2XCU | pdb_00002xcu

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.251 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: 176.67 kDa 
  • Atom Count: 11,835 
  • Modeled Residue Count: 1,410 
  • 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
C5P

Query on C5P



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
O [auth C],
S [auth D]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
K [auth B],
T [auth D]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
CIT

Query on CIT



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
L [auth B],
P [auth C],
U [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
BME

Query on BME



Download:Ideal Coordinates CCD File
M [auth B],
Q [auth C],
R [auth C],
V [auth D]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.251 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.77α = 90
b = 44.67β = 97.15
c = 143.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
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: 2011-05-11
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references, Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Other
  • Version 1.3: 2016-09-28
    Changes: Structure summary
  • Version 1.4: 2018-01-17
    Changes: Data collection
  • Version 1.5: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description