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 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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 LpxI283Caulobacter vibrioides NA1000Mutation(s): 1 
Gene Names: 77330127CCNA_01987CC_1910lpxI
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDG
Query on UDG

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.227 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.297α = 90
b = 107.297β = 90
c = 81.29γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
ELVESrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations