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: 2-Oct-2020
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:
Feature 1                                                   # #                        #         
Q7NE10        55 RGLNMPMLIRFSDILADRIARLNACFVEAIREyDYPGIYKGVYPVKVNQqRHVVEEVVEFGrp--fqYGLEAGSKPELLI 132 Gloeobacter vio...
NP_223679     44 KGYRGPLLVRFPHLVQKQIKSLFDAFSLAIKEyQYSGAFKAVFPLKVNQmPSFVLPLVQGAkg--lnYGLEAGSKSELII 121 Helicobacter py...
YP_843948     53 SGENLPVLLRFPQIIEHRIWEIYRAFTGSISEfGYQGKYQPVFPMKVNQrKEVIEYILNYGre--inIGLEIGTKAELLA 130 Methanosaeta th...
YP_863630     39 RTYGAPLKFTYLPKISQNINRAKDWFKSAIEKhDYKGSYNYCYCTKSSHfEHVLNEALKND------IHIETSSAFDINI 112 Gramella forset...
YP_001040225  48 DKQLPGAHIRILPIIRYMMDQVYEAFMEAFRKfGYKGAFKPVYPLKSNStPIVVDTIWRYGik--ysWGFNAGTYPEVKL 125 Staphylothermus...
ZP_01718184   72 EEYGTPLKLTYLPKISENIQKAKTYFNNAIQAhDYQGKYTYCYCTKSSHfSFVLDEALKND------IHIETSSTFDIPL 145 Algoriphagus sp...
YP_001277158  46 ARYGAPLEVAYCPQITLQIERMLAWADDARMRsGYVGGFIYAYATKANFaEEVVRTAIGAG------AHYETSAAADVTI 119 Roseiflexus sp....
ZP_01886545   38 ETYGTPLRFTYLPMISKKIQQAKLLFQTAIIKnNYRGDYKYCYCTKSSHfRHIVEEALKNG------IHLETSSAFDMPM 111 Pedobacter sp. ...
ZP_01908990   94 RGVHSPFVLRFPGMIVAAMERLHRAFELAAEEnEYQGEHMGMYPLKVNQrRSVVETVVAARer--caYGLEAGSKPELLL 171 Plesiocystis pa...
EDN37327      18 QGATYPLVLYFEHILKNKIDKLYNSFEKAISNlGYTGKYSLAYPIKVNPeQKIIKAIYDYHqhnqvsLDYEVGTKSELLA 97  Francisella tul...
Feature 1                          #                                                       #     
Q7NE10       133 ALATLk----tPGALIICNGYKDS---EYIETALLAQr-lGHTPFVVIERFHELTLLIEaaq--klGIRPLIGVRAKLTA 202 Gloeobacter vio...
NP_223679    122 AMSYTn-----PTAPITVNGFKDK---EMIELGFIAKs-mQHEITLTIEGLNELKTIIAvakqndfVACPKIGIRIRLHS 192 Helicobacter py...
YP_843948    131 ALTLDl----pEDSLLICNGYKDD---DFLRLALMFSd--KHKIIIVVDLFEEIFDILRlar--smEVRPLLGMRVKLFS 199 Methanosaeta th...
YP_863630    113 VEKLKkagkisDDRWVICNGFKRD---QYIENISRLLnggHKNCLPIIDNYEELDLLSEk-----iDDKFQVGIRIASEE 184 Gramella forset...
YP_001040225 126 ISKYIn----eKPRLLVVDGIKDN---KLLDLLSKMCd--SWEIIVDIESMRDADLLSK-------YQDLNIGLRVKVTS 189 Staphylothermus...
ZP_01718184  146 VRSLYakgkitKNTFIICNGFKRDlykQYIAELLNDG---FVNCVPILDNLSEIDYYLEh-----vKVPFQVGIRIAADE 217 Algoriphagus sp...
YP_001277158 120 AHRLWqqgvlpSDRYIFCNGSKDD---AYLAAISALRragFARVVPVIDDLDELETLLAm-----cREPLLLGVRERHAP 191 Roseiflexus sp....
ZP_01886545  112 IEALEkkgaltKDITVICNGFKTYqykQYIIDMLHDG---YKNIIPVLDNKEEFNLFDDev---emDTPCNLGIRIAAEE 185 Pedobacter sp. ...
ZP_01908990  172 AMAQPv-----SKAPLICNGYKDR---EFIRLAFHAAe-lGHEVILVLESMREVQRYLDiyaqgewKATPFLGMRAKLYS 242 Plesiocystis pa...
EDN37327      98 VLSTAa-----KTQKIICNGFKDL---SFYKIAQLAAk-iGYKIIIVIENISEINIIQDlld-nnvNIKFDFGIRTKPFD 167 Francisella tul...
Feature 1                                                    #  #                                
Q7NE10       203 rgigrwgdSTGDRAKFGLSAgEIMEVVAQLKAadLLSSLQLLHFHIGSQISAINVIKTALREASCVYVELAQmg-apMQY 281 Gloeobacter vio...
NP_223679    193 agtgvwakSGGINSKFGLSStEVLEAMRLLEEndLLEHFHMIHFHIGSQISDISPLKKALREAGNLYAELRKmgaknLNS 272 Helicobacter py...
YP_843948    200 kgsgrwaeSGGESAKFGLSTiECLELLKILEEngLLDRLRMIHFHIGSQITDIHRIKHAMNEAARIYAKVRKva--eIEY 277 Methanosaeta th...
YP_863630    185 ep-----kFEFYTSRLGIGYkNIVPFYNKQIKenDQVELKMLHFFINTGIRDTAYYWNELNKCLKVYIALKKva-phLDS 258 Gramella forset...
YP_001040225 190 kssglwshSSGLDSKFGLLInTLDEMVEKHPW--VPNRTVLLHVHAGSQITDKNRLEDIIRETIILYNNLVKtgfknIRY 267 Staphylothermus...
ZP_01718184  218 ep-----kFGFYTSRLGVRYnDIIKLYEEKIKdhPLVSLKMLHFFINSGIKDTAYYWSELTRFIQKYVDLKKva-ptLDT 291 Algoriphagus sp...
YP_001277158 192 adv---daDHPGGERFGLTPdEIEQVVERLRH--TPHRLVMYHAMVGSQIEDADRWNMRLARSAEAYARLRQqa-psLML 265 Roseiflexus sp....
ZP_01886545  186 qp-----dSQFYTSRLGVRMeDVIDFYNNKISanPNFRVKLLHFFINSGITDSPYYWNELEKYVTLYCKFKKin-peLDT 259 Pedobacter sp. ...
ZP_01908990  243 rgsgrwqsSGGERSKFGLTTnEMLEVVRRLEGadALDRLSLLHFHIGSQITQIKRIKVAVREGIRLWCSLRArc-ggLRY 321 Plesiocystis pa...
EDN37327     168 --------NCIHTQKFGLSLsQINECINFLKTnqLQQKLLLLHSHIGSQLKSTDKVVANIQRLMRIYSELKSdf-vnLEY 238 Francisella tul...
Feature 1            ##                                               ####                       
Q7NE10       282 CDVGGGLAIDYDGsktnfraSKNYNMQEYAYDVVAAFQDACrtknVPVPTLVSESGRAITSHQSVLVFDVMGVSHlqfge 361 Gloeobacter vio...
NP_223679    273 VNIGGGLAVEYTQhkh--hqDKNYTLEEFSADVVFLLREIVknkqEIEPDIFIESGRYISANHAVLVAPVLELFSheyne 350 Helicobacter py...
YP_843948    278 FNVGGGLSVDYDGskssgpsSANYTLREYSNDIVYTLQKICeeegVPCPTIVSESGRAIAAYHSFLVFKIIGKKNskdgf 357 Methanosaeta th...
YP_863630    259 LNIGGGFPIKNSL-------AFEYDYAYMVDEIINHIKLTCddaeVDVPNIFTEFGSFTVGESGGAIYEVLYQKQqn--- 328 Gramella forset...
YP_001040225 268 IDFGGGLAYPYIEasn-hvfSANYSLNEYAEILVKELVKSA----ENTPDIVFEGGRYIVAPHRITVTKIIDTRPystsd 342 Staphylothermus...
ZP_01718184  292 MDIGGGWPIKTNV-------FFDYDYQYMADQIVKNIKWMCaknnTTEPNIFTEFGSFTVGESGAVLYSVLDEKLqn--- 361 Algoriphagus sp...
YP_001277158 266 FNFGGGMPTSAYSl------DFRFDYVGFLERLMRTLASTCaahnVPQPTLVGEFGRYTVASHNVFIMEVGRVKRgq--- 336 Roseiflexus sp....
ZP_01886545  260 LDIGGGMPFKDSL-------VFDFDYEYMVNEIVKRIKEICaehdVVEPDIITEFGKYTVAEASGILYKVLGRKQqn--- 329 Pedobacter sp. ...
ZP_01908990  322 IDLGGGIGIDYDGsrtsypsSANYSLEEYASQVVFEIGQVVreleLPAPTIVTESGRVLVAQHAVTVADLREVQGallpv 401 Plesiocystis pa...
EDN37327     239 IDFGGGLAVNYDEy-----dRPSYDFDSYAKTIIKNCKYYAeyynCDMPSIVTESGRAITAESSLLITRPLIKQHesdie 313 Francisella tul...
Feature 1                                                                                        
Q7NE10       362 pepparnehsiirnlyetytqitpdnvqeafndasqfkeeal---slfalgylglgeraraerlywgccekilnlvreld 438 Gloeobacter vio...
NP_223679    351 kslkikennnpplidemldllanineknaieylhdsfdhtes---lftlfdlgyidlidrsntevlahlivkkavqlfyv 427 Helicobacter py...
YP_843948    358 vafplegdpiqiedlyfafkninlknykeyyhdalhyrdell---dsfnlgnigleerakgemlfwmvcqkavslarhag 434 Methanosaeta th...
YP_863630        --------------------------------------------------------------------------------     Gramella forset...
YP_001040225 343 rgetsypiveeikntenikelvyvsrkarevitrlmlkfpiniesrrileklltsineaitskayeiihrdndkaleeli 422 Staphylothermus...
ZP_01718184      --------------------------------------------------------------------------------     Algoriphagus sp...
YP_001277158     --------------------------------------------------------------------------------     Roseiflexus sp....
ZP_01886545      --------------------------------------------------------------------------------     Pedobacter sp. ...
ZP_01908990  402 peaspaedrlitslrecleyinvknieeyfhdavdyrdealq----lfsrgylsledrasaeglfqrirmrcaklirqmr 477 Plesiocystis pa...
EDN37327     314 neilhqqwldr-----------------------------------------------------------------evsl 328 Francisella tul...
Feature 1                                                                    ##                  
Q7NE10       439 yipdeladleknMASTYYCNFSVFQSAPDSWAI-DQLFPIMPIHRLDEePKARGTLADLTCD-------SDGKIDQFIDL 510 Gloeobacter vio...
NP_223679    428 kdhndilriqeqVQERYLLNWSFFQSLPDYWGL-RQNFPVMPLNKLDEkPTRSASLWDITCD-------SDGEIAFDSTK 499 Helicobacter py...
YP_843948    435 dnseefrelkklVGQKYIGNFSLFQSVPDMWGV-GQIFPIMPLHRLREvPSECGTIADITCD-------SDGEIKSFAGG 506 Methanosaeta th...
YP_863630    329 -----------dREKWNMINSSFITTLPDTWAI-SKKFVMLAVNRWND-EYERVLLGGLTCD-------SDDYYNSEQHT 388 Gramella forset...
YP_001040225 423 ktpnyvleelvsPTRRFFASFSLFSHLPDTIIA-DQYFKIIPLQRLNEkPEVLGVISDLTCD-------SMGEYSSFITF 494 Staphylothermus...
ZP_01718184  362 -----------dKELWYMIDGSFITQLPDSWGL-NQKYIMLAINNWDE-TYHNINLGGLTCDsmdyynsEAHQFNIYLPK 428 Algoriphagus sp...
YP_001277158 337 ----------gdAPDWVLINGSLMVSLPDSLIVpGQEFIILPLDGWDRpVRPVRLAGRLTCD-------SDDFFPRPGAP 399 Roseiflexus sp....
ZP_01886545  330 -----------dREKWLMLDGSFITNLPDVWAL-NQKYILLPINNWDA-EYERVNLGGITCDgqd-yynQEAHMNSVFMP 395 Pedobacter sp. ...
ZP_01908990  478 hkpeeildyldrAQVKYLANFSIFQSLPDTWSI-DQVFPAAPLSGHGSaPAYNAEIVDITCD-------SDGCVRTFAHP 549 Plesiocystis pa...
EDN37327     329 gelqsylpqnqkKTQQAWLNFSIFQSLPDHWGI-DQKFPILPLEFFNSyVTSEVKLYDISCD-------VDGVIKSTSEY 400 Francisella tul...
Feature 1                                                             #   #       #           
Q7NE10       511 RDvkgvle--------------------------lhpvrpEEPYYLGMFLNGAYQEILGD----MHNLFGDTNTVHI 557 Gloeobacter violaceus
NP_223679    500 PLflhd------------------------------ididEEEYFLAFFLVGAYQEVLGM----KHNLFTHPTEFSV 542 Helicobacter pylor...
YP_843948    507 KEaielh-----------------------------klsrSEDYYMGIFLLGAYQDTLGD----FHNLLGCVTEVHV 550 Methanosaeta therm...
YP_863630    389 NAiylp------------------------------kfkkEKPLYIGFFNTGAYQDTIGGfgglQHCLIPQPKHILI 435 Gramella forsetii ...
YP_001040225 495 LPnnieyetedlftsldhklmfipgktlrlkgvplhiprkNEDYYIAFLDTGAYQDMLSM----NHNLLNGYPEIII 567 Staphylothermus ma...
ZP_01718184  429 PDn-------------------------------------GKKQYLGFFHTGAYQESLGGyggiQHCLIPAPKHVLI 468 Algoriphagus sp. PR1
YP_001277158 400 PLllp---------------------------------dpYPGQKIAFFGVGAYQQMIAGrggaHHCLTPEMRRIII 443 Roseiflexus sp. RS-1
ZP_01886545  396 KT--------------------------------------RKVQYLGFFNTGAYQEVLSGyggiHHCLLPSPKHVII 434 Pedobacter sp. BAL39
ZP_01908990  550 DDnlkslpl------------------------happarnDEPYFLGFFMTGAYQDSLAN----AHNLFGRCHEVIV 598 Plesiocystis pacif...
EDN37327     401 IEia-----------------------------------tDNIEYIVFMCVGAYQGMLSA----KHNMLGNISAVNI 438 Francisella tulare...

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