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: 2-Oct-2020
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:
Feature 1                                               # #                      #               
1KNW_A        26 CPVWVYDAqIIRRQIAALKQF-------------DVVRFAQKACSnIHILRLMREQGv----KVDSVSLGEIERALAAGy 88  Escherichia coli
1TWI_A        30 TPLYVMSEeQIKINYNRYIEAfkrwee--etgkeFIVAYAYKANAnLAITRLLAKLGc----GADVVSGGELYIAKLSNv 103 Methanocaldococ...
NP_624642     31 PLVGLLDVdGVLAAVDALNEAfeg-------papVQHTFAAKACGlVPVLRLLAEAGm----GCEVASPGELEQALAAGf 99  Streptomyces co...
YP_001356762  16 TPCYVCEEgLLRRNLEILDEVqqk--------sgAKIILALKGFAmWSTFDILKQYLh----GATASGLWEAKLAFEELg 83  Nitratiruptor s...
Q7NE10        59 MPMLIRFSdILADRIARLNACfveaireydypgiYKGVYPVKVNQqRHVVEEVVEFGrpfqyGLEAGSKPELLIALATLk 138 Gloeobacter vio...
ZP_02361551   27 TPCYVFDPqCVLAGYAALRAAl-----------gTRLVVSLKANShADLFLRCAHAFe---dGIELASQGELDTVVGRGk 92  Burkholderia ok...
EDN35336      19 APFFYYDLdMLEAHAKELHRLp------------VKLWYALKANPlSRIIKVFDEQKi----SFDVASIGELDQVLAQGv 82  Francisella tul...
ZP_01078002   17 TPCYLYSVsQVAANYQALTSAl-----------gTKLIYSMKANNnADLLMRASHYLd---gGIEVASIGELNLVAGGDs 82  Marinomonas sp....
EAY66999      32 TPCYVYEPeIAIARYRSLKARl-----------gTRLIVSLKANPnQDMLARCAHAYe---dGVELASRGELDAVIGRIk 97  Burkholderia ce...
BAC16548      26 LCAYLYDLnALEEHIKQLRHVlp---------knVKLFYAAKANPsGPILNTLAPYVd----GFEAASGGELTHLHQQQl 92  Vibrio parahaem...
Feature 1                   #                                                      #             
1KNW_A        89 npqthpdDIVFTADVIDqATLERVSELq----IPVNAGSv-DMLDQLGQvs--------pgHRVWLRVNpgfghghsqkt 155 Escherichia coli
1TWI_A       104 p----skKIVFNGNCKTkEEIIMGIEAn---iRAFNVDSi-SELILINEtake----lgetANVAFRINpnvnpkthpki 171 Methanocaldococ...
NP_624642    100 t----ydRLVFDSPAKTvEELEFALAHg----IAINLDNf-QEMARVDGllag----reaaGPIGLRVNpqvgagaigam 166 Streptomyces co...
YP_001356762  84 k-----eVHTYSPAFKE-DEIELIAKMs----DHIVFNSm-HQFNAFKDivkk----tdpdISIGVRVNpeysaapvdly 148 Nitratiruptor s...
Q7NE10       139 tp---gaLIICNGYKDS-EYIETALLAqrlghTPFVVIErfHELTLLIEaaqk----lgirPLIGVRAKltargigr-wg 209 Gloeobacter vio...
ZP_02361551   93 ------hVKYLNNPAMGdALMRAGIASr----CHFILDGp-DMVRRFIAlasg-----ketEDVMLRINagallga---h 153 Burkholderia ok...
EDN35336      83 n----pkNILHTGPAKSySQLEYFLAQg---vRIFVIESi-NQLKDLSIlvek----kninVKVLLRVQlvwndqennvl 150 Francisella tul...
ZP_01078002   83 -------EKFINNPSADkKFLRAAVASr----STIIVDNl-IQLDALEEfigk-----rplKPILLRLNssvlkrfn-eh 144 Marinomonas sp....
EAY66999      98 ------tPRYLNNPSMDeMFMRAGLASr----CHFVLDNp-DAVARFVPlaresaaggstpGAVLLRVNagalage---q 163 Burkholderia ce...
BAC16548      93 d-----kPLIFGGPGKMpSELQQAIELd---vDAIHVESl-TELQRIGAlter----lnrpASIFLRMNidigditlskl 159 Vibrio parahaem...
Feature 1                                                #  #                                    
1KNW_A       156 ntggenSKHGIWyt---dLPAALDVIqrhh--lqlVGIHMHIGSGv------------dYAHLEQVCGAMVRQVief--- 215 Escherichia coli
1TWI_A       172 stglkkNKFGLDves-giAMKAIKMAleme-yvnvVGVHCHIGSQlt-----------dISPFIEETRKVMDFVvelke- 237 Methanocaldococ...
NP_624642    167 statatSKFGVAlrdegaVDAVIEAFarr---pwlNRLHAHVGSQgc-----------pLPLIAQGVRTAYELAerinre 232 Streptomyces co...
YP_001356762 149 npcgafSRLGVVr-----SEFSWDDAi--------KGLHFHALCEesa---------esLEGVLKAFEERFGEFvp---- 202 Nitratiruptor s...
Q7NE10       210 dstgdrAKFGLSag---eIMEVVAQLkaadllsslQLLHFHIGSQis-----------aINVIKTALREASCVYvelaq- 274 Gloeobacter vio...
ZP_02361551  154 apkslrDHFGMTpa---eALGMANLLtqag--rrvAGLHAFVGSGnfragpt-kggdadSADLAWALAQLAEQIeslv-- 225 Burkholderia ok...
EDN35336     151 ggggcvTPFGLSin---dWRDFFNSApnisnnmsiIGMHCFQWGNilcln----klsqiWEITTKALLDLSEAInv---- 219 Francisella tul...
ZP_01078002  145 hpgvraDQFGMDwd---tVEKAIARCkslq--iplAGFHLFNGSYs-------------FAKVATATAIAGIAIlqever 206 Marinomonas sp....
EAY66999     164 aralwhDHFGMTpn---eAHDAVRTLaaag--lpvAGLHVFSGPHsfirqdptqpdtlvLPELLAALARDLAPAng---- 234 Burkholderia ce...
BAC16548     160 amggkpTPFGLDes---eLSNALMLLrdfp-qvslKGFHFHLMSHql-----------dVERHLALMQRYFQVVkawqq- 223 Vibrio parahaem...
Feature 1                    ##                                               ####               
1KNW_A       216 --gqdLQAISAGGGLSvpyqq------geeavDTEHYYGLWNAAReqiarh-lghpvKLEIEPGRflvAQSGVLITQVRS 286 Escherichia coli
1TWI_A       238 -egieIEDVNLGGGLGipyyk------dkqipTQKDLADAIINTMlkykd--kvempNLILEPGRslvATAGYLLGKVHH 308 Methanocaldococ...
NP_624642    233 lgraqITGLDIGGGLPvnfd---------gedDRPTYADHVAELRsaapgl-fdgryALITEFGRsllAKSGTIASVVEY 302 Streptomyces co...
YP_001356762 203 ----kCKWINFGGGHHitk----------egyNRELLIKLIRDFKkry-------dvEVYLEPGEavgWQTGVLVATVVD 261 Nitratiruptor s...
Q7NE10       275 -mgapMQYCDVGGGLAidydgsktnfrasknyNMQEYAYDVVAAFqdacrtknvpvpTLVSESGRaitSHQSVLVFDVMG 353 Gloeobacter vio...
ZP_02361551  226 --rapVTHLNLGGGFSekgh---------ddaTFERYRARIAPLAkr---------yTLVHEAGRaifANAGVFVTRVRA 285 Burkholderia ok...
EDN35336     220 ----sLKVIDLGGGIGvpyna------gqksiSINDLIFCFNKLKkef------pyiEYWLELGRyavAESGVYVTKIVD 283 Francisella tul...
ZP_01078002  207 lygspLSFVNLGGGFSdhwq--------dqpfDFEAYRALLKEFPsh---------iTLAHETGRglmASAGYFATRVRY 269 Marinomonas sp....
EAY66999     235 ---apLGSLSLGGGFAddhp---------gdaAFDRYAAALAPLAgp---------ySLAHESGRaifADAGVFATRVVA 293 Burkholderia ce...
BAC16548     224 efelgELMINLGGGMGinyqn------peqhfPWMEFCDKLEFLIakeq----vqdwTLRFECGRfitAACGYYVMEVLD 293 Vibrio parahaem...
Feature 1                                                                                        
1KNW_A       287 VKQmgs-------------------------------------------------------------------------- 292 Escherichia coli
1TWI_A       309 IKEtpv-------------------------------------------------------------------------- 314 Methanocaldococ...
NP_624642    303 TKSagg-------------------------------------------------------------------------- 308 Streptomyces co...
YP_001356762 262 IVHng--------------------------------------------------------------------------- 266 Nitratiruptor s...
Q7NE10       354 VSHlqfgepepparnehsiirnlyetytqitpdnvqeafndasqfkeealslfalgylglgeraraerlywgccekilnl 433 Gloeobacter vio...
ZP_02361551  286 VKVwdd-------------------------------------------------------------------------- 291 Burkholderia ok...
EDN35336     284 RKSvnn-------------------------------------------------------------------------- 289 Francisella tul...
ZP_01078002  270 TKQiek-------------------------------------------------------------------------- 275 Marinomonas sp....
EAY66999     294 VKTwqd-------------------------------------------------------------------------- 299 Burkholderia ce...
BAC16548     294 IKQnl--------------------------------------------------------------------------- 298 Vibrio parahaem...
Feature 1                                                                                        
1KNW_A       293 ------------------rhFVLVDAGFNDLMRpam-------------------------------------------y 311 Escherichia coli
1TWI_A       315 ------------------tkWVMIDAGMNDMMRpam-------------------------------------------y 333 Methanocaldococ...
NP_624642    309 ------------------rrIAVTHAGAQVATRtvfm-----------------------------------------pd 329 Streptomyces co...
YP_001356762 267 ------------------mdIAILDTSAETHMPdv--------------------------------------------l 284 Nitratiruptor s...
Q7NE10       434 vreldyipdeladleknmasTYYCNFSVFQSAPdsw------------------------------------------ai 471 Gloeobacter vio...
ZP_02361551  292 ------------------rvIAVCDGGMSHNFLlaktea-------------------------------------vlkt 316 Burkholderia ok...
EDN35336     290 ------------------idLLVTDGGAQHLVRpal-------------------------------------------t 308 Francisella tul...
ZP_01078002  276 ------------------dfFAICDGGINQNFLlaqtenafrrlkqpllwrksemrvaaesgqdassnqgadteqdkahq 337 Marinomonas sp....
EAY66999     300 ------------------rtIAVCDGGLSHAFLlaqtesv----------------------------------mrrlaa 327 Burkholderia ce...
BAC16548     299 ------------------geNFVIARGGTHHFRtpa------------------------------------------aq 318 Vibrio parahaem...
Feature 1                                        ##                                       #   #  
1KNW_A       312 gSYHHISALaadgrsl--ehaptvETVVAGPLCEsgDVFTQqeggnvet-----ralpevkaGDYLVLHDtGAYGASMSs 384 Escherichia coli
1TWI_A       334 eAYHHIINCkvkn--------ekeVVSIAGGLCEssDVFGRdreld------------kvevGDVLAIFDvGAYGISMAn 393 Methanocaldococ...
NP_624642    330 aWPLRVGVFdaagrp---kqgpaeVVDIAGPCCFagDLTATgrelp------------avepGDVVALYDtGAYYFSSHf 394 Streptomyces co...
YP_001356762 285 aMPYRPDVRgaakp-----gekpyTYRLGGNSCLagDIIGDysfde------------plqrGQKLVFEDmIHYTFVKNt 347 Nitratiruptor s...
Q7NE10       472 dQLFPIMPIhrlde------epkaRGTLADLTCDs-DGKIDqfidlrdvkgvlelhpvrpeePYYLGMFLnGAYQEILGd 544 Gloeobacter vio...
ZP_02361551  317 wEAPTLVPAgpadah---rapntlPVTFVGNTCNraDVIGRlerhp-----------rlpqpGDFVVFSQcGAYHHSYTv 382 Burkholderia ok...
EDN35336     309 gESFPIQLLreeac------setnDFQIHGPLCTslDKAGIaslpk------------dtglNDYLIFKQtGAYGFTESm 370 Francisella tul...
ZP_01078002  338 tAGPEATNVsd-----------kgACTYVGSSCSkdDVIGKqnddq-----------prpeaGDICVFADcGAYNASYTm 395 Marinomonas sp....
EAY66999     328 pSLVRRTPAppp---------rgvPTLYVGSTCSraDVIGRddaga------------ppqvGDIAVFERcGAYHRTYSm 386 Burkholderia ce...
BAC16548     319 sHDHPFVILkseqhhdishpiqhaQATFVGQLCTpkDVLARnqhva------------hvdiGDYVVFTLaGAYAWNISh 386 Vibrio parahaem...
Feature 1          #           
1KNW_A       385 -nYNSRPLLPEVLF 397 Escherichia coli
1TWI_A       394 -nYNARGRPRMVLT 406 Methanocaldococcus jannaschii
NP_624642    395 -sYNSLPRPAVYGY 407 Streptomyces coelicolor A3(2)
YP_001356762 348 -tFNGIRLPSLALL 360 Nitratiruptor sp. SB155-2
Q7NE10       545 -mHNLFGDTNTVHI 557 Gloeobacter violaceus
ZP_02361551  383 sgFLSHKPAQVYIR 396 Burkholderia oklahomensis C6786
EDN35336     371 plFLCHNLPAEVIF 384 Francisella tularensis subsp. novicida GA99-3549
ZP_01078002  396 tpFLKLPQAKTYII 409 Marinomonas sp. MED121
EAY66999     387 ahFLSHEAAHVYVR 400 Burkholderia cenocepacia PC184
BAC16548     387 qnFLMHEPPIFHYF 400 Vibrio parahaemolyticus

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