4GGM | pdb_00004ggm

Structure of LpxI

PDB DOI: https://doi.org/10.2210/pdb4GGM/pdb

Classification: HYDROLASE
Organism(s): Caulobacter vibrioides NA1000
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-08-06 Released: 2012-10-03
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.216 (Depositor), 0.213 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 23042606 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2393
Primary Citation 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

Macromolecule Content

Total Structure Weight: 31.11 kDa
Atom Count: 2,148
Modeled Residue Count: 277
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-2,3-diacylglucosamine pyrophosphatase LpxI	A [auth X]	283	Caulobacter vibrioides NA1000	Mutation(s): 0 Gene Names: 7330127, CCNA_01987, lpxI EC: 3.6.1.54
UniProt
Find proteins for A0A0H3C8Q1 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C8Q1 Go to UniProtKB: A0A0H3C8Q1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3C8Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LP5 Query on LP5 Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	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		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth X]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.216 (Depositor), 0.213 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.286	α = 90
b = 74.286	β = 90
c = 364.644	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Center for Structures of Membrane Proteins (CSMP)

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
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary