3HVM

Agmatine Deiminase from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization and inactivation of an agmatine deiminase from Helicobacter pylori.

Jones, J.E.Causey, C.P.Lovelace, L.Knuckley, B.Flick, H.Lebioda, L.Thompson, P.R.

(2010) Bioorg.Chem. 38: 62-73

  • DOI: 10.1016/j.bioorg.2009.11.004

  • PubMed Abstract: 
  • Helicobacter pylori encodes a potential virulence factor, agmatine deiminase (HpAgD), which catalyzes the conversion of agmatine to N-carbamoyl putrescine (NCP) and ammonia - agmatine is decarboxylated arginine. Agmatine is an endogenous human cell s ...

    Helicobacter pylori encodes a potential virulence factor, agmatine deiminase (HpAgD), which catalyzes the conversion of agmatine to N-carbamoyl putrescine (NCP) and ammonia - agmatine is decarboxylated arginine. Agmatine is an endogenous human cell signaling molecule that triggers the innate immune response in humans. Unlike H. pylori, humans do not encode an AgD; it is hypothesized that inhibition of this enzyme would increase the levels of agmatine, and thereby enhance the innate immune response. Taken together, these facts suggest that HpAgD is a potential drug target. Herein we describe the optimized expression, isolation, and purification of HpAgD (10-30 mg/L media). The initial kinetic characterization of this enzyme has also been performed. Additionally, the crystal structure of wild-type HpAgD has been determined at 2.1A resolution. This structure provides a molecular basis for the preferential deimination of agmatine, and identifies Asp198 as a key residue responsible for agmatine recognition, which has been confirmed experimentally. Information gathered from these studies led to the development and characterization of a novel class of haloacetamidine-based HpAgD inactivators. These compounds are the most potent AgD inhibitors ever described.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AGMATINE DEIMINASE
A
330Helicobacter pylori (strain J99 / ATCC 700824)Mutation(s): 0 
Find proteins for Q9ZN18 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZN18
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.082α = 90.00
b = 52.082β = 90.00
c = 246.398γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description