6NC6

Lipid II flippase MurJ, inward closed conformation

PDB DOI: https://doi.org/10.2210/pdb6NC6/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Thermosipho africanus TCF52B
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2018-12-10 Released: 2019-04-17
Deposition Author(s): Kuk, A.C.Y., Lee, S.-Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.278
R-Value Work: 0.255
R-Value Observed: 0.256

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Visualizing conformation transitions of the Lipid II flippase MurJ.

Kuk, A.C.Y., Hao, A., Guan, Z., Lee, S.Y.

(2019) Nat Commun 10: 1736-1736

PubMed: 30988294 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-09658-0
Primary Citation of Related Structures:
6NC6, 6NC7, 6NC8, 6NC9

PubMed Abstract:
The biosynthesis of many polysaccharides, including bacterial peptidoglycan and eukaryotic N-linked glycans, requires transport of lipid-linked oligosaccharide (LLO) precursors across the membrane by specialized flippases. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, and a target of recently discovered antibacterials. However, the flipping mechanism of LLOs including Lipid II remains poorly understood due to a dearth of structural information. Here we report crystal structures of MurJ captured in inward-closed, inward-open, inward-occluded and outward-facing conformations. Together with mutagenesis studies, we elucidate the conformational transitions in MurJ that mediate lipid flipping, identify the key ion for function, and provide a framework for the development of inhibitors.

Organizational Affiliation

Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.

Macromolecule Content

Total Structure Weight: 109 kDa
Atom Count: 7,319
Modelled Residue Count: 927
Deposited Residue Count: 950
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II flippase MurJ	A, B	475	Thermosipho africanus TCF52B	Mutation(s): 0 Gene Names: murJ, mviN, THA_1814 Membrane Entity: Yes
UniProt
Find proteins for B7IE18 (Thermosipho africanus (strain TCF52B)) Explore B7IE18 Go to UniProtKB: B7IE18
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7IE18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLB Query on OLB Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.278
R-Value Work: 0.255
R-Value Observed: 0.256
Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.134	α = 90
b = 101.759	β = 90
c = 158.516	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-17

Deposition Author(s):

Kuk, A.C.Y.

Lee, S.-Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120594

Revision History (Full details and data files)

Version 1.0: 2019-04-17
Type: Initial release
Version 1.1: 2019-05-01
Changes: Data collection, Database references
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description