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Protein

Gingipain R2

Gene

rgpB

Organism
Porphyromonas gingivalis (strain ATCC BAA-308 / W83)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Thiol protease. Acts synergistically with RgpA to catalyze the maturation of fimbrial subunits, such as FimA (By similarity). Its proteolytic activity is a major factor in both periodontal tissue destruction and in evasion of host defense mechanisms (Probable).By similarityCurated

Catalytic activityi

Hydrolysis of proteins and small molecule substrates, with a preference for Arg in P1.2 Publications

Enzyme regulationi

Inhibited by human histatin-3 1/24 (histatin-5).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi307 – 3071Calcium 1Combined sources
Metal bindingi329 – 3291Calcium 2; via carbonyl oxygenCombined sources
Metal bindingi332 – 3321Calcium 2Combined sources
Metal bindingi334 – 3341Calcium 2; via carbonyl oxygenCombined sources
Metal bindingi336 – 3361Calcium 2Combined sources
Metal bindingi390 – 3901Calcium 3Combined sources
Metal bindingi395 – 3951Calcium 3; via pros nitrogenCombined sources
Active sitei440 – 4401Proton donorCombined sources1 Publication
Active sitei473 – 4731NucleophileCombined sources1 Publication1 Publication
Metal bindingi478 – 4781Calcium 1; via carbonyl oxygenCombined sources
Metal bindingi487 – 4871Calcium 1Combined sources
Metal bindingi521 – 5211Calcium 3Combined sources
Metal bindingi522 – 5221Calcium 4Combined sources
Metal bindingi525 – 5251Calcium 4Combined sources
Metal bindingi531 – 5311Calcium 4; via tele nitrogenCombined sources
Metal bindingi613 – 6131Calcium 5Combined sources
Metal bindingi639 – 6391Calcium 5Combined sources

GO - Molecular functioni

  • calcium-dependent cysteine-type endopeptidase activity Source: UniProtKB
  • calcium ion binding Source: UniProtKB

GO - Biological processi

  • pathogenesis Source: UniProtKB-KW
  • proteolysis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Virulence

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciPGIN242619:GHX8-458-MONOMER.
BRENDAi3.4.22.37. 756.
SABIO-RKP95493.

Protein family/group databases

MEROPSiC25.003.

Names & Taxonomyi

Protein namesi
Recommended name:
Gingipain R2 (EC:3.4.22.372 Publications)
Alternative name(s):
Arg-gingipain
Gingipain 2
RGP-2
Gene namesi
Name:rgpB
Synonyms:prtRII, rgp2
Ordered Locus Names:PG_0506
OrganismiPorphyromonas gingivalis (strain ATCC BAA-308 / W83)
Taxonomic identifieri242619 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
Proteomesi
  • UP000000588 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

  • extracellular region Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence analysisAdd
BLAST
Propeptidei25 – 2292051 PublicationPRO_0000026535Add
BLAST
Chaini230 – 736507Gingipain R2PRO_0000026536Add
BLAST

Keywords - PTMi

Zymogen

Proteomic databases

PRIDEiP95493.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
HTN3P155167EBI-8505881,EBI-738783From a different organism.

Protein-protein interaction databases

IntActiP95493. 1 interaction.
MINTiMINT-8415911.
STRINGi242619.PG0506.

Structurei

Secondary structure

1
736
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi36 – 416Combined sources
Beta strandi44 – 507Combined sources
Beta strandi55 – 617Combined sources
Beta strandi64 – 707Combined sources
Beta strandi87 – 937Combined sources
Beta strandi96 – 11217Combined sources
Helixi130 – 1323Combined sources
Helixi139 – 1424Combined sources
Beta strandi151 – 1544Combined sources
Beta strandi158 – 1603Combined sources
Beta strandi163 – 1708Combined sources
Beta strandi173 – 1764Combined sources
Turni177 – 1804Combined sources
Beta strandi181 – 19818Combined sources
Helixi215 – 2217Combined sources
Beta strandi240 – 2456Combined sources
Helixi247 – 2526Combined sources
Helixi254 – 2629Combined sources
Beta strandi266 – 2716Combined sources
Helixi272 – 2754Combined sources
Helixi281 – 29313Combined sources
Beta strandi299 – 3068Combined sources
Turni308 – 3103Combined sources
Beta strandi314 – 3163Combined sources
Beta strandi319 – 3224Combined sources
Helixi323 – 3264Combined sources
Beta strandi329 – 3335Combined sources
Beta strandi336 – 3427Combined sources
Helixi347 – 36216Combined sources
Turni369 – 3724Combined sources
Beta strandi373 – 3786Combined sources
Helixi387 – 3893Combined sources
Helixi392 – 40615Combined sources
Beta strandi409 – 41810Combined sources
Helixi421 – 43010Combined sources
Beta strandi433 – 4397Combined sources
Beta strandi443 – 4464Combined sources
Turni447 – 4493Combined sources
Turni453 – 4553Combined sources
Helixi456 – 4583Combined sources
Beta strandi467 – 4748Combined sources
Beta strandi480 – 4823Combined sources
Helixi485 – 4917Combined sources
Beta strandi502 – 5098Combined sources
Beta strandi512 – 5143Combined sources
Helixi515 – 52713Combined sources
Helixi535 – 5373Combined sources
Helixi539 – 56426Combined sources
Beta strandi565 – 5695Combined sources
Beta strandi589 – 5924Combined sources
Beta strandi596 – 6049Combined sources
Beta strandi608 – 6136Combined sources
Beta strandi616 – 6227Combined sources
Beta strandi627 – 6315Combined sources
Beta strandi640 – 6478Combined sources
Beta strandi654 – 6618Combined sources
Beta strandi675 – 6795Combined sources
Beta strandi682 – 69514Combined sources
Beta strandi701 – 71212Combined sources
Beta strandi715 – 72410Combined sources
Beta strandi727 – 7359Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CVRX-ray2.00A230-664[»]
4IEFX-ray2.30A/C/E/G25-229[»]
B/D/F/H230-662[»]
5AG8X-ray1.90A/B577-736[»]
5AG9X-ray2.11A/B577-736[»]
5HFSX-ray1.97A/B665-736[»]
ProteinModelPortaliP95493.
SMRiP95493. Positions 230-661.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP95493.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase C25 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4108MCP. Bacteria.
ENOG4110H6N. LUCA.
OMAiKENGRMI.
OrthoDBiEOG6BGNW2.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.40.50.10390. 1 hit.
