4GGM

Structure of LpxI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.897 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

LpxI structures reveal how a lipid A precursor is synthesized.

Metzger, L.E.Lee, J.K.Finer-Moore, J.S.Raetz, C.R.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
X
283Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 0 
Gene Names: lpxI
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Hydrolases
Protein: 
LpxI phosphodiester hydrolase for lipid A biosynthesis
Find proteins for A0A0H3C8Q1 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3C8Q1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LP5
Query on LP5

Download SDF File 
Download CCD File 
X
(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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.897 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.286α = 90.00
b = 74.286β = 90.00
c = 364.644γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Blu-Icedata collection
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references
  • Version 1.2: 2012-11-21
    Type: Database references
  • Version 1.3: 2013-04-17
    Type: Structure summary
  • Version 1.4: 2017-10-25
    Type: Author supporting evidence