2VD4

Structure of small-molecule inhibitor of Glmu from Haemophilus influenzae reveals an allosteric binding site

Summary for 2VD4

• Entry DOI: 10.2210/pdb2vd4/pdb
• Related: 2V0H 2V0I 2V0J 2V0K 2V0L
• Descriptor: BIFUNCTIONAL PROTEIN GLMU, 4-chloro-N-(3-methoxypropyl)-N-[(3S)-1-(2-phenylethyl)piperidin-3-yl]benzamide, SULFATE ION, ... (7 entities in total)
• Functional Keywords: glmu, inhibitor, magnesium, cell shape, peptidoglycan synthesis, allosteric, transferase, active site, metal-binding, cell wall biogenesis/degradation, multifunctional enzyme, nucleotidyltransferase, acyltransferase, uridyltransferase
• Biological source: HAEMOPHILUS INFLUENZAE
• Cellular location: Cytoplasm (By similarity): P43889
• Total number of polymer chains: 1
• Total formula weight: 50924.64

Authors

Mochalkin, I.,Lightle, S.,McDowell, L. (deposition date: 2007-09-28, release date: 2008-01-15, Last modification date: 2023-12-13)

Primary citation

Mochalkin, I.,Lightle, S.,Narasimhan, L.,Bornemeier, D.,Melnick, M.,Vanderroest, S.,Mcdowell, L.
Structure of a Small-Molecule Inhibitor Complexed with Glmu from Haemophilus Influenzae Reveals an Allosteric Binding Site.
Protein Sci., 17:577-, 2008

PubMed Abstract: N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine-diphospho-N-acetylglucosamine (UDP-GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram-negative and Gram-positive bacteria. Here we disclose a 1.9 A resolution crystal structure of a synthetic small-molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high-throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC(50) approximately 18 microM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc-1-P substrate-binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure-guided design of a new class of mechanism-based inhibitors of GlmU.

PubMed: 18218712
DOI: 10.1110/PS.073271408

Experimental method

X-RAY DIFFRACTION (1.9 Å)