4MDZ: Metallo-enzyme From P. Marina

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.
PDB ID: 4MDZDownload
MMDB ID: 117670
PDB Deposition Date: 2013/8/23
Updated in MMDB: 2014/02
Experimental Method:
x-ray diffraction
Resolution: 2.68  Å
Source Organism:
Similar Structures:
Biological Unit for 4MDZ: dimeric; determined by author and by software (PISA)
Molecular Components in 4MDZ
Label Count Molecule
Proteins (2 molecules)
Metal Dependent Phosphohydrolase
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB