5T77 | pdb_00005t77

Crystal structure of the MOP flippase MurJ

PDB DOI: https://doi.org/10.2210/pdb5T77/pdb

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

Deposited: 2016-09-02 Released: 2016-12-28
Deposition Author(s): Kuk, A.C.Y., Lee, S.-Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.189 (Depositor), 0.191 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the MOP flippase MurJ in an inward-facing conformation.

Kuk, A.C., Mashalidis, E.H., Lee, S.Y.

(2017) Nat Struct Mol Biol 24: 171-176

PubMed: 28024149 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3346
Primary Citation Related Structures:
5T77

PubMed Abstract:
Peptidoglycan (PG) protects bacteria from osmotic lysis, and its biogenesis is a key antibiotic target. A central step in PG biosynthesis is flipping of the lipid-linked PG precursor lipid II across the cytoplasmic membrane for subsequent incorporation into PG. MurJ, part of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) transporter superfamily, was recently shown to carry out this process. However, understanding of how MurJ flips lipid II, and of how MOP transporters operate in general, remains limited due to a lack of structural information. Here we present a crystal structure of MurJ from Thermosipho africanus in an inward-facing conformation at 2.0-Å resolution. A hydrophobic groove is formed by two C-terminal transmembrane helices, which leads into a large central cavity that is mostly cationic. Our studies not only provide the first structural glimpse of MurJ but also suggest that alternating access is important for MurJ function, which may be applicable to other MOP superfamily transporters.

Organizational Affiliation

Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.

Macromolecule Content

Total Structure Weight: 69.17 kDa
Atom Count: 4,404
Modeled Residue Count: 467
Deposited Residue Count: 475
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipid II flippase MurJ	A	475	Thermosipho africanus TCF52B	Mutation(s): 0 Gene Names: 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7IE18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLB Query on OLB Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A]	P [auth A] Q [auth A] R [auth A] S [auth A] T [auth A] P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] SDF format, chain Y [auth A] SDF format, chain VA [auth A] SDF format, chain SA [auth A] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain GA [auth A] SDF format, chain FA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A]	AA [auth A] AB [auth A] BA [auth A] BB [auth A] CA [auth A] AA [auth A], AB [auth A], BA [auth A], BB [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	M [auth A], N [auth A], O [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214 (Depositor), 0.216 (DCC)
R-Value Work: 0.189 (Depositor), 0.191 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.163	α = 90
b = 99.573	β = 112.91
c = 74.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Kuk, A.C.Y.

Lee, S.-Y.

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2017-01-04
Changes: Database references
Version 1.2: 2017-02-15
Changes: Database references
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Derived calculations