1KNW,2OO0,1D7K,1TWI,3BTN,2J66,1F3T,1QU4,1HKV,2PLJ,2TOD,2ON3,3BTN,2P3E,2YXX,3C5Q


Conserved Protein Domain Family
PLPDE_III_ODC_DapDC_like

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cd06810: PLPDE_III_ODC_DapDC_like 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes
This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to L-lysine, which is the final step of lysine biosynthesis. CANSDC catalyzes the decarboxylation of carboxynorspermidine, which is the last step in the synthesis of norspermidine. The PLP-dependent decarboxylases in this family 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. Prokaryotic ornithine, lysine and biodegradative arginine decarboxylases are fold type I PLP-dependent enzymes and are not included in this family.
Statistics
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PSSM-Id: 143485
View PSSM: cd06810
Aligned: 28 rows
Threshold Bit Score: 294.596
Threshold Setting Gi: 48474347
Created: 17-Dec-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 18 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:1TWI_AB; Methanocaldococcus jannaschii Diaminopimelate decarboxylase dimer binds two cofactors (PLP) and two substrates (L-lysine); defined at 4A contacts.
    View structure with Cn3D
  • Structure:1F3T_AB; Trypanosoma Brucei Ornithine decarboxylase dimer binds two cofactor-substrate (PLP-putrescine) complexes; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                               # #                      #               
1KNW_A        26 CPVWVYDAqIIRRQIAALKQF-------------DVVRFAQKACSnIHILRLMREQGv----KVDSVSLGEIERALAAGy 88
1TWI_A        30 TPLYVMSEeQIKINYNRYIEAfkrwee--etgkeFIVAYAYKANAnLAITRLLAKLGc----GADVVSGGELYIAKLSNv 103
gi 21218863   31 PLVGLLDVdGVLAAVDALNEAfeg-------papVQHTFAAKACGlVPVLRLLAEAGm----GCEVASPGELEQALAAGf 99
gi 152991040  16 TPCYVCEEgLLRRNLEILDEVqqk--------sgAKIILALKGFAmWSTFDILKQYLh----GATASGLWEAKLAFEELg 83
gi 48474347   59 MPMLIRFSdILADRIARLNACfveaireydypgiYKGVYPVKVNQqRHVVEEVVEFGrpfqyGLEAGSKPELLIALATLk 138
gi 167568677  27 TPCYVFDPqCVLAGYAALRAAl-----------gTRLVVSLKANShADLFLRCAHAFe---dGIELASQGELDTVVGRGk 92
gi 151569682  19 APFFYYDLdMLEAHAKELHRLp------------VKLWYALKANPlSRIIKVFDEQKi----SFDVASIGELDQVLAQGv 82
gi 87122118   17 TPCYLYSVsQVAANYQALTSAl-----------gTKLIYSMKANNnADLLMRASHYLd---gGIEVASIGELNLVAGGDs 82
gi 124879643  32 TPCYVYEPeIAIARYRSLKARl-----------gTRLIVSLKANPnQDMLARCAHAYe---dGVELASRGELDAVIGRIk 97
gi 23307119   26 LCAYLYDLnALEEHIKQLRHVlp---------knVKLFYAAKANPsGPILNTLAPYVd----GFEAASGGELTHLHQQQl 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                   #                                                      #             
1KNW_A        89 npqthpdDIVFTADVIDqATLERVSELq----IPVNAGSv-DMLDQLGQvs--------pgHRVWLRVNpgfghghsqkt 155
1TWI_A       104 p----skKIVFNGNCKTkEEIIMGIEAn---iRAFNVDSi-SELILINEtake----lgetANVAFRINpnvnpkthpki 171
gi 21218863  100 t----ydRLVFDSPAKTvEELEFALAHg----IAINLDNf-QEMARVDGllag----reaaGPIGLRVNpqvgagaigam 166
gi 152991040  84 k-----eVHTYSPAFKE-DEIELIAKMs----DHIVFNSm-HQFNAFKDivkk----tdpdISIGVRVNpeysaapvdly 148
gi 48474347  139 tp---gaLIICNGYKDS-EYIETALLAqrlghTPFVVIErfHELTLLIEaaqk----lgirPLIGVRAKltargigr-wg 209
gi 167568677  93 ------hVKYLNNPAMGdALMRAGIASr----CHFILDGp-DMVRRFIAlasg-----ketEDVMLRINagallga---h 153
