1Y7M

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

1Y7M の概要

• エントリーDOI: 10.2210/pdb1y7m/pdb
• 分子名称: hypothetical protein BSU14040, CADMIUM ION, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: surface mutagenesis, cysteine proteases, cell wall catabolism, structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• 由来する生物種: Bacillus subtilis subsp. subtilis str. 168
• 細胞内の位置: Spore wall (Probable): O34816
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 35984.80

構造登録者

Bielnicki, J.A.,Devedjiev, Y.,Derewenda, U.,Dauter, Z.,Joachimiak, A.,Derewenda, Z.S.,Midwest Center for Structural Genomics (MCSG) (登録日: 2004-12-09, 公開日: 2005-03-01, 最終更新日: 2024-11-06)

主引用文献

Bielnicki, J.,Devedjiev, Y.,Derewenda, U.,Dauter, Z.,Joachimiak, A.,Derewenda, Z.S.
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
Proteins, 62:144-151, 2006

PubMed 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 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.

PubMed: 16287140
DOI: 10.1002/prot.20702

実験手法

X-RAY DIFFRACTION (2.05 Å)