3.40.50.1460. 1 hit.
InterProiIPR029030. Caspase-like_dom.
IPR001769. Gingipain.
IPR029031. Gingipain_N.
IPR013783. Ig-like_fold.
IPR014756. Ig_E-set.
IPR005536. Peptidase_C25_Ig-like_domain.
IPR012600. Propeptide_C25.
IPR026444. Secre_tail.
[Graphical view]
PfamiPF01364. Peptidase_C25. 1 hit.
PF03785. Peptidase_C25_C. 1 hit.
PF08126. Propeptide_C25. 1 hit.
[Graphical view]
SUPFAMiSSF52129. SSF52129. 1 hit.
SSF81296. SSF81296. 1 hit.
TIGRFAMsiTIGR04183. Por_Secre_tail. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P95493-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKNFSRIVS IVAFSSLLGG MAFAQPAERG RNPQVRLLSA EQSMSKVQFR
60 70 80 90 100
MDNLQFTGVQ TSKGVAQVPT FTEGVNISEK GTPILPILSR SLAVSETRAM
110 120 130 140 150
KVEVVSSKFI EKKDVLIAPS KGVISRAENP DQIPYVYGQS YNEDKFFPGE
160 170 180 190 200
IATLSDPFIL RDVRGQVVNF APLQYNPVTK TLRIYTEIVV AVSETAEAGQ
210 220 230 240 250
NTISLVKNST FTGFEDIYKS VFMNYEATRY TPVEEKENGR MIVIVPKKYE
260 270 280 290 300
EDIEDFVDWK NQRGLRTEVK VAEDIASPVT ANAIQQFVKQ EYEKEGNDLT
310 320 330 340 350
YVLLVGDHKD IPAKITPGIK SDQVYGQIVG NDHYNEVFIG RFSCESKEDL
360 370 380 390 400
KTQIDRTIHY ERNITTEDKW LGQALCIASA EGGPSADNGE SDIQHENIIA
410 420 430 440 450
NLLTQYGYTK IIKCYDPGVT PKNIIDAFNG GISLANYTGH GSETAWGTSH
460 470 480 490 500
FGTTHVKQLT NSNQLPFIFD VACVNGDFLY NVPCFAEALM RAQKDGKPTG
510 520 530 540 550
TVAIIASTIN QSWASPMRGQ DEMNEILCEK HPNNIKRTFG GVTMNGMFAM
560 570 580 590 600
VEKYKKDGEK MLDTWTVFGD PSLLVRTLVP TKMQVTAPAN ISASAQTFEV
610 620 630 640 650
ACDYNGAIAT LSDDGDMVGT AIVKDGKAII KLNESIADET NLTLTVVGYN
660 670 680 690 700
KVTVIKDVKV EGTSIADVAN DKPYTVAVSG KTITVESPAA GLTIFDMNGR
710 720 730
RVATAKNRMV FEAQNGVYAV RIATEGKTYT EKVIVK
Length:736
Mass (Da):80,967
Last modified:October 3, 2003 - v2
Checksum:iC848DD3FAB420833
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti58 – 581G → D in AAB41892 (PubMed:9705298).Curated
Sequence conflicti246 – 2461P → A in AAB41892 (PubMed:9705298).Curated
Sequence conflicti251 – 2511E → G in AAB41892 (PubMed:9705298).Curated
Sequence conflicti254 – 2541E → K in AAB41892 (PubMed:9705298).Curated
Sequence conflicti398 – 3981I → V in AAB41892 (PubMed:9705298).Curated
Sequence conflicti435 – 4351A → V in AAB41892 (PubMed:9705298).Curated
Sequence conflicti480 – 4823YNV → FSM in AAB41892 (PubMed:9705298).Curated
Sequence conflicti510 – 5101N → D AA sequence (PubMed:9705298).Curated
Sequence conflicti512 – 5121S → Y AA sequence (PubMed:9705298).Curated
Sequence conflicti515 – 5151S → P AA sequence (PubMed:9705298).Curated
Sequence conflicti560 – 5601K → N in AAB41892 (PubMed:9705298).Curated
Sequence conflicti582 – 5821K → E in AAB41892 (PubMed:9705298).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U85038 Genomic DNA. Translation: AAB41892.1.
AF007124 Genomic DNA. Translation: AAC26371.1.
AE015924 Genomic DNA. Translation: AAQ65700.1.
RefSeqiWP_010956050.1. NC_002950.2.

