2H1H

E. coli heptosyltransferase WaaC with ADP-2-deoxy-2-fluoro heptose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 

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This is version 1.3 of the entry. See complete history


Literature

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

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

(2006) J Mol Biol 363: 383-394

  • DOI: https://doi.org/10.1016/j.jmb.2006.07.057
  • Primary Citation of Related Structures:  
    2GT1, 2H1F, 2H1H

  • PubMed 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.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS, Université Paris Descartes, Faculté de Pharmacie, 4, Avenue de l'Observatoire, F-75270 Paris cedex 06, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide heptosyltransferase 1
A, B
334Escherichia coli RS218Mutation(s): 0 
Gene Names: rfaCrfa-2waaC
EC: 2
Membrane Entity: Yes 
UniProt
Find proteins for P24173 (Escherichia coli (strain K12))
Explore P24173 
Go to UniProtKB:  P24173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24173
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AFH
Query on AFH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ADENOSINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO HEPTOSE
C17 H26 F N5 O15 P2
SUPCMUQXGKOKIM-FJBXLJLUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AFH Binding MOAD:  2H1H IC50: 3.00e+4 (nM) from 1 assay(s)
PDBBind:  2H1H IC50: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.53α = 90
b = 88.9β = 90
c = 90.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description