1CVR


Conserved Protein Domain Family
Peptidase_C25_N_gingipain

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cd10913: Peptidase_C25_N_gingipain 
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gingipain subgroup of the Peptidase C25 family N-terminal domain
Gingipain, produced by Porphyromonas gingivalis, exemplifies the Peptidase family C25, a unique class of cysteine proteases. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease also associated with other diseases such as diabetes and cardiovascular disease. The gingipain subgroup contains 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. It has been suggested that they 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: 199211
Aligned: 13 rows
Threshold Bit Score: 365.573
Created: 8-Aug-2011
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active site
Conserved site includes 7 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          2 TPVEEKen---gRMIVIVAKKy----EGDIKDFVDWKNQRG--LRTEVKVAEDIASpvt-anAIQQFVKQEYEKeg---n 68   Porphyromonas...
2182812       235 GDLYNTp----vRMLVVAGAKf----KEALKPWLTWKAQKGfyLDVHYTDEAEVGTtn---aSIKAFIHKKYNDglaasa 303  Porphyromonas...
P28784        229 TPVEEKqn---gRMIVIVAKKy----EGDIKDFVDWKNQRG--LRTEVKVAEDIASpvt-anAIQQFVKQEYEKeg---n 295  Porphyromonas...
YP_001741285  224 TPVDDSy----gKLLVICHSSf----LTQIAPYINWKRQKG--IDTELVEFSTIGTta---nQLKAYIQNRYNAdn---- 286  Candidatus Cl...
YP_004342858  216 TPMEESg-----SMLVISAPNl----IEEITPLVHWKNQKG--IRTELVSTTTAGTsd---aDIHTFIQNYYSThp---- 277  Fluviicola ta...
YP_001741063  226 PSLDEEg-----RILVIKHSMf----DATIQPWVDWKRQLG--FTVDVVDVTTAGSta---aNIKTYIQNQYNLnd---- 287  Candidatus Cl...
YP_001741767  240 ERLNVNry--ptKMVILCPPNy----VSTMQTFVNWKTQQG--YKVIVTTVGTGGTvannttAIKNYMQTLWNSatasdp 311  Candidatus Cl...
YP_001741369  173 RDIPFSr----pKMLIITHSQl----TNYQQDYIAWKKSIG--FDVYTANKSDIGStv---qDIKNFIANHYQTy----- 234  Candidatus Cl...
YP_001741062  275 SFLRYPi-----GYVIILPDNf----IAPMQPFIDWKKQEG--YNVIVAPTSITGTtt---tSIKAYMQNLWNSatsenp 340  Candidatus Cl...
YP_001740552  215 YYRNANlapepaRILLIYGNNtdpifTAKLNEFVAWKRQKG--YDVNFVSTAETGGas--tqAIKNYIQTQYDNps---t 287  Candidatus Cl...
YP_133595     214 ADLTPAqk---aDYLIITADRf----QQTVEPLAAWKRKKG--YQVHVATITEVGNtq---aQIKAYIKDAYSNgt---- 277  Photobacteriu...
YP_001740968  218 REIDYRn----pVMLVIYGNYtdtnyLSKINEFVTWKKQRG--FIVNAVSTGVTGItn---tNIKSYIQTAYNNpa---t 285  Candidatus Cl...
YP_001740722  226 DAVVTNtp---pSYLIIYGNNsdinfTSALNEYVLWKKQKG--ADVMVASTAANEAgnt-ttSIKNYIQTKYNNpe---t 296  Candidatus Cl...
Feature 1                                                                                         
1CVR_A         69 dLTYVLLVGDHKDIPAKITP----------GIKSDQVYGQIVGNDhYNEVFIGRFSCESkEDLKTQIDRTIHYERnitt- 137  Porphyromonas...
2182812       304 aPVFLALVGDTDVISGEKGKk--------tKKVTDLYYSAVDGDY-FPEMYTFRMSASSpEELTNIIDKVLMYEKatmp- 373  Porphyromonas...
P28784        296 dLTYVLLVGDHKDIPAKITP----------GIKSDQVYGQIVGNDhYNEVFIGRFSCESkEDLKTQIDRTIHYERnitt- 364  Porphyromonas...
YP_001741285  287 sITFVQLVGDAPQIPTLSYS----------GGGSDPSFSLVAGSDnYPDIFIGRFSAQTtAEVTAQVNKTIQYERdlnt- 355  Candidatus Cl...
YP_004342858  278 eLIYVLLVGDDADIPAHTYGlsg-----geQLYSDSYYGQLSGSDyYPEVFVGRFSGSE-ANITTMVNRTLEYEKnpl-- 349  Fluviicola ta...
YP_001741063  288 gLMFVQLVGDAPQIPTLTYS----------GGGSDPSYALLAGNDnYYDIFVGRFSAQTvAELETQVTRSIYYERdiap- 356  Candidatus Cl...
YP_001741767  312 aPTYLLIVGDTSTSGDNIIAntgg---tssSHITDLTYVQLNGTDyLPELYFGRFSVASaTELTNVINKTITFEKttmp- 387  Candidatus Cl...
YP_001741369  235 kCDYLFLWGDVNGTYAIPTNfivspeypteNDADDNYYTMLEGDDyFPEMIAGRFSFADaSEFITMINKTIAYEKtpfm- 313  Candidatus Cl...
YP_001741062  341 aPSYLLIVGDVAQVPTNNGNa--------gSHPTDLTYVRLQGTDyMPEMYFGRFSATSvAEVTNQVNKTLMYEQytmp- 411  Candidatus Cl...
YP_001740552  288 rPDFIILLGDTNGSYTIPTYteqm---styGGEGDYPYTFLAGNDyLGDAFIGRISAENiSQLDVLFTKIYAVEKninvs 364  Candidatus Cl...
YP_133595     278 mTSYVLLVGDHEDIPGYEIVghpyh-gknhRWHTDYEYTLVDGDDkYSDVVIGRLPGDTeSQITTMVNRSLNYEQnpt-- 354  Photobacteriu...
YP_001740968  286 rPDYIVLIGDTDGTIAVTSN----------NTYVDYQYTWLAGNDnLGDVMIGRISVTStADLDVILAKIFSLEKnigq- 354  Candidatus Cl...
YP_001740722  297 rPDFVVLIGDTSGSYTIPANsa------anSGVTDYNYTFLAGNDqLGDCFIGRISVENlSQFLVVLNKIYLYERdinl- 369  Candidatus Cl...
Feature 1                                                                                         
1CVR_A        138 --edkWLGQALCIASAeggpsa----------------------------dngesDIQHENVIANLLTqyg-------yt 180  Porphyromonas...
2182812       374 --dksYLEKVLLIAGAdyswnsqv-----------------------gqptikygMQYYYNQEHGYTDv----------y 418  Porphyromonas...
P28784        365 --edkWLGQALCIASAeggpsa----------------------------dngesDIQHENVIANLLTqyg-------yt 407  Porphyromonas...
YP_001741285  356 --satWLSKAMGIASAegtsgegdng-------------------esdithmnliRTKLLNYGYTSVD------------ 402  Candidatus Cl...
YP_004342858  350 --agdWMEKAIGLGSDegsgignddepd----------------wqhlrnirsvlMSSGYSEVSEFYDgshgg---sdvs 408  Fluviicola ta...
YP_001741063  357 --gatWLEKAIGIASAegggg-----------------------------qgdmgESDIAHMNNIRTDllnyg--yttvd 403  Candidatus Cl...
YP_001741767  388 --dlsYLGKTVLIAGAdatygpth-----------------------gngainygTTQYFNSAHNITSnty-------ly 435  Candidatus Cl...
YP_001741369  314 -tdtnWMKRALAVAGNyaegglrpt---------------------tpiymskwlRDKMLNFGYTQVDtv--------fc 363  Candidatus Cl...
YP_001741062  412 --sdaYLSEVVMIAGVdsyystth-----------------------angqinygTNNYFNPAHNITShty-------ly 459  Candidatus Cl...
YP_001740552  365 gnagaWVNKMLLIGDPgn------------------------------------sGISTIYVNKFIKElakrtnpdytfl 408  Candidatus Cl...
YP_133595     355 ---dsDRYKHVLLAGQyqdrdadrvadrmfmedlhraadflgpdydffsglgdrfNKGYSVHTALQWDad--------lt 423  Photobacteriu...
YP_001740968  355 -hptdWLNRMVLVGDTgs------------------------------------sGISTIYTNRYIRDi----------s 387  Candidatus Cl...
YP_001740722  370 -atanWLNRMMLSGDNap------------------------------------sGISTMYIHKYIKEmsllt--npdyt 410  Candidatus Cl...
Feature 1                                                          ####                           
1CVR_A        181 KIIKCYdpgv---------------------tpkNIIDAFNGGisLVNYTGHGSetawgt--shfgtTHVKQLTNs---n 234  Porphyromonas...
2182812       419 NYLKAPy--------------------------tGCYSHLNTGvsFANYTAHGSetawad--pllttSQLKALTNk---d 467  Porphyromonas...
P28784        408 KIIKCYdpgv---------------------tpkNIIDAFNGGisLVNYTGHGSetawgt--shfgtTHVKQLTNs---n 461  Porphyromonas...
YP_001741285  403 QIYDPGas------------------------asTVTTNVNAGrgFINYVGHGSntswgt--tgfsnTNASALTNg---n 453  Candidatus Cl...
YP_004342858  409 GSPNPG----------------------------IILPVVNNGvgLFNYTGHGDvnlcvt--gnfqsSNINQATNn---g 455  Fluviicola ta...
YP_001741063  404 QIYDPGat------------------------aaQVTTSVNQGrgFINYVGHGAdtywvt--tnfnnNNANALTNd---y 454  Candidatus Cl...
YP_001741767  436 PASGSSn--------------------------aQIIANASEGrgYINYTAHGSqtswad--ptftiSDINGLNNt---n 484  Candidatus Cl...
YP_001741369  364 PPTYPGt--------------------------tSIQQSINQGvqFISYRGWGDangw-----hypsFHIPDLTNtfnga 412  Candidatus Cl...
YP_001741062  460 PASGSSa--------------------------sAIVQNASNGmgYINYTAHGDvtewyn--pnfsiSNINSLQNt---n 508  Candidatus Cl...
YP_001740552  409 ENYSSGfp-------------------------aYINNGFNQGvaFFNYRGWLGls---------gwSPSASLINg---n 451  Candidatus Cl...
YP_133595     424 KELKYGgwnygsarvnppssvpqvwkdqgngdrvQIADAINQGvgFVMHRDHGYgngsgwadphytaTEVNALTNg---n 500  Photobacteriu...
YP_001740968  388 EEINPAytytevy--------------gsspsstTINSAINQGvmCYNYRGYIGmsg--------wpGTMSSMYNs---h 442  Candidatus Cl...
YP_001740722  411 FTEDYGasp----------------------nytIINQALNQGvgFYSFRGYIDwv----------pPSESELFNa---y 455  Candidatus Cl...
Feature 1                # #                                                                      
1CVR_A        235 QLPFIFDVACVNGDFLfs-mpCFAEALMRAqkdg--kptGTVAIIastid------------------------------ 281  Porphyromonas...
2182812       468 KYFLAIGNCCITAQFDyv-qpCFGEVITRVke------kGAYAYIgsspnsywgedyywsvganavfgvqptfegtsmgs 540  Porphyromonas...
P28784        462 QLPFIFDVACVNGDFLfs-mpCFAEALMRAqkdg--kptGTVAIIastin------------------------------ 508  Porphyromonas...
YP_001741285  454 KVPFIMDVACVNGNFVsy--tCFAEAWMRNan------gGAVGIYassin------------------------------ 495  Candidatus Cl...
YP_004342858  456 KYPFVISVACNNGTFTsg--tCISEAWTRAvkng--tpsGAIAAAgssil------------------------------ 501  Fluviicola ta...
YP_001741063  455 MLPFIVSVACVNGNFVsq--tCFAEAWMRSvnettnapaGAIAFWgstin------------------------------ 502  Candidatus Cl...
YP_001741767  485 KYSVVVGNCCLTNAFDtg--vCFGEAFLRAnn------kGAVTYIggtnstywdedywwa-----------------vgs 539  Candidatus Cl...
YP_001741369  413 KMPIVYSIVCNTGDFAntvnpNFGEKWMRMgtms--npgGCVAFVgp--------------------------------- 457  Candidatus Cl...
YP_001741062  509 KYSYVVGNCCLTSKFDnp--iCFAEAWLRAtn------kGAIIYIggtnstywdedyww------------------gvg 562  Candidatus Cl...
YP_001740552  452 KLPHSTILTCSTGNFEns--nATTEDLIRLgtsa--apaGAITAIgmatsg----------------------------- 498  Candidatus Cl...
YP_133595     501 MAPFVFSLNCATGWFDgk--dSFAESWMRNan------gGAVGFTgavrvsys--------------------------- 545  Photobacteriu...
YP_001740968  443 KLFHAVFITCSTGSFGgs--tSTTEQVIRYgtaa--slgGAITAIgmatss----------------------------- 489  Candidatus Cl...
YP_001740722  456 KLFHTVNITCGTNNYN-----GAGEVETFVrygttaapkGAVTGIgmctss----------------------------- 501  Candidatus Cl...
Feature 1                     #                                                                   
1CVR_A        282 ------qywapPMRGQDEMNEILcekhpn----nikrtFGGVTMNGMFAMvekykkd------genmldTWTVFGDPSLL 345  Porphyromonas...
2182812       541 ydatfledsynTVNSIMWAGNLAath---------agnIGNITHIGAHYYw-----------------eAYHVLGDGSVM 594  Porphyromonas...
P28784        509 ------qswasPMRGQDEMNEILcekhpn----nikrtFGGVTMNGMFAMvekykkd------gekmldTWTVFGDPSLL 572  Porphyromonas...
YP_001741285  496 ------qswasPMRAQDEVTDLLtgev--------httLGGLYYNGSCKMmdvygsd------gvnmfkTWHIFGDASLQ 555  Candidatus Cl...
YP_004342858  502 ------mawaePMQTQDEMAEIIaetnpv----nqkttLGGLFYNSQLSMleeypsg-----sgeevmqTWILFGDPSAQ 566  Fluviicola ta...
YP_001741063  503 ------qswapPMRAQDEVTDLLvgnf--------khrIGSLLFNGAHKMlevygsq------glddarTWTIFGDASLM 562  Candidatus Cl...
YP_001741767  540 kgtangsapayDASKLGAYDAMFhthseaf--tnwattVGEAVMMGNSAVvqagssl------snyyweIYSIMGDPSLM 611  Candidatus Cl...
YP_001741369  458 ----------sDLHTKTRFNNSIasgafrsimdwdvrsFGSSVLMGKIELyknfpndlapnqyvafyfhVFNILSDPSLN 527  Candidatus Cl...
YP_001741062  563 ykppvvgtgspFVAGRTGAYDALfhdhnep-fadwagnAGSNVVMGNMAVvqsnssr------inyyweIYSIMGDPSLV 635  Candidatus Cl...
YP_001740552  499 -----thttfnNCLNAGIYDGIFtyg---------mrsMGEALLNAKLYIkqvygstfd--qqanyfahWCNLMGDPTVE 562  Candidatus Cl...
YP_133595     546 ----gyndlmhAAILDSLWDDYDgawssav--ypvswrPAMALNRAKDRLfghygaed---shailtarFFSWFGDPELE 616  Photobacteriu...
YP_001740968  490 -----thtpmnNCLDVGIFHGIYnlg---------mreMSSPMLYAKLYLhsvygvshp--tqaqdfaaYCNLMGDPTAM 553  Candidatus Cl...
YP_001740722  502 -----thttfnNAIHGGIFAGIFasd---------mrtMGEALLNGRLYLrqlfgvssp--tnatnfaaWCNLMGDPTME 565  Candidatus Cl...
Feature 1          
1CVR_A        346 V 346  Porphyromonas gingivalis
2182812       595 P 595  Porphyromonas gingivalis
P28784        573 V 573  Porphyromonas gingivalis
YP_001741285  556 V 556  Candidatus Cloacamonas acidaminovorans
YP_004342858  567 F 567  Fluviicola taffensis DSM 16823
YP_001741063  563 V 563  Candidatus Cloacamonas acidaminovorans
YP_001741767  612 P 612  Candidatus Cloacamonas acidaminovorans
YP_001741369  528 M 528  Candidatus Cloacamonas acidaminovorans
YP_001741062  636 P 636  Candidatus Cloacamonas acidaminovorans
YP_001740552  563 V 563  Candidatus Cloacamonas acidaminovorans
YP_133595     617 L 617  Photobacterium profundum SS9
YP_001740968  554 V 554  Candidatus Cloacamonas acidaminovorans
YP_001740722  566 V 566  Candidatus Cloacamonas acidaminovorans

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