4MDZ

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Summary for 4MDZ

• Entry DOI: 10.2210/pdb4mdz/pdb
• Related: 4MCW 4ME4
• Descriptor: Metal dependent phosphohydrolase, FE (III) ION, SUCCINIC ACID, ... (5 entities in total)
• Functional Keywords: structural genomics, oxford protein production facility, oppf, phosphohydrolase, hydrolase
• Biological source: Persephonella marina
• Total number of polymer chains: 2
• Total formula weight: 87035.79

Authors

Bellini, D.,Walsh, M.A.,Oxford Protein Production Facility (OPPF) (deposition date: 2013-08-23, release date: 2014-02-19, Last modification date: 2023-09-20)

Primary citation

Bellini, D.,Caly, D.L.,McCarthy, Y.,Bumann, M.,An, S.Q.,Dow, J.M.,Ryan, R.P.,Walsh, M.A.
Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.
Mol.Microbiol., 91:26-38, 2014

PubMed 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.

PubMed: 24176013
DOI: 10.1111/mmi.12447

Experimental method

X-RAY DIFFRACTION (2.68 Å)