Genome annotation databases

EnsemblBacteriaiAAQ65700; AAQ65700; PG_0506.
GeneIDi2552233.
PATRICi22978106. VBIPorGin134034_0464.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U85038 Genomic DNA. Translation: AAB41892.1.
AF007124 Genomic DNA. Translation: AAC26371.1.
AE015924 Genomic DNA. Translation: AAQ65700.1.
RefSeqiWP_010956050.1. NC_002950.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CVRX-ray2.00A230-664[»]
4IEFX-ray2.30A/C/E/G25-229[»]
B/D/F/H230-662[»]
5AG8X-ray1.90A/B577-736[»]
5AG9X-ray2.11A/B577-736[»]
5HFSX-ray1.97A/B665-736[»]
ProteinModelPortaliP95493.
SMRiP95493. Positions 230-661.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP95493. 1 interaction.
MINTiMINT-8415911.
STRINGi242619.PG0506.

Protein family/group databases

MEROPSiC25.003.

Proteomic databases

PRIDEiP95493.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAQ65700; AAQ65700; PG_0506.
GeneIDi2552233.
PATRICi22978106. VBIPorGin134034_0464.

Phylogenomic databases

eggNOGiENOG4108MCP. Bacteria.
ENOG4110H6N. LUCA.
OMAiKENGRMI.
OrthoDBiEOG6BGNW2.

Enzyme and pathway databases

BioCyciPGIN242619:GHX8-458-MONOMER.
BRENDAi3.4.22.37. 756.
SABIO-RKP95493.

Miscellaneous databases

EvolutionaryTraceiP95493.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.40.50.10390. 1 hit.
3.40.50.1460. 1 hit.
InterProiIPR029030. Caspase-like_dom.
IPR001769. Gingipain.
IPR029031. Gingipain_N.
IPR013783. Ig-like_fold.
IPR014756. Ig_E-set.
IPR005536. Peptidase_C25_Ig-like_domain.
IPR012600. Propeptide_C25.
IPR026444. Secre_tail.
[Graphical view]
PfamiPF01364. Peptidase_C25. 1 hit.
PF03785. Peptidase_C25_C. 1 hit.
PF08126. Propeptide_C25. 1 hit.
[Graphical view]
SUPFAMiSSF52129. SSF52129. 1 hit.
SSF81296. SSF81296. 1 hit.
TIGRFAMsiTIGR04183. Por_Secre_tail. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Comparative properties of two cysteine proteinases (gingipains R), the products of two related but individual genes of Porphyromonas gingivalis."
    Potempa J., Mikolajczyk-Pawlinska J., Brassell D., Nelson D., Thoegersen I.B., Enghild J.J., Travis J.
    J. Biol. Chem. 273:21648-21657(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 230-651, PROPEPTIDE, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY.
    Strain: HG66.
  2. "Characterization of a second cell-associated Arg-specific cysteine proteinase of Porphyromonas gingivalis and identification of an adhesin-binding motif involved in association of the prtR and prtK proteinases and adhesins into large complexes."
    Slakeski N., Bhogal P.S., O'Brien-Simpson N.M., Reynolds E.C.
    Microbiology 144:1583-1592(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 53978 / W50.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-308 / W83.
  4. "Salivary histatin 5 is an inhibitor of both host and bacterial enzymes implicated in periodontal disease."
    Gusman H., Travis J., Helmerhorst E.J., Potempa J., Troxler R.F., Oppenheim F.G.
    Infect. Immun. 69:1402-1408(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION, CATALYTIC ACTIVITY.
  5. "Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold."
    Eichinger A., Beisel H.-G., Jacob U., Huber R., Medrano F.-J., Banbula A., Potempa J., Travis J., Bode W.
    EMBO J. 18:5453-5462(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 230-664, ACTIVE SITE.
  6. "Porphyromonas gingivalis virulence factor gingipain RgpB shows a unique zymogenic mechanism for cysteine peptidases."
    de Diego I., Veillard F.T., Guevara T., Potempa B., Sztukowska M., Potempa J., Gomis-Ruth F.X.
    J. Biol. Chem. 288:14287-14296(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 25-229 AND 230-662 IN COMPLEX WITH CALCIUM, ACTIVE SITE.
    Strain: ATCC BAA-308 / W831 Publication.
  7. "The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal beta-sandwich domain."
    de Diego I., Ksiazek M., Mizgalska D., Koneru L., Golik P., Szmigielski B., Nowak M., Nowakowska Z., Potempa B., Houston J.A., Enghild J.J., Thogersen I.B., Gao J., Kwan A.H., Trewhella J., Dubin G., Gomis-Ruth F.X., Nguyen K.A., Potempa J.
    Sci. Rep. 6:23123-23123(2016) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 577-736.
    Strain: ATCC BAA-308 / W831 Publication.

Entry informationi

Entry nameiCPG2_PORGI
AccessioniPrimary (citable) accession number: P95493
Secondary accession number(s): O33441
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: October 3, 2003
Last modified: July 6, 2016
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.