4J6E

Structure of LPXI D225A Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

LpxI structures reveal how a lipid A precursor is synthesized.

Metzger IV, L.E.Lee, J.K.Finer-Moore, J.S.Raetz, C.R.H.Stroud, R.M.

(2012) Nat.Struct.Mol.Biol. 19: 1132-1138

  • DOI: 10.1038/nsmb.2393
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymes in lipid metabolism acquire and deliver hydrophobic substrates and products from within lipid bilayers. The structure at 2.55 Å of one isozyme of a constitutive enzyme in lipid A biosynthesis, LpxI from Caulobacter crescentus, has a novel fol ...

    Enzymes in lipid metabolism acquire and deliver hydrophobic substrates and products from within lipid bilayers. The structure at 2.55 Å of one isozyme of a constitutive enzyme in lipid A biosynthesis, LpxI from Caulobacter crescentus, has a novel fold. Two domains close around a completely sequestered substrate, UDP-2,3-diacylglucosamine, and open to release products either to the neighboring enzyme in a putative multienzyme complex or to the bilayer. Mutation analysis identifies Asp225 as key to Mg(2+)-catalyzed diphosphate hydrolysis. These structures provide snapshots of the enzymatic synthesis of a critical lipid A precursor.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, The University of California San Francisco, San Francisco, California, USA. metzger@msg.ucsf.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-2,3-diacylglucosamine pyrophosphatase LpxI
A
283Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 1 
Gene Names: lpxI
Find proteins for A0A0H3C8Q1 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3C8Q1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDG
Query on UDG

Download SDF File 
Download CCD File 
A
(2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[(3R)-3-hydroxytetradecanoyl]amino}tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate
C43 H77 N3 O20 P2
KOJCFMYSTWNMQW-RUAJDYCTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.297α = 90.00
b = 107.297β = 90.00
c = 81.290γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
ELVESrefinement
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description