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

Dom Bellini, Delphine L. Caly, Yvonne McCarthy, Mario Bumann, Shi-Qi An, J. Maxwell Dow (Lead / Corresponding author), Robert P. Ryan (Lead / Corresponding author), Martin A. Walsh (Lead / Corresponding author)

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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.
Original languageEnglish
Pages (from-to)26-38
Number of pages13
JournalMolecular Microbiology
Volume91
Issue number1
Early online date24 Nov 2013
DOIs
Publication statusPublished - Jan 2014

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