Characterization and inactivation of an agmatine deiminase from Helicobacter pylori

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Agmatine; Amidines; Amino Acid Sequence; Binding Sites; Crystallography, X-Ray; Helicobacter pylori; Humans; Hydrolases; Kinetics; Recombinant Proteins; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Substrate Specificity


Biochemistry | Enzymes and Coenzymes | Medicinal-Pharmaceutical Chemistry | Therapeutics


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.


Deiminase, Haloacetamidine, Inactivator

DOI of Published Version



Bioorg Chem. 2010 Apr;38(2):62-73. doi: 10.1016/j.bioorg.2009.11.004. Link to article on publisher's site. Epub 2009 Nov 29.

Journal/Book/Conference Title

Bioorganic chemistry


At the time of publication, Paul Thompson was not yet affiliated with UMass Medical School.

Related Resources

Link to Article in PubMed