4J6E

Structure of LPXI D225A Mutant

• PDB DOI: https://doi.org/10.2210/pdb4J6E/pdb
• Entry: 4J6E supersedes: 4GGI

• Classification: HYDROLASE
• Organism(s): Caulobacter vibrioides NA1000
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-11 Released: 2013-05-08 
• Deposition Author(s): Metzger IV, L.E., Lee, J.K., Finer-Moore, J.S., Raetz, C.R.H., Stroud, R.M., Center for Structures of Membrane Proteins (CSMP)

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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 

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

• PubMed: 23042606 
• 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.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, The University of California San Francisco, San Francisco, California, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.98 kDa 
• Atom Count: 2,064 
• Modelled Residue Count: 273 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-2,3-diacylglucosamine pyrophosphatase LpxI	A	283	Caulobacter vibrioides NA1000	Mutation(s): 1  Gene Names: 77330127, CCNA_01987, CC_1910, lpxI EC: 3.6.1.54
UniProt
Find proteins for A0A0H3C8Q1 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C8Q1  Go to UniProtKB:  A0A0H3C8Q1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDG	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 = 107.297	α = 90
b = 107.297	β = 90
c = 81.29	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
ELVES	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Metzger IV, L.E., Lee, J.K., Finer-Moore, J.S., Raetz, C.R.H., Stroud, R.M., Center for Structures of Membrane Proteins (CSMP)
• This entry supersedes: 4GGI

Revision History  

• 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