PDBsum entry: 1y7m

Structural genomics, unknown function

PDB id: 1y7m

Contents

Protein chains

164 a.a. *

Ligands

SO4 ×4

Metals

_CD ×2

Waters ×156

* Residue conservation analysis

PDB id:

1y7m

Name:

Structural genomics, unknown function

Title:

Crystal structure of the b. Subtilis ykud protein at 2 a resolution

Structure:

Hypothetical protein bsu14040. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Strain: subsp. Subtilis str. 168. Gene: ykud. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.05Å R-factor: 0.214 R-free: 0.270

Authors:

J.A.Bielnicki,Y.Devedjiev,U.Derewenda,Z.Dauter,A.Joachimiak, Z.S.Derewenda,Midwest Center For Structural Genomics (Mcsg)

Key ref:

J.Bielnicki et al. (2006). 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. PubMed id: 16287140 DOI: 10.1002/prot.20702

Date:

09-Dec-04 Release date: 01-Mar-05

Protein chains

O34816  (YKUD_BACSU) -  Putative L,D-transpeptidase YkuD

Seq: 164 a.a.

Struc: 164 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: spore wall (1 term)
• Biological process: cell wall organization (5 terms)
• Biochemical function: transferase activity (3 terms)

DOI no: 10.1002/prot.20702

Proteins 62:144-151 (2006)

PubMed id: 16287140

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.

J.Bielnicki, Y.Devedjiev, U.Derewenda, Z.Dauter, A.Joachimiak, Z.S.Derewenda.

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.

Selected figure(s)

Figure 2.
Figure 2. The molecular architecture of ykuD. (A) A stereodiagram showing the head-to-tail noncrystallographic dimer of ykuD molecules; the two molecules are labeled A and B. (B) A comparison of the NMR structure of the LysM domain from murein transglycosylase D (PDB entry: 1E0G), orange, and the LysM domain of ykuD, blue; for details see text. (C) The tertiary structure of the ErfK/YbiS/YhnG domain of ykuD with the fingerprint conserved stretch shown in red; the side-chains of His123, Gly124, Ser136, Cys139, and Arg141 are shown in full. (D) A schematic representation of the teriary fold of the ErfK/YbiS/YhnG domain.

Figure 3.
Figure 3. The ykuD putative active site involved in a crystal contact. Side-chains of select residues, as well as Gly124, are shown in full; sulfate ions are represented by spheres: red (oxygen) and green (sulfur).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 144-151) copyright 2006.

Figures were selected by an automated process.