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B. subtilis ykuD protein at 2.0 Å resolution: Insights into the structure and function of a novel, ubiquitous family of bacterial enzymes
Author(s) -
Bielnicki Jakub,
Devedjiev Yancho,
Derewenda Urszula,
Dauter Zbigniew,
Joachimiak Andrzej,
Derewenda Zygmunt S.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20702
Subject(s) - bacillus subtilis , enzyme , biology , protein structure , escherichia coli , biochemistry , mutant , peptide sequence , active site , protein domain , gene , stereochemistry , chemistry , genetics , bacteria
Abstract 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 Å 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 β‐sandwich with two mixed sheets, one containing five strands and the other, six strands. The two β‐sheets form a cradle capped by an α‐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. Proteins 2006. © 2005 Wiley‐Liss, Inc.