2XCI

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Mechanistic Analysis of the Membrane-Embedded Glycosyltransferase Waaa Required for Lipopolysaccharide Synthesis.

Schmidt, H.Hansen, G.Singh, S.Hanuszkiewicz, A.Lindner, B.Fukase, K.Woodard, R.W.Holst, O.Hilgenfeld, R.Mamat, U.Mesters, J.R.

(2012) Proc.Natl.Acad.Sci.USA 109: 6253

  • DOI: 10.1073/pnas.1119894109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • WaaA is a key enzyme in the biosynthesis of LPS, a critical component of the outer envelope of Gram-negative bacteria. Embedded in the cytoplasmic face of the inner membrane, WaaA catalyzes the transfer of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) to ...

    WaaA is a key enzyme in the biosynthesis of LPS, a critical component of the outer envelope of Gram-negative bacteria. Embedded in the cytoplasmic face of the inner membrane, WaaA catalyzes the transfer of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) to the lipid A precursor of LPS. Here we present crystal structures of the free and CMP-bound forms of WaaA from Aquifex aeolicus, an ancient Gram-negative hyperthermophile. These structures reveal details of the CMP-binding site and implicate a unique sequence motif (GGS/TX(5)GXNXLE) in Kdo binding. In addition, a cluster of highly conserved amino acid residues was identified which represents the potential membrane-attachment and acceptor-substrate binding site of WaaA. A series of site-directed mutagenesis experiments revealed critical roles for glycine 30 and glutamate 31 in Kdo transfer. Our results provide the structural basis of a critical reaction in LPS biosynthesis and allowed the development of a detailed model of the catalytic mechanism of WaaA.


    Related Citations: 
    • Waaa of the Hyperthermophilic Bacterium Aquifex Aeolicus is a Monofunctional 3-Deoxy-D-Manno-Oct-2- Ulosonic Acid Transferase Involved in Lipopolysaccharide Biosynthesis.
      Mamat, U.,Schmidt, H.,Munoz, E.,Lindner, B.,Fukase, K.,Hanuszkiewicz, A.,Wu, J.,Meredith, T.C.,Woodard, R.W.,Hilgenfeld, R.,Mesters, J.R.,Holst, O.
      (2009) J.Biol.Chem. 284: 22248


    Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lübeck, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
A, B, C, D
374Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: kdtA
EC: 2.4.99.12
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Glycosyltransferases
Protein: 
Monofunctional glycosyltransferase WaaA, substrate free
Find proteins for O66663 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66663
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
C
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 132.500α = 90.00
b = 45.820β = 97.23
c = 144.070γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
autoSHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2012-05-02
    Type: Other
  • Version 1.3: 2018-01-17
    Type: Data collection