4J72 | pdb_00004j72

Crystal Structure of polyprenyl-phosphate N-acetyl hexosamine 1-phosphate transferase

• PDB DOI: https://doi.org/10.2210/pdb4J72/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-02-12 Released: 2013-09-11 
• Deposition Author(s): Lee, S.Y., Chung, B.C., Gillespie, R.A., Kwon, D.Y., Guan, Z., Zhou, P., Hong, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.265 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.223 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of MraY, an essential membrane enzyme for bacterial cell wall synthesis.

Chung, B.C., Zhao, J., Gillespie, R.A., Kwon, D.Y., Guan, Z., Hong, J., Zhou, P., Lee, S.Y.

(2013) Science 341: 1012-1016

• PubMed: 23990562 
• DOI: https://doi.org/10.1126/science.1236501
• Primary Citation Related Structures: 
  4J72


• PubMed Abstract: 
  

  MraY (phospho-MurNAc-pentapeptide translocase) is an integral membrane enzyme that catalyzes an essential step of bacterial cell wall biosynthesis: the transfer of the peptidoglycan precursor phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl phosphate. MraY has long been considered a promising target for the development of antibiotics, but the lack of a structure has hindered mechanistic understanding of this critical enzyme and the enzyme superfamily in general. The superfamily includes enzymes involved in bacterial lipopolysaccharide/teichoic acid formation and eukaryotic N-linked glycosylation, modifications that are central in many biological processes. We present the crystal structure of MraY from Aquifex aeolicus (MraYAA) at 3.3 Å resolution, which allows us to visualize the overall architecture, locate Mg(2+) within the active site, and provide a structural basis of catalysis for this class of enzyme.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University Medical Center, 2 Genome Ct, Durham, NC 27710, USA.
Department of Chemistry, Duke University, Durham, NC 27708, USA.
Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.08 kDa 
• Atom Count: 4,770 
• Modeled Residue Count: 620 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospho-N-acetylmuramoyl-pentapeptide-transferase	A, B	365	Aquifex aeolicus	Mutation(s): 0  Gene Names: aq_053, mraY EC: 2.7.8.13 Membrane Entity: Yes
UniProt
Find proteins for O66465 (Aquifex aeolicus (strain VF5)) Explore O66465  Go to UniProtKB:  O66465

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.265 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.223 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.799	α = 90
b = 101.491	β = 90
c = 138.313	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Lee, S.Y., Chung, B.C., Gillespie, R.A., Kwon, D.Y., Guan, Z., Zhou, P., Hong, J.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations