1CVR


Conserved Protein Domain Family
Peptidase_C25_N

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cd02258: Peptidase_C25_N 
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Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins
Peptidase family C25 is a unique class of cysteine proteases, exemplified by gingipain, which is produced by Porphyromonas gingivalis. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease that is also associated with other diseases such as diabetes and cardiovascular disease. Gingipains are a group of extracellular Arg- and Lys-specific proteinases called Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and RgpB are homologous Arg-specific gingipains encoded by two closely related genes, rgpA and rgpB, while Lys-specific gingipain is encoded by the single kgp gene. Mutant studies have shown that, among the large quantities of proteolytic enzymes produced by P. gingivalis, these three proteases are major virulence factors of this bacterium. All three genes encode an N-terminal pre-pro fragment, followed by the protease domain; however, rgpA and kgp also encode additional C-terminal HA (hemaglutinin/adhesion) subunits which consist of several sequence-related adhesion domains. Although unique, their cysteine protease active site residues (His and Cys) forming the catalytic dyad are well-conserved, cleaving the C-terminal peptide bond with Arg or Lys residues. Gingipains are evolutionarily related to other highly specific proteases including caspases, clostripain, legumains, and separase. Gingipains function by dysregulating host defense and inflammatory responses, and degrading host proteins, e.g. tissue, cells, matrix, plasma and immunological proteins. They are proposed to enhance gingival crevicular fluid (GCF) production through activation of the kallikrein/kinin pathways, thus increasing vascular permeability and causing gingival inflammation, a distinctive feature of periodontitis. RgpA and RgpB are also able to cleave and activate coagulation factors IX and X in order to activate prothrombin to produce thrombin, which in turn increases production of GCF. The gingipains also play a pivotal role in the survival of P. gingivalis in the host by attacking the host defense system through cleavage of several immunological molecules, while at the same time evading the host-immune response by dysregulating the cytokine network.
Statistics
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PSSM-Id: 199210
Aligned: 39 rows
Threshold Bit Score: 226.447
Created: 13-Dec-2003
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active site
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Gingipain catalytic site includes the conserved Cys and His residues that form the catalytic dyad
  • Structure:1CVR: Porphyromonas gingivalis Gingipain R (Rgpb) binds D-Phe-Phe-Arg-chloroketone (FFRCMK) inhibitor; contacts at 4.0A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
1CVR_A          3 PVEEKen----gRMIVIVAKKy----EGDIKDFVDWKNQRg------LRTEVKVAEDIASpvt-anAIQQFVKQEYEKeg 67   Porphyromonas...
YP_002429182  244 KLKDPgn----hGDFVIVTTGdlkdaFKNFIDIRNLDHTVk-----lALLNDIKKEFPATgd--dvSIKDFLTYAYNNwa 312  Desulfatibaci...
YP_004252183  241 TLKNPan----cAELLIVTKPdlrpaFDDFLEFKSRDFKVa-----lADTGQIISEFGGQsgm-deQIREFLCYAAENwr 310  Odoribacter s...
YP_003087816  385 EPHDPk-----aGNYIIITTDelrdgAAAFAEYRSSPAGGsfk-pliVNIRDIYDQFNYGeps-pvGIKRFMSYMLSDs- 456  Dyadobacter f...
YP_003088908  385 PLNLEvie-pkqPNYIIITTQglmqgANQYAAYRSSADGGgfk-tiiLNVADLYDQFNYGeps-plGIRNFMAYMLGEgg 461  Dyadobacter f...
YP_004345282  404 GMFTNfsalnidSALLFVYHPslsssTESYKNYRASSAGGghn-vikANIEELYLQFSSGilkhpvSIRRFADFIYDNst 482  Fluviicola ta...
YP_678179     379 ELVNMslp-nlsKDYFIIYPEvfnssALSYDQYRSSNAGGnyd-verCSFEKLCNLYSYGeys-siAIKRYCSEIIQVns 455  Cytophaga hut...
ADQ15878      371 VVVRYskp-sieANYLIVTHPtlrssAEEYKTYRTSILGGsyk-veiMETQEIYDQFNYGers-piAIKEYLRYQLQKsq 447  Leadbetterell...
YP_004273603  394 RFNVSd-----iRKAIIISNKnlstgAENYLNYNQQVRNIpt---llAYTEDIYNEFYYGfhh-plAINNFIKWNIDKsg 464  Pedobacter sa...
YP_003088907  406 QINKSd------YDYMIVSSEslieaADSIALYRSAETAGrkfktgiFKIRDIYNQFNYGeps-piAIRRFVDFMISDlk 478  Dyadobacter f...
Feature 1                                                                                         
1CVR_A         68 -----ndLTYVLLVGdhk------------------------------diPAKITP-------------------GIKSD 93   Porphyromonas...
YP_002429182  313 -----lrPKWVILGG-----------------------------------DVDKIPthhtacatwndpgdephhgLMASD 352  Desulfatibaci...
YP_004252183  311 -----isPRYILLGG-----------------------------------NITDIPthwey----------flgaRISSD 340  Odoribacter s...
YP_003087816  457 ------kDKYLFLIGksitqn-----------------------ekmvreLPGEVPti----------------gYPGSD 491  Dyadobacter f...
YP_003088908  462 -----ktDKHLFLIGksithn-----------------------ermtreLPDEVPti----------------gYPASD 497  Dyadobacter f...
YP_004345282  483 -----qkPEGLFLIGkglnfset--------------------rysdpgfVACLIPpl----------------gYPASD 521  Fluviicola ta...
YP_678179     456 ------kEKYLLILGkgvvpsmsnfinnvgsvvyrknpsfywtntdfknhFVNLVPpf----------------gEPGSD 513  Cytophaga hut...
ADQ15878      448 -----ngEKFLFLIGkpntyps----------------------tlfsqpEIDLVPsf----------------gYPGSD 484  Leadbetterell...
YP_004273603  465 -----glSTSLLLLGrgmtn-------------------------pkdnlSSDLVPty----------------gYPASD 498  Pedobacter sa...
YP_003088907  479 kdnlgrlDKYLLLLGisvtrn-----------------------drinkeLLNEVPtf----------------sFPGSD 519  Dyadobacter f...
Feature 1                                                                                         
1CVR_A         94 --QVYGQIVGNDh-yNEVFIGRFSCESkEDLKTQIDRTIHYErnit-------tedkWLGQALCIASAeggpsa------ 157  Porphyromonas...
YP_002429182  353 --HFYADISGDIl--PELLVGRFPASDsDTMKKICARALAFGrhg----------sqWRDVIMLTTYQrndyeqckd-ai 417  Desulfatibaci...
YP_004252183  341 --HFYADLKGDLs--PDVVVSRFPASEpEEMKNMCDYFIRYAqtr----------keWGKSVLLSSYNre---------- 396  Odoribacter s...
YP_003087816  492 i-LLVEGIAGAPvnaPAIPVGRLSANTnQQIMDYLEKVKAYEsnqs-------geyaWRKKVLHLSGGk----------- 552  Dyadobacter f...
YP_003088908  498 v-LLVEGLAGTAaeiPAIPVGRLSAISnQNVLDYLTKVKEYEhnai-------gdygWRKNFLHLNGGk----------- 558  Dyadobacter f...
YP_004345282  522 naITAGLIDPFTw-ePLIPTGRLSMRTnTEVENYLSKVEQYEdaqnntglnfsetkkWQKQILHFVGGssvn-------- 592  Fluviicola ta...
YP_678179     514 --LMFSVDNKYA---AQIHTGRVPARTnSEVLGYLEKVQAHEslds--------tllWRKNLIHLSGGedaa-------- 572  Cytophaga hut...
ADQ15878      485 v-LLSSGINGSHidvSTYLTGRIEATNnAEVLNYLEKVKEFEdpkn--------hgsWIKKVLHMNGGnnineisnf--k 553  Leadbetterell...
YP_004273603  499 --NLLAIFNGEKa--ARLAVGRIPAKTnEEINTYLVKLKTYInlp---------dslWRKKMINVTGGa----------- 554  Pedobacter sa...
YP_003088907  520 l-LLIEGLQGTPrdvPAIPVGRIPATNnAQALAYLRKVKQYEnatt--------nlaWRKNVAHISGGktsseindhvsn 590  Dyadobacter f...
Feature 1                                                                                        #
1CVR_A        158 --dngesDIQHENVIANLLTqyg--------ytKIIKCYdpgv----------------tpkNIIDAFNGGi--sLVNYT 209  Porphyromonas...
YP_002429182  418 avaidgeKRRDYNAALKYYGs-----------dPAATKAkiier-------------lnerdNHHVAKNGGv--dIVNYR 471  Desulfatibaci...
YP_004252183  397 -----dyNECTEEVAGIIASdf---------qiYKCYDGqat------------------keEIIETINQGv--gFINYR 442  Odoribacter s...
YP_003087816  553 -------TTSEILQLKNHLRgl----------ePYVMNGllrgkvthyvk--qqpmeetesvNITKEVNEGv--gLITLF 611  Dyadobacter f...
YP_003088908  559 -------NTGEITQLKEFLSdl----------ePTVANGvvggkvipfvk--qqpiaevesvNITAEVNAGa--gLITYF 617  Dyadobacter f...
YP_004345282  593 ---eqnsFQGQMNIMKGIVE-------------DTVFAGnvtnyfktss----npldpnvvsTVTQKIEDGv--sIMTFF 650  Fluviicola ta...
YP_678179     573 ---qvtlFKKYVDTYKAYVEgphlggkvvktyvKNLQNGavdd---------------qlisGVADDLNKGi--sLMTFF 632  Cytophaga hut...
ADQ15878      554 nfmynlgQKSIGSISNTHVDfl----------tKSTTESve-------------------niNIGKYLNEGv--gVISYF 602  Leadbetterell...
YP_004273603  555 -------TISEYQTFSNYLKnl----------gNIAKNGflgaysvsfdkkvseavtenltdGIIANTNSGt--sLISFL 615  Pedobacter sa...
YP_003088907  591 lntaalkVKANVFQGRVYTAk------------KPVATDqvlqmdt---------lakhvnvNVTAAADSAgglgMITYF 649  Dyadobacter f...
Feature 1         ###                                 # #                                         
1CVR_A        210 GHGSetawgt-shfgtTHVKQLTNs---nQLPFIFDVACVNGDFLfs-------------mpCFAEALMRAqkdgkptGT 272  Porphyromonas...
YP_002429182  472 GHGSqtawq---asngLNINDVTNlktgsKTPLVLSICCLNNFIDwt-------------gpCFGETWISKl------KS 529  Desulfatibaci...
YP_004252183  443 GHGLptgwqagngltsDDLVQLKNv---dKIPQVLSIACSNNALEke--------------hCFGCEWIRQg------KA 499  Odoribacter s...
YP_003087816  612 GHGAavivdpnigyarEAARGYNNv---nKYPVMFFLGCGVGNVFgnrfnvnppnpksadriPLSLDWLLApg----rGA 684  Dyadobacter f...
YP_003088908  618 GHGSatvtdldmgyitDVKRGYNNf---gKYPMMYFNGCGVGNIFagrfnpnp--natsdriTLSLDWLLAkd----rGS 688  Dyadobacter f...
YP_004345282  651 GHAAasnng--feiniDEPSNWDNf---gKYPVVIGNSCYNGNIFss-------------vnSTSENFVNIpn----eGA 708  Fluviicola ta...
YP_678179     633 GHSSalindvdigfvsNPVYGYKNf---gKYPMMLVNGCTSANIFsn--------------ySFAEDWINTpg----vGA 691  Cytophaga hut...
ADQ15878      603 GHGSstildfnlgfasDPKLGYANk---gKYPFMLFNGCGVGNIFhr-------------yePLSSDWLFTpn----kGA 662  Leadbetterell...
YP_004273603  616 GHGSvslt----avslGIPGNLNNa---yKPTNYLVNGCSTGNAFst-------------apSYAENMILNe-----rGA 670  Pedobacter sa...
YP_003088907  650 GHSVpyqtdynfgyvsDGAKKYNNp---nRYPIIFYNGCDILNVFsnnfnet---vntntsrPQSLDWLLSan----kGA 719  Dyadobacter f...
Feature 1                                                                                         
1CVR_A        273 VAIIastid-qywapPMRGQDEMNEILcekhpn-----nikrtFGGVTMNGMFAMvekykkd--------------genm 332  Porphyromonas...
YP_002429182  530 AGFWgas-----rpsYTAVNHKFDKFLwegiin-----erytsIGDIAQYGTAKLwqndtsd-------------lakqn 586  Desulfatibaci...
YP_004252183  500 VSFLgaa-----vpsYTVVNHEFDKWLwegial-----kklkrAGEIFNYGIQKLymnnpend------------lvkht 557  Odoribacter s...
YP_003087816  685 IAVVag-------syESFANTGINHLEalyqhalanptsadlsIGKIHWLVSNEIlekfkdk-------------hhiah 744  Dyadobacter f...
YP_003088908  689 VAIIans-----yesFVSPSAQYLEQLyknmfav--pstvnfsIGKIQIAVAEAIisktkdk-------------yavan 748  Dyadobacter f...
YP_004345282  709 IAFLssisv-gyeyyLAIYSKELYRQFsyks--------ygstFGSQIKKTIKKMytdygtstpms------gqaylest 773  Fluviicola ta...
YP_678179     692 INVLght-----digYTNNLYQFSLYFynfqfnd--yryinkpVGFIHKKVIDSInsinasid-----------vtsqaq 753  Cytophaga hut...
ADQ15878      663 IAVLans-----yyaYSNTSMDFFEIFynkly------ndeetLGKPIAKVYLESvkthilrpny--------ekyaqsn 723  Leadbetterell...
YP_004273603  671 ISWIgtssegvgsylYNFSSKFYTRWFvnny---------sepIAEGFRLGLNDQtnltdrl--------------nlah 727  Pedobacter sa...
YP_003088907  720 IAVFgnsw----agyASSCNNYMQKIYtelftkn---dadrdlMGRVLQVVAAQTkagggfrmgfenartaevyvadqaq 792  Dyadobacter f...
Feature 1                       
1CVR_A        333 ldTWTVFGDPSLLV 346  Porphyromonas gingivalis
YP_002429182  587 ikMYLLLGDPTADA 600  Desulfatibacillum alkenivorans AK-01
YP_004252183  558 iyAYLLVGDATAEC 571  Odoribacter splanchnicus DSM 20712
YP_003087816  745 vhQSLLQGDPALKL 758  Dyadobacter fermentans DSM 18053
YP_003088908  749 ihQSLLQGDPALKL 762  Dyadobacter fermentans DSM 18053
YP_004345282  774 ctQMTLHGDPILRI 787  Fluviicola taffensis DSM 16823
YP_678179     754 itQMNLTGDPALRL 767  Cytophaga hutchinsonii ATCC 33406
ADQ15878      724 sqQMILQGDPAVVV 737  Leadbetterella byssophila DSM 17132
YP_004273603  728 srQYIFFGDPNITF 741  Pedobacter saltans DSM 12145
YP_003088907  793 ihQTVLLGDPALKV 806  Dyadobacter fermentans DSM 18053

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