4GGM

Structure of LpxI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/nsmb.2393
  • Primary Citation of Related Structures:  
    4GGM, 4J6E

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-2,3-diacylglucosamine pyrophosphatase LpxIA [auth X]283Caulobacter vibrioides NA1000Mutation(s): 0 
Gene Names: 7330127CCNA_01987lpxI
EC: 3.6.1.54
UniProt
Find proteins for A0A0H3C8Q1 (Caulobacter vibrioides (strain NA1000 / CB15N))
Explore A0A0H3C8Q1 
Go to UniProtKB:  A0A0H3C8Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3C8Q1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LP5
Query on LP5

Download Ideal Coordinates CCD File 
C [auth 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
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth X]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth X]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.286α = 90
b = 74.286β = 90
c = 364.644γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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