2W27

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM

Summary for 2W27

• Entry DOI: 10.2210/pdb2w27/pdb
• Related: 2BAS
• Descriptor: YKUI PROTEIN, GUANOSINE-5'-MONOPHOSPHATE, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: protein structure initiative, signaling protein, structural genomics, psi, mcsg, eal domain, ykui protein, cyclic di-gmp
• Biological source: BACILLUS SUBTILIS
• Total number of polymer chains: 2
• Total formula weight: 103035.06

Authors

Padavattan, S.,AndERSON, W.F.,Schirmer, T. (deposition date: 2008-10-24, release date: 2009-02-24, Last modification date: 2023-12-13)

Primary citation

Minasov, G.,Padavattan, S.,Shuvalova, L.,Brunzelle, J.S.,Miller, D.J.,Basle, A.,Massa, C.,Collart, F.R.,Schirmer, T.,Anderson, W.F.
Crystal Structures of Ykui and its Complex with Second Messenger C-Di-Gmp Suggests Catalytic Mechanism of Phosphodiester Bond Cleavage by Eal Domains.
J.Biol.Chem., 284:13174-, 2009

PubMed Abstract: Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca(2+). The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca(2+) defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.

PubMed: 19244251
DOI: 10.1074/JBC.M808221200

Experimental method

X-RAY DIFFRACTION (2.8 Å)