PDBsum entry 2h1h

Transferase

PDB id: 2h1h

Contents

Protein chains

322 a.a. *

Ligands

AFH ×2

Waters ×43

* Residue conservation analysis

PDB id:

2h1h

Name:

Transferase

Title:

E. Coli heptosyltransferase waac with adp-2-deoxy-2-fluoro heptose

Structure:

Lipopolysaccharide heptosyltransferase 1. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 439184. Strain: rs218. Gene: rfac, rfa-2, waac. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.222 R-free: 0.269

Authors:

S.Grizot,M.Salem,V.Vongsouthi,L.Durand,F.Moreau,H.Dohi,S.Vincent, S.Escaich,A.Ducruix

Key ref:

S.Grizot et al. (2006). Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose. J Mol Biol, 363, 383-394. PubMed id: 16963083 DOI: 10.1016/j.jmb.2006.07.057

Date:

16-May-06 Release date: 22-May-07

Protein chains

P24173  (RFAC_ECOLI) -  Lipopolysaccharide heptosyltransferase 1 from Escherichia coli (strain K12)

Seq: 319 a.a.

Struc: 322 a.a.*

* PDB and UniProt seqs differ at 16 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.-.-.-

DOI no: 10.1016/j.jmb.2006.07.057

J Mol Biol 363:383-394 (2006)

PubMed id: 16963083

Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose.

S.Grizot, M.Salem, V.Vongsouthi, L.Durand, F.Moreau, H.Dohi, S.Vincent, S.Escaich, A.Ducruix.

ABSTRACT

Lipopolysaccharides constitute the outer leaflet of the outer membrane of Gram-negative bacteria and are therefore essential for cell growth and viability. The heptosyltransferase WaaC is a glycosyltransferase (GT) involved in the synthesis of the inner core region of LPS. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) residue of the Kdo2-lipid A molecule. Heptose is an essential component of the LPS core domain; its absence results in a truncated lipopolysaccharide associated with the deep-rough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria. Thus, WaaC represents a promising target in antibacterial drug design. Here, we report the structure of WaaC from the Escherichia coli pathogenic strain RS218 alone at 1.9 A resolution, and in complex with either ADP or the non-cleavable analog ADP-2-deoxy-2-fluoro-heptose of the sugar donor at 2.4 A resolution. WaaC adopts the GT-B fold in two domains, characteristic of one glycosyltransferase structural superfamily. The comparison of the three different structures shows that WaaC does not undergo a domain rotation, characteristic of the GT-B family, upon substrate binding, but allows the substrate analog and the reaction product to adopt remarkably distinct conformations inside the active site. In addition, both binary complexes offer a close view of the donor subsite and, together with results from site-directed mutagenesis studies, provide evidence for a model of the catalytic mechanism.

Selected figure(s)

Figure 1.
Figure 1. Structure of the ADP-L-glycero-β-d-manno-heptose. Figure 1. Structure of the ADP-L-glycero-β-d-manno-heptose.

Figure 4.
Figure 4. Observed electron density for the ADP-2F-heptose at 2.4 Å resolution. On the left is a 2F[o] – F[c] omit map contoured at 1σ superimposed with the F[o] – F[c] omit map contoured at 3σ, and on the right is the final 2F[o] – F[c] contoured at 1σ. ADP-2F-heptose is colored light gray and in atom colors. Figure 4. Observed electron density for the ADP-2F-heptose at 2.4 Å resolution. On the left is a 2F[o] – F[c] omit map contoured at 1σ superimposed with the F[o] – F[c] omit map contoured at 3σ, and on the right is the final 2F[o] – F[c] contoured at 1σ. ADP-2F-heptose is colored light gray and in atom colors.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 383-394) copyright 2006.

Figures were selected by an automated process.