWLAGVLDSR 393 Rhodopirellula ...
CAJ89577     245 AIDIGGGFGVGYvadaeEWERWTTALSEAVLggrppltwrghgyglrneggtvrgsvALYPGHRPH-AGPGYLDELLSLP 323 Streptomyces am...
YP_118776    228 VLDIGGGLRQVFtadadRFDGYVRALRAGLAgrgpamswpgqtfgyhvaggaahgtpVFHKYGNTV-GAADMLAELLAAP 306 Nocardia farcin...
YP_001319484 236 VLDIGGGFKVSYiedakEWNDSISYLKESILgyqegvtwnnqtfgiqqekgvlkgtlNIYNYHDNL-TGPKYLDALLSTR 314 Alkaliphilus me...
ZP_00956997  242 FLDIGGGIPMNYlddaaEWETWLAELDRALIgdrdpitqhndg---lgrkvggegkvDSYPVAQTL-VQEDWMRRILDHM 317 Sulfitobacter s...
NP_601336    216 FIDLGGGVPMSYieseeDWIRYQSAKSATSAgyaesft------------wkddplsNTYPFYQTP-VRGNWLKDVLSKG 282 Corynebacterium...
YP_251780    235 TLDIGGGFSVRYsa-daDWEAFQPTLTDASAfhag------------------htpsTSYPYGGEKaTGPEMLRAILNTP 295 Corynebacterium...
Feature 1                              ####                                                      
P55709       293 Mnqg--rsvAGYLAREGLTLAMEPGRALADQAAITVFRISRVKAlg---------------pDSHVIFVEGSSFSACEtw 355 Rhizobium sp. N...
NP_864470    345 L--------AYEINRRELILKCEPGRALLDGCGLTIAEVLFVKRdq---------------nQNHLIGLMMNSSQCRT-- 399 Rhodopirellula ...
ZP_01857207  339 Ceag---tiADSLRKRQIQLRCEPGRSLLDGCGFTAARVEFRKQqp---------------tGDWLIGLSMNRTQCRT-- 398 Planctomyces ma...
NP_866065    394 Iegk---tiADRLVELNVQLRCEPGRSILDGCGLTVARVEFRKQna---------------eGDWLIGLSMNRTQCRT-- 453 Rhodopirellula ...
CAJ89577     324 Apvlg-rapGTLLLEHLHDLHIEPGRALADQCGLSLARVLDVRPtge-------------gpDQYLVRLGMNAGDVSL-- 387 Streptomyces am...
YP_118776    307 LaehegrplGTVLADNLLELWLEPGKALVDHAGLTLASVEFVKElg---------------dGTVLVTLDLSRDTVTP-- 369 Nocardia farcin...
YP_001319484 315 LpkfenrtiGTILSENMIDLFIEPGKALVNQLGLSAAKVNFIKQss---------------dDEILIGLDLKRTDVVM-- 377 Alkaliphilus me...
ZP_00956997  318 Adgq---tvAAHLRDAHISLRCEPGRSLLDGCGMTLARVAFCKRds---------------aGTPVIGVQMNRTQSRS-- 377 Sulfitobacter s...
NP_601336    283 V--------AQMLIDRGLRLHLEPGRSLLDGCGVTLAEVAFVKTrs---------------dGLPLVGLAMNRTQCRT-- 337 Corynebacterium...
YP_251780    296 TkqvdgqtlAERLRTEGVKLALEPGRALLAGCGLTVFPVQGVKSaeterkspdlnpqenshyRYQILTAAGLSMSLSEqw 375 Corynebacterium...
Feature 1                                              ##                             #   #    # 
P55709       356 FASEFLIDPILVPatkat------vqlpPVRAYLAGHSCLDEDVISNRWLTFPTaPRAGDLLVYANTGGYQMDLLENeFH 429 Rhizobium sp. N...
NP_864470    400 TRDDFLVDPIVISasnesakptnqtdhaEIEGYFVGGYCTESEYLMQRRFRFPRgISRGDFVLIPNTAAYQMHFAESrAH 479 Rhodopirellula ...
ZP_01857207  399 SSDDFLVDPLLIPateesl---lprtpaGISGYLVGAYCTESELLCLRKLQFPHgVGIGDLIVFPNTAGYFMHFLESrSH 475 Planctomyces ma...
NP_866065    454 SSDDFLVDPILVPkqssfg---ratetkPMLGYLVGAYCTESELISLRKMQFPSgVQRGDLIAFPNTAGYFMHFLESrSH 530 Rhodopirellula ...
CAJ89577     388 EEHGVLVDPVLLPrggpe-----dggqgPVGVHLVGNLCLEADLITRRLVFLPAlPRAGDLLAFVNTAGYAMDFHAHrAQ 462 Streptomyces am...
YP_118776    370 ADQEVMVDPLVLPgarr-------ddgpAVGVYFAGRLCLERDLITTRQVFLPGlPAPGDVVVFPNTAAYHMDLSAStAA 442 Nocardia farcin...
YP_001319484 378 GDQELFIDPIIIHrskvt------dlqeDKGVYFIGNLCLESDLIFKHKIFINQlPANGDIVIFPNTAGYFMDFNATdSI 451 Alkaliphilus me...
ZP_00956997  378 GFAEFALDPLMVPapgp--------rkgPIEGYLAGTYCTESEWLTRRKMSFPQgVKAGDLMVFPNTAGYLMHFLESrSH 449 Sulfitobacter s...
NP_601336    338 TSDDFLIDPLHITdgd---------vgeEIEAYLVGAYCIEDELILRRRIRFPRgVKPGDIIGIPNTAGYFMHILESaSH 408 Corynebacterium...
YP_251780    376 KSSEFLPDPTLWPqre----------gtPTRACVGGSSCMEYDMLTWRTICFPRaPKRGDLLIYHNTAGYQMDKNESsFH 445 Corynebacterium...
Feature 1                  
P55709       430 RHPMPARFCV 439 Rhizobium sp. NGR234
NP_864470    480 QMPLAENVFL 489 Rhodopirellula baltica SH 1
ZP_01857207  476 QFPLAQNVVY 485 Planctomyces maris DSM 8797
NP_866065    531 QFPLAKNLIV 540 Rhodopirellula baltica SH 1
CAJ89577     463 RQPLARTVAV 472 Streptomyces ambofaciens ATCC 23877
YP_118776    443 RWAPPRRWVV 452 Nocardia farcinica IFM 10152
YP_001319484 452 MQPIAKKVAV 461 Alkaliphilus metalliredigens QYMF
ZP_00956997  450 QFPLARNVFV 459 Sulfitobacter sp. EE-36
NP_601336    409 QIPLAKNVVW 418 Corynebacterium glutamicum ATCC 13032
YP_251780    446 QLPLPSRFVW 455 Corynebacterium jeikeium K411

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