2XCU

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 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 10.1073/pnas.1119894109
  • Primary Citation of 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 ...

    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 TRANSFERASEA, B, C, D374Aquifex 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • 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

View Full Validation Report



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