2XCI | pdb_00002xci

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 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2XCI

This is version 1.5 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: https://doi.org/10.1073/pnas.1119894109
  • Primary Citation Related Structures: 
    2XCI, 2XCU

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 175.3 kDa 
  • Atom Count: 11,857 
  • Modeled Residue Count: 1,411 
  • Deposited Residue Count: 1,496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
A, B, C, D
374Aquifex aeolicusMutation(s): 0 
EC: 2.4.99.12
Membrane Entity: Yes 
UniProt
Find proteins for O66663 (Aquifex aeolicus (strain VF5))
Explore O66663 
Go to UniProtKB:  O66663
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66663
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
X [auth D],
Y [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth D]
G [auth A]
H [auth A]
I [auth A]
N [auth B]
AA [auth D],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
R [auth C],
S [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME

Query on BME



Download:Ideal Coordinates CCD File
T [auth C],
U [auth C]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
CA [auth D],
J [auth A],
O [auth B],
V [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth D]
DA [auth D]
K [auth A]
L [auth A]
M [auth A]
BA [auth D],
DA [auth D],
K [auth A],
L [auth A],
M [auth A],
P [auth B],
Q [auth B],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.254 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary