4LKV

Determinants of lipid substrate and membrane binding for the tetraacyldisaccharide-1-phosphate 4 -kinase LpxK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.273 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Basis of Lipid Binding for the Membrane-embedded Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK.

Emptage, R.P.Tonthat, N.K.York, J.D.Schumacher, M.A.Zhou, P.

(2014) J Biol Chem 289: 24059-24068

  • DOI: https://doi.org/10.1074/jbc.M114.589986
  • Primary Citation of Related Structures:  
    4LKV

  • PubMed Abstract: 

    The membrane-bound tetraacyldisaccharide-1-phosphate 4'-kinase, LpxK, catalyzes the sixth step of the lipid A (Raetz) biosynthetic pathway and is a viable antibiotic target against emerging Gram-negative pathogens. We report the crystal structure of lipid IVA, the LpxK product, bound to the enzyme, providing a rare glimpse into interfacial catalysis and the surface scanning strategy by which many poorly understood lipid modification enzymes operate. Unlike the few previously structurally characterized proteins that bind lipid A or its precursors, LpxK binds almost exclusively to the glucosamine/phosphate moieties of the lipid molecule. Steady-state kinetic analysis of multiple point mutants of the lipid-binding pocket pinpoints critical residues involved in substrate binding, and characterization of N-terminal helix truncation mutants uncovers the role of this substructure as a hydrophobic membrane anchor. These studies make critical contributions to the limited knowledge surrounding membrane-bound enzymes that act upon lipid substrates and provide a structural template for designing small molecule inhibitors targeting this essential kinase.


  • Organizational Affiliation

    From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetraacyldisaccharide 4'-kinase
A, B, C, D
315Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: lpxKaq_1656
EC: 2.7.1.130
UniProt
Find proteins for O67572 (Aquifex aeolicus (strain VF5))
Explore O67572 
Go to UniProtKB:  O67572
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67572
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LP5
Query on LP5

Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]
(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
C34 H66 N O12 P
HEHQDWUWJVPREQ-XQJZMFRCSA-N
LP4
Query on LP4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]
2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose
C34 H66 N O12 P
AJRPJFBMHCTNGK-XQJZMFRCSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.273 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.632α = 90
b = 140.691β = 90
c = 173.846γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2014-09-24
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description