3TMD
Bd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus
3TMD の概要
エントリーDOI | 10.2210/pdb3tmd/pdb |
関連するPDBエントリー | 3TM8 3TMB 3TMC |
分子名称 | Uncharacterized protein, FE (III) ION, PHOSPHATE ION, ... (4 entities in total) |
機能のキーワード | hd-gyp, phosphodiesterase, unknown function, hydrolase, signaling protein |
由来する生物種 | Bdellovibrio bacteriovorus |
タンパク質・核酸の鎖数 | 1 |
化学式量合計 | 37220.58 |
構造登録者 | |
主引用文献 | 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 Cited by 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: 21990613DOI: 10.1128/mBio.00163-11 主引用文献が同じPDBエントリー |
実験手法 | X-RAY DIFFRACTION (2.641 Å) |
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