2XCI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 U S A 109: 6253

  • DOI: 10.1073/pnas.1119894109
  • Primary Citation of Related Structures:  
    2XCU, 2XCI

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASEABCD374Aquifex aeolicusMutation(s): 0 
EC: 2.4.99.12
Membrane protein
Mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Glycosyltransferases
Protein: 
Monofunctional glycosyltransferase WaaA, substrate free
Find proteins for O66663 (Aquifex aeolicus (strain VF5))
Explore O66663 
Go to UniProtKB:  O66663
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

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

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A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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

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A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.5α = 90
b = 45.82β = 97.23
c = 144.07γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Other
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation