2BAS

Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain.

Summary for 2BAS

• Entry DOI: 10.2210/pdb2bas/pdb
• Descriptor: YkuI protein, BETA-MERCAPTOETHANOL (3 entities in total)
• Functional Keywords: ykui protein, eal domain, structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, signaling protein
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 102611.84

Authors

Minasov, G.,Brunzelle, J.S.,Shuvalova, L.,Miller, D.J.,Collart, F.R.,Joachimiak, A.,Anderson, W.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2005-10-14, release date: 2005-11-29, Last modification date: 2024-03-06)

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 cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.
J.Biol.Chem., 284:13174-13184, 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 (2.61 Å)