PDBsum entry: 2w27

Signaling protein

PDB id: 2w27

Contents

Protein chains

401 a.a. *

Ligands

5GP-5GP ×2

Metals

_CA ×2

Waters ×7

* Residue conservation analysis

PDB id:

2w27

Name:

Signaling protein

Title:

Crystal structure of the bacillus subtilis ykui protein, with an eal domain, in complex with substratE C-di-gmp and calcium

Structure:

Ykui protein. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.80Å R-factor: 0.228 R-free: 0.275

Authors:

S.Padavattan,W.F.Anderson,T.Schirmer

Key ref:

G.Minasov et al. (2009). 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. PubMed id: 19244251 DOI: 10.1074/jbc.M808221200

Date:

24-Oct-08 Release date: 24-Feb-09

Protein chains

O35014  (YKUI_BACSU) -  Uncharacterized EAL-domain containing protein ykuI

Seq: 407 a.a.

Struc: 401 a.a.

DOI no: 10.1074/jbc.M808221200

J Biol Chem 284:13174-13184 (2009)

PubMed id: 19244251

Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains.

G.Minasov, S.Padavattan, L.Shuvalova, J.S.Brunzelle, D.J.Miller, A.Baslé, C.Massa, F.R.Collart, T.Schirmer, W.F.Anderson.

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.

Selected figure(s)

Figure 1.
Crystal structure of YkuI. A, the monomer consists of two domains connected by a long helix (residues 246-289). The ribbon is colored from blue at the N terminus to red at the C terminus. The N-terminal EAL domain is folded to a TIM-barrel, and the C-terminal domain shows a PAS-like fold. Chain termini and secondary structure elements are labeled (see also Fig. 2). B, two monomers of YkuI form a noncrystallographic tight dimer. The 2-fold axis is vertical. The A-chain is colored in yellow (EAL domain), green (linking helix), and magenta (C-terminal PAS-like domain). The B-chain is shown in gray. The two EAL domains interact via isologous interactions across the molecular 2-fold axis involving the β5-α5 loop and the α6-helix.

Figure 4.
Stereo view of the active site of the YkuI EAL domain with bound substrate c-di-GMP and Ca^2^+. The omit map for substrate and the divalent cation has been contoured at 3σ. Coordinating atoms are joint with the Ca^2+ by dashed lines in magenta. Asp-152 has a distance of 3.7 Å to the metal, indicated by the blue line. Superimposed on the YkuI structure, the water molecule Wat1 of the tdEAL structure (PDB code 2r6o) is shown with its ligands Mg^2+ (largely concealed by the YkuI calcium ion) and Glu-535, Asp-646, and Glu-703. These tdEAL residues are shown in aquamarine and labeled in blue. For clarity, the residues that are homologous to Asn-88, Glu-122, and Lys-173 of YkuI (Glu-616 and Lys-667 of tdEAL), are not shown, but would also superimpose closely. H-bonds and the Wat-Mg^2+ coordination in tdEAL are drawn in light blue.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 13174-13184) copyright 2009.

Figures were selected by the author.