1y7m

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Revision as of 04:30, 21 November 2007

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spinqualitylabelsall models 1y7m, resolution 2.05Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

Overview

The crystal structure of the product of the Bacillus subtilis ykuD gene, was solved by the multiwavelength anomalous dispersion (MAD) method and, refined using data to 2.0 A resolution. The ykuD protein is a, representative of a distinctly prokaryotic and ubiquitous family found, among both pathogenic and nonpathogenic Gram-positive and Gram-negative, bacteria. The deduced amino acid sequence reveals the presence of an, N-terminal LysM domain, which occurs among enzymes involved in cell wall, metabolism, and a novel, putative catalytic domain with a highly conserved, His/Cys-containing motif of hitherto unknown structure. As the wild-type, protein did not crystallize, a double mutant was designed, (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As, expected, the structure of the LysM domain is similar to the NMR structure, reported for an analogous domain from Escherichia coli murein, transglycosylase MltD. The molecular model also shows that the, 112-residue-long C-terminal domain has a novel tertiary fold consisting of, a beta-sandwich with two mixed sheets, one containing five strands and the, other, six strands. The two beta-sheets form a cradle capped by an, alpha-helix. This domain contains a putative catalytic site with a tetrad, of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of, this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important, role in cell wall biology.

About this Structure

1Y7M is a Single protein structure of sequence from Bacillus subtilis subsp. subtilis str. 168 with CD and SO4 as ligands. Full crystallographic information is available from OCA.

Reference

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes., Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS, Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140

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