2QIV

Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase

Williams, A.H.Raetz, C.R.H.

(2007) Proc Natl Acad Sci U S A 104: 13543-13550

  • DOI: https://doi.org/10.1073/pnas.0705833104
  • Primary Citation of Related Structures:  
    2QIA, 2QIV

  • PubMed Abstract: 

    UDP-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes the first step of lipid A biosynthesis, the reversible transfer of the R-3-hydroxyacyl chain from R-3-hydroxyacyl acyl carrier protein to the glucosamine 3-OH group of UDP-GlcNAc. Escherichia coli LpxA is highly selective for R-3-hydroxymyristate. The crystal structure of the E. coli LpxA homotrimer, determined previously in the absence of lipid substrates or products, revealed that LpxA contains an unusual, left-handed parallel beta-helix fold. We have now solved the crystal structures of E. coli LpxA with the bound product UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc at a resolution of 1.74 A and with bound UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc at 1.85 A. The structures of these complexes are consistent with the catalytic mechanism deduced by mutagenesis and with a recent 3.0-A structure of LpxA with bound UDP-GlcNAc. Our structures show how LpxA selects for 14-carbon R-3-hydroxyacyl chains and reveal two modes of UDP binding.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Box 3711 DUMC, Durham, NC 27710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine acyltransferaseA [auth X]262Escherichia coli K-12Mutation(s): 0 
Gene Names: lpxa
EC: 2.3.1.129
UniProt
Find proteins for P0A722 (Escherichia coli (strain K12))
Explore P0A722 
Go to UniProtKB:  P0A722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A722
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U21
Query on U21

Download Ideal Coordinates CCD File 
B [auth X]uridine-5'-diphosphate-3-O-(R-3-hydroxydecanoyl)-N-acetyl-D-glucosamine
C27 H45 N3 O19 P2
MQPZMQHQQMJGDE-MCDYFTFASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.72α = 90
b = 96.72β = 90
c = 96.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary