Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.48 kDa 
• Atom Count: 5506 
• Modelled Residue Count: 646 
• Deposited Residue Count: 666 
• Unique protein chains: 1

6B10

C. Jejuni Agmatine Deiminase

• PDB DOI: 10.2210/pdb6B10/pdb

• Classification: HYDROLASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-15 Released: 2017-12-13 
• Deposition Author(s): Shek, R., Hicks, K.A., French, J.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structural and Functional Basis for Targeting Campylobacter jejuni Agmatine Deiminase To Overcome Antibiotic Resistance.

Shek, R., Dattmore, D.A., Stives, D.P., Jackson, A.L., Chatfield, C.H., Hicks, K.A., French, J.B.

(2017) Biochemistry 56: 6734-6742

• PubMed: 29190068 
• DOI: 10.1021/acs.biochem.7b00982
• Primary Citation of Related Structures:  
  6B10, 6B2W


• PubMed Abstract: 
  

Campylobacter jejuni is the most common bacterial cause of gastroenteritis and a major contributor to infant mortality in the developing world. The increasing incidence of antibiotic-resistant C. jejuni only adds to the urgency to develop effective therapies. Because of the essential role that polyamines play, particularly in protection from oxidative stress, enzymes involved in the biosynthesis of these metabolites are emerging as promising antibiotic targets. The recent description of an alternative pathway for polyamine synthesis, distinct from that in human cells, in C. jejuni suggests this pathway could be a target for novel therapies. To that end, we determined X-ray crystal structures of C. jejuni agmatine deiminase (CjADI) and demonstrated that loss of CjADI function contributes to antibiotic sensitivity, likely because of polyamine starvation. The structures provide details of key molecular features of the active site of this protein. Comparison of the unliganded structure (2.1 Å resolution) to that of the CjADI-agmatine complex (2.5 Å) reveals significant structural rearrangements that occur upon substrate binding. The shift of two helical regions of the protein and a large conformational change in a loop near the active site generate a narrow binding pocket around the bound substrate. This change optimally positions the substrate for catalysis. In addition, kinetic analysis of this enzyme demonstrates that CjADI is an iminohydrolase that effectively deiminates agmatine. Our data suggest that C. jejuni agmatine deiminase is a potentially important target for combatting antibiotic resistance, and these results provide a valuable framework for guiding future drug development.

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Organizational Affiliation: 

Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative peptidyl-arginine deiminase family protein	A, B	333	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: Cj0949c
UniProt
Find proteins for Q0P9V0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9V0  Go to UniProtKB:  Q0P9V0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], F [auth B], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.4	α = 90
b = 80.296	β = 97.36
c = 83.923	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-15 
• Released Date: 2017-12-13 
Deposition Author(s): Shek, R., Hicks, K.A., French, J.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM124898

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2018-01-03
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence