3TMB

Bd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus

Summary for 3TMB

• Entry DOI: 10.2210/pdb3tmb/pdb
• Related: 3TM8 3TMC 3TMD
• Descriptor: Uncharacterized protein Bd1817, FE (III) ION, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: hd-gyp, phosphodiesterase, unknown function, hydrolase, signaling protein
• Biological source: Bdellovibrio bacteriovorus
• Total number of polymer chains: 2
• Total formula weight: 74441.16

Authors

Lovering, A.L. (deposition date: 2011-08-31, release date: 2011-10-19, Last modification date: 2024-02-28)

Primary citation

Lovering, A.L.,Capeness, M.J.,Lambert, C.,Hobley, L.,Sockett, R.E.
The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases.
MBio, 2:-, 2011

PubMed Abstract: Cyclic-di-GMP is a near-ubiquitous bacterial second messenger that is important in localized signal transmission during the control of various processes, including virulence and switching between planktonic and biofilm-based lifestyles. Cyclic-di-GMP is synthesized by GGDEF diguanylate cyclases and hydrolyzed by EAL or HD-GYP phosphodiesterases, with each functional domain often appended to distinct sensory modules. HD-GYP domain proteins have resisted structural analysis, but here we present the first structural representative of this family (1.28 Å), obtained using the unusual Bd1817 HD-GYP protein from the predatory bacterium Bdellovibrio bacteriovorus. Bd1817 lacks the active-site tyrosine present in most HD-GYP family members yet remains an excellent model of their features, sharing 48% sequence similarity with the archetype RpfG. The protein structure is highly modular and thus provides a basis for delineating domain boundaries in other stimulus-dependent homologues. Conserved residues in the HD-GYP family cluster around a binuclear metal center, which is observed complexed to a molecule of phosphate, providing information on the mode of hydroxide ion attack on substrate. The fold and active site of the HD-GYP domain are different from those of EAL proteins, and restricted access to the active-site cleft is indicative of a different mode of activity regulation. The region encompassing the GYP motif has a novel conformation and is surface exposed and available for complexation with binding partners, including GGDEF proteins.

PubMed: 21990613
DOI: 10.1128/mBio.00163-11

Experimental method

X-RAY DIFFRACTION (1.7 Å)