PDBsum entry: 1pn3

Transferase/antibiotic

PDB id: 1pn3

Contents

Protein chains

391 a.a. *

Ligands

MLU-OMZ-ASN-GHP-GHP-OMY-3FG ×2

TYD

BGC ×2

Waters ×162

* Residue conservation analysis

PDB id:

1pn3

Name:

Transferase/antibiotic

Title:

Crystal structure of tdp-epi-vancosaminyltransferase gtfa in with tdp and the acceptor substrate dvv.

Structure:

Glycosyltransferase gtfa. Chain: a, b. Engineered: yes. Desvancosaminyl vancomycin. Chain: c, d

Source:

Amycolatopsis orientalis. Organism_taxid: 31958. Gene: gtfa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Organism_taxid: 31958

Resolution:

2.80Å R-factor: 0.212 R-free: 0.249

Authors:

A.M.Mulichak,H.C.Losey,W.Lu,Z.Wawrzak,C.T.Walsh,R.M.Garavito

Key ref:

A.M.Mulichak et al. (2003). Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway. Proc Natl Acad Sci U S A, 100, 9238-9243. PubMed id: 12874381 DOI: 10.1073/pnas.1233577100

Date:

12-Jun-03 Release date: 12-Aug-03

Protein chains

P96558  (P96558_AMYOR) -  Glycosyltransferase GtfA

Seq: 396 a.a.

Struc: 391 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (2 terms)
• Biochemical function: transferase activity (2 terms)

DOI no: 10.1073/pnas.1233577100

Proc Natl Acad Sci U S A 100:9238-9243 (2003)

PubMed id: 12874381

Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway.

A.M.Mulichak, H.C.Losey, W.Lu, Z.Wawrzak, C.T.Walsh, R.M.Garavito.

ABSTRACT

During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases from this pathway are potential tools for the combinatorial design of new antibiotics that are effective against vancomycin-resistant bacterial strains. These enzymes are members of the GT-B glycosyltransferase superfamily, which share a homologous bidomain topology. We present the 2.8-A crystal structures of GtfA complexes with vancomycin and the natural monoglycosylated peptide substrate, representing the first direct observation of acceptor substrate binding among closely related glycosyltransferases. The acceptor substrates bind to the N-terminal domain such that the aglycone substrate's reactive hydroxyl group hydrogen bonds to the side chains of Ser-10 and Asp-13, thus identifying these as residues of potential catalytic importance. As well as an open form of the enzyme, the crystal structures have revealed a closed form in which a TDP ligand is bound at a donor substrate site in the interdomain cleft, thereby illustrating not only binding interactions, but the conformational changes in the enzyme that accompany substrate binding.

Selected figure(s)

Figure 3.
Fig. 3. (a) Stereoview comparing the open (blue) and closed (green) forms of GtfA, with bound TDP (gold) and DVV (red) as observed in closed conformation. The flexible loop, unobserved in open form, is shown in magenta. (b) An expanded view looking into cleft of closed form (molecule B). Positions of bound DVV (red) and vancomycin (blue) are superimposed, highlighting the altered binding at the glycosylation site (arrow). The figure was prepared by using MOLSCRIPT (27) and RASTER3D (28).

Figure 5.
Fig. 5. (a) Difference electron density (3 level) for TDP in the interdomain cleft. (b) Binding interactions of TDP (gold) with residues of the N-terminal (cyan) and C-terminal (green) domains including the 292HHXXAGT298 loop. Ribose moiety interacts only via buried water molecules (blue spheres). Interdomain aromatic capping interaction between Arg-11 and Glu-277 and position of attacking hydroxyl (asterisk) of the bound DVV (red) are also shown. The images were prepared by using SETOR (29).

Figures were selected by the author.