PDBsum entry 4me4

Hydrolase

PDB id: 4me4

Contents

Protein chains

361 a.a.

Ligands

SIN ×5

IMD ×2

5GP

Metals

_FE ×6

Waters ×140

References listed in PDB file

Key reference

• Title: Crystal structure of an hd-Gyp domain cyclic-Di-Gmp phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.
• Authors: D.Bellini, D.L.Caly, Y.Mccarthy, M.Bumann, S.Q.An, J.M.Dow, R.P.Ryan, M.A.Walsh.
• Ref.: Mol Microbiol, 2014, 91, 26-38. [DOI no: 10.1111/mmi.12447]
• PubMed id: 24176013

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.