5JNQ | pdb_00005jnq

MraY tunicamycin complex

• PDB DOI: https://doi.org/10.2210/pdb5JNQ/pdb

• Classification: Transferase/Antibiotic
• Organism(s): Enterocloster bolteae 90A9
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-04-30 Released: 2017-01-11 
• Deposition Author(s): Johansson, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.252 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

MraY-antibiotic complex reveals details of tunicamycin mode of action.

Hakulinen, J.K., Hering, J., Branden, G., Chen, H., Snijder, A., Ek, M., Johansson, P.

(2017) Nat Chem Biol 13: 265-267

• PubMed: 28068312 
• DOI: https://doi.org/10.1038/nchembio.2270
• Primary Citation Related Structures: 
  5JNQ


• PubMed Abstract: 
  

  The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl-pentapeptide translocase (MraY) in complex with the nucleoside antibiotic tunicamycin. The structure not only reveals the mode of action of several related natural-product antibiotics but also gives an indication on the binding mode of the MraY UDP-MurNAc-pentapeptide and undecaprenyl-phosphate substrates.

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Organizational Affiliation: 
• Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, Gothenburg, Sweden.
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.57 kDa 
• Atom Count: 2,440 
• Modeled Residue Count: 307 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospho-N-acetylmuramoyl-pentapeptide-transferase	A	376	Enterocloster bolteae 90A9	Mutation(s): 0  Gene Names: mraY, HMPREF1085_00623 EC: 2.7.8.13 Membrane Entity: Yes
UniProt
Find proteins for R0BTE9 (Enterocloster bolteae 90A9) Explore R0BTE9  Go to UniProtKB:  R0BTE9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TUM	B [auth A]	Tunicamycin C37 H60 N4 O16 YJQCOFNZVFGCAF-DCSBULBVSA-N
BOG	E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	C [auth A], D [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.252 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.64	α = 90
b = 105.54	β = 90
c = 134.96	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Johansson, P.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-01-18
  Changes: Database references
• Version 1.2: 2017-02-22
  Changes: Database references
• Version 1.3: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary