1Y7M

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

Summary for 1Y7M

• Entry DOI: 10.2210/pdb1y7m/pdb
• Descriptor: hypothetical protein BSU14040, CADMIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: surface mutagenesis, cysteine proteases, cell wall catabolism, structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Bacillus subtilis subsp. subtilis str. 168
• Cellular location: Spore wall (Probable): O34816
• Total number of polymer chains: 2
• Total formula weight: 35984.80

Authors

Bielnicki, J.A.,Devedjiev, Y.,Derewenda, U.,Dauter, Z.,Joachimiak, A.,Derewenda, Z.S.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2004-12-09, release date: 2005-03-01, Last modification date: 2024-11-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.05 Å)