gi 151569682  83 n----pkNILHTGPAKSySQLEYFLAQg---vRIFVIESi-NQLKDLSIlvek----kninVKVLLRVQlvwndqennvl 150
gi 87122118   83 -------EKFINNPSADkKFLRAAVASr----STIIVDNl-IQLDALEEfigk-----rplKPILLRLNssvlkrfn-eh 144
gi 124879643  98 ------tPRYLNNPSMDeMFMRAGLASr----CHFVLDNp-DAVARFVPlaresaaggstpGAVLLRVNagalage---q 163
gi 23307119   93 d-----kPLIFGGPGKMpSELQQAIELd---vDAIHVESl-TELQRIGAlter----lnrpASIFLRMNidigditlskl 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                #  #                                    
1KNW_A       156 ntggenSKHGIWyt---dLPAALDVIqrhh--lqlVGIHMHIGSGv------------dYAHLEQVCGAMVRQVief--- 215
1TWI_A       172 stglkkNKFGLDves-giAMKAIKMAleme-yvnvVGVHCHIGSQlt-----------dISPFIEETRKVMDFVvelke- 237
gi 21218863  167 statatSKFGVAlrdegaVDAVIEAFarr---pwlNRLHAHVGSQgc-----------pLPLIAQGVRTAYELAerinre 232
gi 152991040 149 npcgafSRLGVVr-----SEFSWDDAi--------KGLHFHALCEesa---------esLEGVLKAFEERFGEFvp---- 202
gi 48474347  210 dstgdrAKFGLSag---eIMEVVAQLkaadllsslQLLHFHIGSQis-----------aINVIKTALREASCVYvelaq- 274
gi 167568677 154 apkslrDHFGMTpa---eALGMANLLtqag--rrvAGLHAFVGSGnfragpt-kggdadSADLAWALAQLAEQIeslv-- 225
gi 151569682 151 ggggcvTPFGLSin---dWRDFFNSApnisnnmsiIGMHCFQWGNilcln----klsqiWEITTKALLDLSEAInv---- 219
gi 87122118  145 hpgvraDQFGMDwd---tVEKAIARCkslq--iplAGFHLFNGSYs-------------FAKVATATAIAGIAIlqever 206
gi 124879643 164 aralwhDHFGMTpn---eAHDAVRTLaaag--lpvAGLHVFSGPHsfirqdptqpdtlvLPELLAALARDLAPAng---- 234
gi 23307119  160 amggkpTPFGLDes---eLSNALMLLrdfp-qvslKGFHFHLMSHql-----------dVERHLALMQRYFQVVkawqq- 223
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    ##                                               ####               
1KNW_A       216 --gqdLQAISAGGGLSvpyqq------geeavDTEHYYGLWNAAReqiarh-lghpvKLEIEPGRflvAQSGVLITQVRS 286
1TWI_A       238 -egieIEDVNLGGGLGipyyk------dkqipTQKDLADAIINTMlkykd--kvempNLILEPGRslvATAGYLLGKVHH 308
gi 21218863  233 lgraqITGLDIGGGLPvnfd---------gedDRPTYADHVAELRsaapgl-fdgryALITEFGRsllAKSGTIASVVEY 302
gi 152991040 203 ----kCKWINFGGGHHitk----------egyNRELLIKLIRDFKkry-------dvEVYLEPGEavgWQTGVLVATVVD 261
gi 48474347  275 -mgapMQYCDVGGGLAidydgsktnfrasknyNMQEYAYDVVAAFqdacrtknvpvpTLVSESGRaitSHQSVLVFDVMG 353
gi 167568677 226 --rapVTHLNLGGGFSekgh---------ddaTFERYRARIAPLAkr---------yTLVHEAGRaifANAGVFVTRVRA 285
gi 151569682 220 ----sLKVIDLGGGIGvpyna------gqksiSINDLIFCFNKLKkef------pyiEYWLELGRyavAESGVYVTKIVD 283
gi 87122118  207 lygspLSFVNLGGGFSdhwq--------dqpfDFEAYRALLKEFPsh---------iTLAHETGRglmASAGYFATRVRY 269
gi 124879643 235 ---apLGSLSLGGGFAddhp---------gdaAFDRYAAALAPLAgp---------ySLAHESGRaifADAGVFATRVVA 293
gi 23307119  224 efelgELMINLGGGMGinyqn------peqhfPWMEFCDKLEFLIakeq----vqdwTLRFECGRfitAACGYYVMEVLD 293
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1KNW_A       287 VKQmgs-------------------------------------------------------------------------- 292
1TWI_A       309 IKEtpv-------------------------------------------------------------------------- 314
gi 21218863  303 TKSagg-------------------------------------------------------------------------- 308
gi 152991040 262 IVHng--------------------------------------------------------------------------- 266
gi 48474347  354 VSHlqfgepepparnehsiirnlyetytqitpdnvqeafndasqfkeealslfalgylglgeraraerlywgccekilnl 433
