5K8K

Structure of the Haemophilus influenzae LpxH-lipid X complex

PDB DOI: https://doi.org/10.2210/pdb5K8K/pdb

Classification: HYDROLASE
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2016-05-30 Released: 2016-08-10
Deposition Author(s): Cho, J., Lee, C.-J., Zhou, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.227
R-Value Work: 0.192
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis.

Cho, J., Lee, C.J., Zhao, J., Young, H.E., Zhou, P.

(2016) Nat Microbiol 1: 16154-16154

PubMed: 27780190 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nmicrobiol.2016.154
Primary Citation of Related Structures:
5K8K

PubMed Abstract:
In most Gram-negative pathogens, the hydrolysis of UDP-2,3-diacylglucosamine to generate lipid X in lipid A biosynthesis is catalysed by the membrane-associated enzyme LpxH. We report the crystal structure of LpxH in complex with its product, lipid X, unveiling a unique insertion lid above the conserved architecture of calcineurin-like phosphoesterases. This structure reveals elaborate interactions surrounding lipid X and provides molecular insights into the substrate selectivity, catalysis and inhibition of LpxH.

Organizational Affiliation

Department of Biochemistry, Duke University Medical Center, Research Drive, Durham, North Carolina 27710, USA.

Macromolecule Content

Total Structure Weight: 31.64 kDa
Atom Count: 2,004
Modelled Residue Count: 237
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-2,3-diacylglucosamine hydrolase	A	256	Haemophilus influenzae Rd KW20	Mutation(s): 0 Gene Names: lpxH, HI_0735 EC: 3.6.1.54 Membrane Entity: Yes
UniProt
Find proteins for P44046 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44046 Go to UniProtKB: P44046
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P44046
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LP5 Query on LP5 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(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 D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.227
R-Value Work: 0.192
R-Value Observed: 0.195
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.84	α = 90
b = 99.84	β = 90
c = 200.85	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Cho, J.

Lee, C.-J.

Zhou, P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115355
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM51310

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-09-21
Changes: Database references
Version 1.2: 2016-11-09
Changes: Database references
Version 1.3: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.4: 2019-12-25
Changes: Author supporting evidence
Version 1.5: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary