Conserved Protein Domain Family
PLPDE_III_ADC

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cd06830: PLPDE_III_ADC 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase
This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which 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. Homodimer formation and the presence of both PLP and Mg2+ cofactors may be required for catalytic activity. Prokaryotic ADCs (biodegradative), which are fold type I PLP-dependent enzymes, are not included in this family.
Statistics
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PSSM-Id: 143503
View PSSM: cd06830
Aligned: 37 rows
Threshold Bit Score: 425.446
Threshold Setting Gi: 151571673
Created: 28-Feb-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
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 48474347   55 RGLNMPMLIRFSDILADRIARLNACFVEAIREyDYPGIYKGVYPVKVNQqRHVVEEVVEFGrp--fqYGLEAGSKPELLI 132
gi 15612027   44 KGYRGPLLVRFPHLVQKQIKSLFDAFSLAIKEyQYSGAFKAVFPLKVNQmPSFVLPLVQGAkg--lnYGLEAGSKSELII 121
gi 116754830  53 SGENLPVLLRFPQIIEHRIWEIYRAFTGSISEfGYQGKYQPVFPMKVNQrKEVIEYILNYGre--inIGLEIGTKAELLA 130
gi 120437944  39 RTYGAPLKFTYLPKISQNINRAKDWFKSAIEKhDYKGSYNYCYCTKSSHfEHVLNEALKND------IHIETSSAFDINI 112
gi 126465116  48 DKQLPGAHIRILPIIRYMMDQVYEAFMEAFRKfGYKGAFKPVYPLKSNStPIVVDTIWRYGik--ysWGFNAGTYPEVKL 125
gi 126645640  72 EEYGTPLKLTYLPKISENIQKAKTYFNNAIQAhDYQGKYTYCYCTKSSHfSFVLDEALKND------IHIETSSTFDIPL 145
gi 148656953  46 ARYGAPLEVAYCPQITLQIERMLAWADDARMRsGYVGGFIYAYATKANFaEEVVRTAIGAG------AHYETSAAADVTI 119
gi 149280425  38 ETYGTPLRFTYLPMISKKIQQAKLLFQTAIIKnNYRGDYKYCYCTKSSHfRHIVEEALKNG------IHLETSSAFDMPM 111
gi 149920522  94 RGVHSPFVLRFPGMIVAAMERLHRAFELAAEEnEYQGEHMGMYPLKVNQrRSVVETVVAARer--caYGLEAGSKPELLL 171
gi 151571673  18 QGATYPLVLYFEHILKNKIDKLYNSFEKAISNlGYTGKYSLAYPIKVNPeQKIIKAIYDYHqhnqvsLDYEVGTKSELLA 97
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                          #                                                       #     
gi 48474347  133 ALATLk----tPGALIICNGYKDS---EYIETALLAQr-lGHTPFVVIERFHELTLLIEaaq--klGIRPLIGVRAKLTA 202
gi 15612027  122 AMSYTn-----PTAPITVNGFKDK---EMIELGFIAKs-mQHEITLTIEGLNELKTIIAvakqndfVACPKIGIRIRLHS 192
gi 116754830 131 ALTLDl----pEDSLLICNGYKDD---DFLRLALMFSd--KHKIIIVVDLFEEIFDILRlar--smEVRPLLGMRVKLFS 199
gi 120437944 113 VEKLKkagkisDDRWVICNGFKRD---QYIENISRLLnggHKNCLPIIDNYEELDLLSEk-----iDDKFQVGIRIASEE 184
gi 126465116 126 ISKYIn----eKPRLLVVDGIKDN---KLLDLLSKMCd--SWEIIVDIESMRDADLLSK-------YQDLNIGLRVKVTS 189
gi 126645640 146 VRSLYakgkitKNTFIICNGFKRDlykQYIAELLNDG---FVNCVPILDNLSEIDYYLEh-----vKVPFQVGIRIAADE 217
gi 148656953 120 AHRLWqqgvlpSDRYIFCNGSKDD---AYLAAISALRragFARVVPVIDDLDELETLLAm-----cREPLLLGVRERHAP 191
gi 149280425 112 IEALEkkgaltKDITVICNGFKTYqykQYIIDMLHDG---YKNIIPVLDNKEEFNLFDDev---emDTPCNLGIRIAAEE 185
gi 149920522 172 AMAQPv-----SKAPLICNGYKDR---EFIRLAFHAAe-lGHEVILVLESMREVQRYLDiyaqgewKATPFLGMRAKLYS 242
gi 151571673  98 VLSTAa-----KTQKIICNGFKDL---SFYKIAQLAAk-iGYKIIIVIENISEINIIQDlld-nnvNIKFDFGIRTKPFD 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                    #  #                                
gi 48474347  203 rgigrwgdSTGDRAKFGLSAgEIMEVVAQLKAadLLSSLQLLHFHIGSQISAINVIKTALREASCVYVELAQmg-apMQY 281
gi 15612027  193 agtgvwakSGGINSKFGLSStEVLEAMRLLEEndLLEHFHMIHFHIGSQISDISPLKKALREAGNLYAELRKmgaknLNS 272
gi 116754830 200 kgsgrwaeSGGESAKFGLSTiECLELLKILEEngLLDRLRMIHFHIGSQITDIHRIKHAMNEAARIYAKVRKva--eIEY 277
gi 120437944 185 ep-----kFEFYTSRLGIGYkNIVPFYNKQIKenDQVELKMLHFFINTGIRDTAYYWNELNKCLKVYIALKKva-phLDS 258
gi 126465116 190 kssglwshSSGLDSKFGLLInTLDEMVEKHPW--VPNRTVLLHVHAGSQITDKNRLEDIIRETIILYNNLVKtgfknIRY 267
gi 126645640 218 ep-----kFGFYTSRLGVRYnDIIKLYEEKIKdhPLVSLKMLHFFINSGIKDTAYYWSELTRFIQKYVDLKKva-ptLDT 291
gi 148656953 192 adv---daDHPGGERFGLTPdEIEQVVERLRH--TPHRLVMYHAMVGSQIEDADRWNMRLARSAEAYARLRQqa-psLML 265
gi 149280425 186 qp-----dSQFYTSRLGVRMeDVIDFYNNKISanPNFRVKLLHFFINSGITDSPYYWNELEKYVTLYCKFKKin-peLDT 259
gi 149920522 243 rgsgrwqsSGGERSKFGLTTnEMLEVVRRLEGadALDRLSLLHFHIGSQITQIKRIKVAVREGIRLWCSLRArc-ggLRY 321
gi 151571673 168 --------NCIHTQKFGLSLsQINECINFLKTnqLQQKLLLLHSHIGSQLKSTDKVVANIQRLMRIYSELKSdf-vnLEY 238
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1            ##                                               ####                       
gi 48474347  282 CDVGGGLAIDYDGsktnfraSKNYNMQEYAYDVVAAFQDACrtknVPVPTLVSESGRAITSHQSVLVFDVMGVSHlqfge 361
gi 15612027  273 VNIGGGLAVEYTQhkh--hqDKNYTLEEFSADVVFLLREIVknkqEIEPDIFIESGRYISANHAVLVAPVLELFSheyne 350
gi 116754830 278 FNVGGGLSVDYDGskssgpsSANYTLREYSNDIVYTLQKICeeegVPCPTIVSESGRAIAAYHSFLVFKIIGKKNskdgf 357
gi 120437944 259 LNIGGGFPIKNSL-------AFEYDYAYMVDEIINHIKLTCddaeVDVPNIFTEFGSFTVGESGGAIYEVLYQKQqn--- 328
gi 126465116 268 IDFGGGLAYPYIEasn-hvfSANYSLNEYAEILVKELVKSA----ENTPDIVFEGGRYIVAPHRITVTKIIDTRPystsd 342
gi 126645640 292 MDIGGGWPIKTNV-------FFDYDYQYMADQIVKNIKWMCaknnTTEPNIFTEFGSFTVGESGAVLYSVLDEKLqn--- 361
gi 148656953 266 FNFGGGMPTSAYSl------DFRFDYVGFLERLMRTLASTCaahnVPQPTLVGEFGRYTVASHNVFIMEVGRVKRgq--- 336
gi 149280425 260 LDIGGGMPFKDSL-------VFDFDYEYMVNEIVKRIKEICaehdVVEPDIITEFGKYTVAEASGILYKVLGRKQqn--- 329
gi 149920522 322 IDLGGGIGIDYDGsrtsypsSANYSLEEYASQVVFEIGQVVreleLPAPTIVTESGRVLVAQHAVTVADLREVQGallpv 401
gi 151571673 239 IDFGGGLAVNYDEy-----dRPSYDFDSYAKTIIKNCKYYAeyynCDMPSIVTESGRAITAESSLLITRPLIKQHesdie 313
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 48474347  362 pepparnehsiirnlyetytqitpdnvqeafndasqfkeeal---slfalgylglgeraraerlywgccekilnlvreld 438
gi 15612027  351 kslkikennnpplidemldllanineknaieylhdsfdhtes---lftlfdlgyidlidrsntevlahlivkkavqlfyv 427
gi 116754830 358 vafplegdpiqiedlyfafkninlknykeyyhdalhyrdell---dsfnlgnigleerakgemlfwmvcqkavslarhag 434
gi 120437944     --------------------------------------------------------------------------------
gi 126465116 343 rgetsypiveeikntenikelvyvsrkarevitrlmlkfpiniesrrileklltsineaitskayeiihrdndkaleeli 422
gi 126645640     --------------------------------------------------------------------------------
gi 148656953     --------------------------------------------------------------------------------
gi 149280425     --------------------------------------------------------------------------------
gi 149920522 402 peaspaedrlitslrecleyinvknieeyfhdavdyrdealq----lfsrgylsledrasaeglfqrirmrcaklirqmr 477
gi 151571673 314 neilhqqwldr-----------------------------------------------------------------evsl 328
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                    ##                  
gi 48474347  439 yipdeladleknMASTYYCNFSVFQSAPDSWAI-DQLFPIMPIHRLDEePKARGTLADLTCD-------SDGKIDQFIDL 510
gi 15612027  428 kdhndilriqeqVQERYLLNWSFFQSLPDYWGL-RQNFPVMPLNKLDEkPTRSASLWDITCD-------SDGEIAFDSTK 499
gi 116754830 435 dnseefrelkklVGQKYIGNFSLFQSVPDMWGV-GQIFPIMPLHRLREvPSECGTIADITCD-------SDGEIKSFAGG 506
gi 120437944 329 -----------dREKWNMINSSFITTLPDTWAI-SKKFVMLAVNRWND-EYERVLLGGLTCD-------SDDYYNSEQHT 388
gi 126465116 423 ktpnyvleelvsPTRRFFASFSLFSHLPDTIIA-DQYFKIIPLQRLNEkPEVLGVISDLTCD-------SMGEYSSFITF 494
gi 126645640 362 -----------dKELWYMIDGSFITQLPDSWGL-NQKYIMLAINNWDE-TYHNINLGGLTCDsmdyynsEAHQFNIYLPK 428
gi 148656953 337 ----------gdAPDWVLINGSLMVSLPDSLIVpGQEFIILPLDGWDRpVRPVRLAGRLTCD-------SDDFFPRPGAP 399
gi 149280425 330 -----------dREKWLMLDGSFITNLPDVWAL-NQKYILLPINNWDA-EYERVNLGGITCDgqd-yynQEAHMNSVFMP 395
gi 149920522 478 hkpeeildyldrAQVKYLANFSIFQSLPDTWSI-DQVFPAAPLSGHGSaPAYNAEIVDITCD-------SDGCVRTFAHP 549
gi 151571673 329 gelqsylpqnqkKTQQAWLNFSIFQSLPDHWGI-DQKFPILPLEFFNSyVTSEVKLYDISCD-------VDGVIKSTSEY 400
                        490       500       510       520       530       540       550
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
Feature 1                                                             #   #       #           
gi 48474347  511 RDvkgvle--------------------------lhpvrpEEPYYLGMFLNGAYQEILGD----MHNLFGDTNTVHI 557
gi 15612027  500 PLflhd------------------------------ididEEEYFLAFFLVGAYQEVLGM----KHNLFTHPTEFSV 542
gi 116754830 507 KEaielh-----------------------------klsrSEDYYMGIFLLGAYQDTLGD----FHNLLGCVTEVHV 550
gi 120437944 389 NAiylp------------------------------kfkkEKPLYIGFFNTGAYQDTIGGfgglQHCLIPQPKHILI 435
gi 126465116 495 LPnnieyetedlftsldhklmfipgktlrlkgvplhiprkNEDYYIAFLDTGAYQDMLSM----NHNLLNGYPEIII 567
gi 126645640 429 PDn-------------------------------------GKKQYLGFFHTGAYQESLGGyggiQHCLIPAPKHVLI 468
gi 148656953 400 PLllp---------------------------------dpYPGQKIAFFGVGAYQQMIAGrggaHHCLTPEMRRIII 443
gi 149280425 396 KT--------------------------------------RKVQYLGFFNTGAYQEVLSGyggiHHCLLPSPKHVII 434
gi 149920522 550 DDnlkslpl------------------------happarnDEPYFLGFFMTGAYQDSLAN----AHNLFGRCHEVIV 598
gi 151571673 401 IEia-----------------------------------tDNIEYIVFMCVGAYQGMLSA----KHNMLGNISAVNI 438

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