gi 167568677 286 VKVwdd-------------------------------------------------------------------------- 291
gi 151569682 284 RKSvnn-------------------------------------------------------------------------- 289
gi 87122118  270 TKQiek-------------------------------------------------------------------------- 275
gi 124879643 294 VKTwqd-------------------------------------------------------------------------- 299
gi 23307119  294 IKQnl--------------------------------------------------------------------------- 298
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1KNW_A       293 ------------------rhFVLVDAGFNDLMRpam-------------------------------------------y 311
1TWI_A       315 ------------------tkWVMIDAGMNDMMRpam-------------------------------------------y 333
gi 21218863  309 ------------------rrIAVTHAGAQVATRtvfm-----------------------------------------pd 329
gi 152991040 267 ------------------mdIAILDTSAETHMPdv--------------------------------------------l 284
gi 48474347  434 vreldyipdeladleknmasTYYCNFSVFQSAPdsw------------------------------------------ai 471
gi 167568677 292 ------------------rvIAVCDGGMSHNFLlaktea-------------------------------------vlkt 316
gi 151569682 290 ------------------idLLVTDGGAQHLVRpal-------------------------------------------t 308
gi 87122118  276 ------------------dfFAICDGGINQNFLlaqtenafrrlkqpllwrksemrvaaesgqdassnqgadteqdkahq 337
gi 124879643 300 ------------------rtIAVCDGGLSHAFLlaqtesv----------------------------------mrrlaa 327
gi 23307119  299 ------------------geNFVIARGGTHHFRtpa------------------------------------------aq 318
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                        ##                                       #   #  
1KNW_A       312 gSYHHISALaadgrsl--ehaptvETVVAGPLCEsgDVFTQqeggnvet-----ralpevkaGDYLVLHDtGAYGASMSs 384
1TWI_A       334 eAYHHIINCkvkn--------ekeVVSIAGGLCEssDVFGRdreld------------kvevGDVLAIFDvGAYGISMAn 393
gi 21218863  330 aWPLRVGVFdaagrp---kqgpaeVVDIAGPCCFagDLTATgrelp------------avepGDVVALYDtGAYYFSSHf 394
gi 152991040 285 aMPYRPDVRgaakp-----gekpyTYRLGGNSCLagDIIGDysfde------------plqrGQKLVFEDmIHYTFVKNt 347
gi 48474347  472 dQLFPIMPIhrlde------epkaRGTLADLTCDs-DGKIDqfidlrdvkgvlelhpvrpeePYYLGMFLnGAYQEILGd 544
gi 167568677 317 wEAPTLVPAgpadah---rapntlPVTFVGNTCNraDVIGRlerhp-----------rlpqpGDFVVFSQcGAYHHSYTv 382
gi 151569682 309 gESFPIQLLreeac------setnDFQIHGPLCTslDKAGIaslpk------------dtglNDYLIFKQtGAYGFTESm 370
gi 87122118  338 tAGPEATNVsd-----------kgACTYVGSSCSkdDVIGKqnddq-----------prpeaGDICVFADcGAYNASYTm 395
gi 124879643 328 pSLVRRTPAppp---------rgvPTLYVGSTCSraDVIGRddaga------------ppqvGDIAVFERcGAYHRTYSm 386
gi 23307119  319 sHDHPFVILkseqhhdishpiqhaQATFVGQLCTpkDVLARnqhva------------hvdiGDYVVFTLaGAYAWNISh 386
                        570
                 ....*....|....
Feature 1          #           
1KNW_A       385 -nYNSRPLLPEVLF 397
1TWI_A       394 -nYNARGRPRMVLT 406
gi 21218863  395 -sYNSLPRPAVYGY 407
gi 152991040 348 -tFNGIRLPSLALL 360
gi 48474347  545 -mHNLFGDTNTVHI 557
gi 167568677 383 sgFLSHKPAQVYIR 396
gi 151569682 371 plFLCHNLPAEVIF 384
gi 87122118  396 tpFLKLPQAKTYII 409
gi 124879643 387 ahFLSHEAAHVYVR 400
gi 23307119  387 qnFLMHEPPIFHYF 400

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