Characterization and inactivation of an agmatine deiminase from Helicobacter pylori

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology



Document Type


Medical Subject Headings

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.

Rights and Permissions

Citation: 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.


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

Related Resources

Link to Article in PubMed


Deiminase, Haloacetamidine, Inactivator