B. subtilis ykuD Protein at 2.0 Angstrom Resolution: Insights into the Structure and Function of a Novel, Ubiquitous Family of Bacterial Enzymes

Journal Article · Sun Jan 01 04:00:00 EST 2006 · Proteins: Struc. Func. Bioinformatics

DOI:https://doi.org/10.1002/prot.20702· OSTI ID:914091

Bielnicki, J; Devedjiev, Y; Derewenda, U; Dauter, Z; Joachimiak, A; Derewenda, Z

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 Angstroms 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.

• Research Organization: Brookhaven National Laboratory (BNL) National Synchrotron Light Source
• Sponsoring Organization: Doe - Office Of Science
• DOE Contract Number: AC02-98CH10886
• OSTI ID: 914091
• Report Number(s): BNL--78659-2007-JA
• Journal Information: Proteins: Struc. Func. Bioinformatics, Journal Name: Proteins: Struc. Func. Bioinformatics Vol. 62
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
43 PARTICLE ACCELERATORS
AMINO ACID SEQUENCE
BACILLUS SUBTILIS
CELL WALL
CRYSTAL STRUCTURE
ENZYMES
ESCHERICHIA COLI
MOLECULAR MODELS
NSLS
PROTEINS
RESOLUTION
national synchrotron light source