6DFE

The structure of a ternary complex of E. coli WaaC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 2.1 of the entry. See complete history


Literature

Insights into Heptosyltransferase I Catalysis and Inhibition through the Structure of Its Ternary Complex.

Blaukopf, M.Worrall, L.Kosma, P.Strynadka, N.C.J.Withers, S.G.

(2018) Structure 26: 1399-1407.e5

  • DOI: https://doi.org/10.1016/j.str.2018.07.001
  • Primary Citation of Related Structures:  
    6DFE

  • PubMed Abstract: 

    Heptosyltransferase I (WaaC) is a highly conserved glycosyltransferase found in Gram-negative bacteria that transfers a heptose residue onto the endotoxin inner core structure (ReLPS) of the outer membrane. Knockouts of WaaC have decreased virulence and increased susceptibility to antibiotics, making WaaC a potential drug target. While previous studies have elucidated the structure of the holoenzyme and a donor analog complex, no information on the binding mode of the acceptor has been available so far. By soaking of a chemically modified functional acceptor, along with a stable donor analog, the crystal structure of a pseudo-ternary complex of WaaC was obtained at 2.3-Å resolution. The acceptor is bound in an unusual horseshoe conformation stabilized by interaction of the anionic carboxylate and phosphate groups at its center and tips with highly conserved Lys and Arg residues. This binding is accompanied by both inter- and intra-domain movements within the protein.


  • Organizational Affiliation

    University of Natural Resources and Life Sciences - Vienna, Department of Chemistry, Muthgasse 18, 1190 Vienna, Austria. Electronic address: markus.blaukopf@boku.ac.at.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-heptose--LPS heptosyltransferase
A, B
326Escherichia coliMutation(s): 0 
Gene Names: AL530_003015AZZ83_001895C1N95_02680CT143_12860CT146_13830WM48_19965
UniProt
Find proteins for A0A152KUZ3 (Escherichia coli)
Explore A0A152KUZ3 
Go to UniProtKB:  A0A152KUZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A152KUZ3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
C, D
4N/A
Glycosylation Resources
GlyTouCan:  G89241LN
GlyCosmos:  G89241LN
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GA7 (Subject of Investigation/LOI)
Query on GA7

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R)-1-{(2S,3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl}propan-2-yl hydrogen (R)-phosphate (non-preferred name)
C20 H32 N5 O13 P
KMYAQBXCNBRSNR-VHKXYEKJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.82α = 90
b = 92.33β = 90
c = 94.94γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary