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Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre

DOI: 10.1111/mmi.12447 DOI Help
PMID: 24176013 PMID Help

Authors: Domenico Bellini (Diamond Light Source) , Delphine L. Caly (University College Cork) , Yvonne Mccarthy (University College Cork) , Mario Bumann (ESRF) , Shi-qi An (University of Dundee) , J. Maxwell Dow (University College Cork) , Robert P. Ryan (University of Dundee) , Martin A. Walsh (Diamond Light Source)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Molecular Microbiology

State: Published (Approved)
Published: November 2013

Open Access Open Access

Abstract: Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.

Journal Keywords: Amino; Bacterial; Catalytic; Crystallography; X-Ray; Cyclic; Evolution; Molecular; Gram-Negative; Iron; Mutation; Protein; Tertiary; Sequence Alignment

Subject Areas: Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography , I03-Macromolecular Crystallography , I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography

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