PDBsum entry 4mdz

Hydrolase

PDB id: 4mdz

Contents

Protein chains

361 a.a.

Ligands

SIN ×5

C2E

Metals

_FE ×4

Waters ×96

PDB id:

4mdz

Name:

Hydrolase

Title:

Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre

Structure:

Metal dependent phosphohydrolase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Persephonella marina. Organism_taxid: 123214. Strain: dsm 14350 / ex-h1. Gene: perma_0986. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.68Å R-factor: 0.186 R-free: 0.228

Authors:

D.Bellini,M.A.Walsh,Oxford Protein Production Facility (Oppf)

Key ref:

D.Bellini et al. (2014). 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. PubMed id: 24176013 DOI: 10.1111/mmi.12447

Date:

23-Aug-13 Release date: 19-Feb-14

Protein chains

C0QQ26  (C0QQ26_PERMH) -  Metal dependent phosphohydrolase from Persephonella marina (strain DSM 14350 / EX-H1)

Seq: 363 a.a.

Struc: 361 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1111/mmi.12447

Mol Microbiol 91:26-38 (2014)

PubMed id: 24176013

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

D.Bellini, D.L.Caly, Y.McCarthy, M.Bumann, S.Q.An, J.M.Dow, R.P.Ryan, M.A.Walsh.

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.