5AK7

Structure of wt Porphyromonas gingivalis peptidylarginine deiminase

• PDB DOI: https://doi.org/10.2210/pdb5AK7/pdb

• Classification: HYDROLASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-02 Released: 2015-07-22 
• Deposition Author(s): Kopec, J., Montgomery, A., Shrestha, L., Kiyani, W., Nowak, R., Burgess-Brown, N., Venables, P.J., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.154 
• R-Value Work: 0.128 
• R-Value Observed: 0.130 

Literature

Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.

Montgomery, A.B., Kopec, J., Shrestha, L., Thezenas, M.L., Burgess-Brown, N.A., Fischer, R., Yue, W.W., Venables, P.J.

(2016) Ann Rheum Dis 75: 1255

• PubMed: 26209657 
• DOI: https://doi.org/10.1136/annrheumdis-2015-207656
• Primary Citation of Related Structures:  
  5AK7, 5AK8


• PubMed Abstract: 
  

  Periodontitis (PD) is a known risk factor for rheumatoid arthritis (RA) and there is increasing evidence that the link between the two diseases is due to citrullination by the unique bacterial peptidylarginine deiminase (PAD) enzyme expressed by periodontal pathogen Pophyromonas gingivalis (PPAD). However, the precise mechanism by which PPAD could generate potentially immunogenic peptides has remained controversial due to lack of information about the structural and catalytic mechanisms of the enzyme.

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Organizational Affiliation: 

Kennedy institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.28 kDa 
• Atom Count: 3,889 
• Modelled Residue Count: 419 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYLARGININE DEIMINASE	A	438	Porphyromonas gingivalis	Mutation(s): 0  EC: 3.5.3
UniProt
Find proteins for Q9RQJ2 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q9RQJ2  Go to UniProtKB:  Q9RQJ2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	C [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
ALA	B [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	U [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.154 
• R-Value Work: 0.128 
• R-Value Observed: 0.130 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.86	α = 90
b = 84.66	β = 92.5
c = 55.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Kopec, J., Montgomery, A., Shrestha, L., Kiyani, W., Nowak, R., Burgess-Brown, N., Venables, P.J., Yue, W.W.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 1.2: 2015-08-19
  Changes: Structure summary
• Version 1.3: 2016-05-25
  Changes: Database references
• Version 1.4: 2019-10-30
  Changes: Advisory, Data collection, Derived calculations, Other