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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)DescriptionActionsGraphical viewLength
Metal bindingi307Calcium 1Combined sources1
Metal bindingi329Calcium 2; via carbonyl oxygenCombined sources1
Metal bindingi332Calcium 2Combined sources1
Metal bindingi334Calcium 2; via carbonyl oxygenCombined sources1
Metal bindingi336Calcium 2Combined sources1
Metal bindingi390Calcium 3Combined sources1
Metal bindingi395Calcium 3; via pros nitrogenCombined sources1
Active sitei440Proton donorCombined sources1 Publication1
Active sitei473NucleophileCombined sources1 Publication1 Publication1
Metal bindingi478Calcium 1; via carbonyl oxygenCombined sources1
Metal bindingi487Calcium 1Combined sources1
Metal bindingi521Calcium 3Combined sources1
Metal bindingi522Calcium 4Combined sources1
Metal bindingi525Calcium 4Combined sources1
Metal bindingi531Calcium 4; via tele nitrogenCombined sources1
Metal bindingi613Calcium 5Combined sources1
Metal bindingi639Calcium 5Combined sources1

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

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
PropeptideiPRO_000002653525 – 2291 PublicationAdd BLAST205
ChainiPRO_0000026536230 – 736Gingipain R2Add BLAST507

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 interactor.
MINTiMINT-8415911.
STRINGi242619.PG0506.

Structurei

Secondary structure

1736
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 41Combined sources6
Beta strandi44 – 50Combined sources7
Beta strandi55 – 61Combined sources7
Beta strandi64 – 70Combined sources7
Beta strandi87 – 93Combined sources7
Beta strandi96 – 112Combined sources17
Helixi130 – 132Combined sources3
Helixi139 – 142Combined sources4
Beta strandi151 – 154Combined sources4
Beta strandi158 – 160Combined sources3
Beta strandi163 – 170Combined sources8
Beta strandi173 – 176Combined sources4
Turni177 – 180Combined sources4
Beta strandi181 – 198Combined sources18
Helixi215 – 221Combined sources7
Beta strandi240 – 245Combined sources6
Helixi247 – 252Combined sources6
Helixi254 – 262Combined sources9
Beta strandi266 – 271Combined sources6
Helixi272 – 275Combined sources4
Helixi281 – 293Combined sources13
Beta strandi299 – 306Combined sources8
Turni308 – 310Combined sources3
Beta strandi314 – 316Combined sources3
Beta strandi319 – 322Combined sources4
Helixi323 – 326Combined sources4
Beta strandi329 – 333Combined sources5
Beta strandi336 – 342Combined sources7
Helixi347 – 362Combined sources16
Turni369 – 372Combined sources4
Beta strandi373 – 378Combined sources6
Helixi387 – 389Combined sources3
Helixi392 – 406Combined sources15
Beta strandi409 – 418Combined sources10
Helixi421 – 430Combined sources10
Beta strandi433 – 439Combined sources7
Beta strandi443 – 446Combined sources4
Turni447 – 449Combined sources3
Turni453 – 455Combined sources3
Helixi456 – 458Combined sources3
Beta strandi467 – 474Combined sources8
Beta strandi480 – 482Combined sources3
Helixi485 – 491Combined sources7
Beta strandi502 – 509Combined sources8
Beta strandi512 – 514Combined sources3
Helixi515 – 527Combined sources13
Helixi535 – 537Combined sources3
Helixi539 – 564Combined sources26
Beta strandi565 – 569Combined sources5
Beta strandi589 – 592Combined sources4
Beta strandi596 – 604Combined sources9
Beta strandi608 – 613Combined sources6
Beta strandi616 – 622Combined sources7
Beta strandi627 – 631Combined sources5
Beta strandi640 – 647Combined sources8
Beta strandi654 – 661Combined sources8
Beta strandi675 – 679Combined sources5
Beta strandi682 – 695Combined sources14
Beta strandi701 – 712Combined sources12
Beta strandi715 – 724Combined sources10
Beta strandi727 – 735Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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.
KOiK08589.
OMAiKENGRMI.

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)DescriptionActionsGraphical viewLength
Sequence conflicti58G → D in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti246P → A in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti251E → G in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti254E → K in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti398I → V in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti435A → V in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti480 – 482YNV → FSM in AAB41892 (PubMed:9705298).Curated3
Sequence conflicti510N → D AA sequence (PubMed:9705298).Curated1
Sequence conflicti512S → Y AA sequence (PubMed:9705298).Curated1
Sequence conflicti515S → P AA sequence (PubMed:9705298).Curated1
Sequence conflicti560K → N in AAB41892 (PubMed:9705298).Curated1
Sequence conflicti582K → E in AAB41892 (PubMed:9705298).Curated1

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.
KEGGipgi:PG_0506.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP95493. 1 interactor.
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.
KEGGipgi:PG_0506.
PATRICi22978106. VBIPorGin134034_0464.

Phylogenomic databases

eggNOGiENOG4108MCP. Bacteria.
ENOG4110H6N. LUCA.
KOiK08589.
OMAiKENGRMI.

Enzyme and pathway databases

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...

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: November 2, 2016
This is version 129 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.