PDBsum entry: 2olu

Transferase

PDB id: 2olu

Contents

Protein chain

608 a.a. *

Ligands

EDO

Waters ×22

* Residue conservation analysis

PDB id:

2olu

Name:

Transferase

Title:

Structural insight into the transglycosylation step of bacte wall biosynthesis : apoenzyme

Structure:

Penicillin-binding protein 2. Chain: a. Fragment: residues 60-727. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Gene: pbp2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å R-factor: 0.194 R-free: 0.246

Authors:

A.L.Lovering,L.H.De Castro,D.Lim,N.C.Strynadka

Key ref:

A.L.Lovering et al. (2007). Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis. Science, 315, 1402-1405. PubMed id: 17347437 DOI: 10.1126/science.1136611

Date:

19-Jan-07 Release date: 20-Mar-07

Protein chain

Q2YY56  (Q2YY56_STAAB) -  Penicillin-binding protein 2

Seq: 727 a.a.

Struc: 608 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: peptidoglycan-based cell wall (1 term)
• Biological process: cellular cell wall organization (4 terms)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1126/science.1136611

Science 315:1402-1405 (2007)

PubMed id: 17347437

Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis.

A.L.Lovering, L.H.de Castro, D.Lim, N.C.Strynadka.

ABSTRACT

Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.

Selected figure(s)

Figure 3.
Fig. 3. Detail of moenomycin binding. (A) Interactions of moenomycin with the donor substrate site of GT[51], with selected side chains shown. The phosphoric acid diester group is positioned in a region of high positive charge, and the sugar rings form an extended plane in the active-site cleft. Ring D projects out into solution, and ring A is located closest to the linker region. (B) Chemical structure of moenomycin. For clarity, an R1 group is used in place of the C[25] moenocinol lipid unit. (C) Electron density of the moenomycin molecule. The map is of a 2fo-fc format, contoured at 1 , from the final model at 2.8 Å resolution. For reference, the putative catalytic residues E114 and E171 are shown in stick form.

Figure 4.
Fig. 4. Proposed mechanism for lipid II polymerization. To simplify these diagrams, the peptide substituents on lipid II have been omitted. (A) Schematic for lipid II polymerization. For clarity, R1 and R2 groups are used in place of the OAc and NHAc groups, respectively. For comparative purposes, the respective lysozyme sugar subsites are labeled in parentheses (the traditional nomenclature using subsites a to f has been avoided to prevent confusion with the moenomycin ring labeling). In this model, lipid II is the acceptor (right side), and the growing glycan chain is the donor (left side). Residue E114 acts to deprotonate the acceptor 4-OH group, which concomitantly attacks C1 of the donor, in an S[N]2-like reaction that inverts the -linked precursors into a ß1,4-linked product. Residue E171 may assist this process by direct protonation of the phosphate-sugar bond or by stabilizing the pyrophosphate group through interaction with a divalent cation. (B) Spatial representation of the lipid II polymerization model. The membrane interface (horizontal black line), transmembrane region (vertical blue rectangle), and missing polypeptide (dotted blue line) are shown for effect. The protein structure is unmodified from the moenomycin-bound complex, with the growing glycan-chain donor (left side) modeled over moenomycin rings E and F and the lipid II acceptor (right side) fitted manually between the glycan-chain donor and the E114 catalytic residue (shown with E171 in stick form). After polymerization, the product would be translocated in the direction denoted by the yellow arrow. Any sugar chain larger than four sugar units (discounting the incoming two sugar units of the acceptor) would project out from the GT[51] domain, and there are no steric barriers in our structure to prevent this from occurring. The stronger positive charge on the left side of the active site, relative to that on the right side [see (C)], may assist in movement of the retained acceptor lipid-pyrophosphate group into the donor position. (C) Detail of active-site pockets and cleft. Residues E114 and E171 are shown in space-filling form. The electrostatic potentials (red, negative; blue, positive) indicate a conserved region of positive charge across the middle of the pocket. This region binds the phosphoric acid diester group of moenomycin in our structure and is located in a position to bind both pyrophosphates in our substrate model. (D) Details of the hydrophobic platform of the GT[51] fold. The view is approximately 90° from (C), with residues shown in stick form. Green, hydrophobic platform; gray, E114 and E171.

The above figures are reprinted by permission from the AAAs: Science (2007, 315, 1402-1405) copyright 2007.

Figures were selected by an automated process.