4LQE | pdb_00004lqe

Crystal Structure of MepB

• PDB DOI: https://doi.org/10.2210/pdb4LQE/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-17 Released: 2014-03-12 
• Deposition Author(s): Faham, S., Agah, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.279 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases.

Agah, S., Poulos, S., Banchs, C., Faham, S.

(2014) Protein Sci 23: 594-602

• PubMed: 24501097 
• DOI: https://doi.org/10.1002/pro.2438
• Primary Citation Related Structures: 
  4LQE


• PubMed Abstract: 
  

  The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance. Although the functions of MepA and MepR are known, little information is available on the function of MepB. Here we report the X-ray structure of MepB to 2.1 Å revealing its structural similarity to the PD-(D/E)XK family of endonucleases. We further show that MepB binds DNA and RNA, with a higher affinity towards RNA and single stranded DNA than towards double stranded DNA. Notably, the PD-(D/E)XK catalytic active site residues are not conserved in MepB. MepB's association with a drug resistance operon suggests that it plays a role in responding to antimicrobials. This role is likely carried out through MepB's interactions with nucleic acids.

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Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.35 kDa 
• Atom Count: 1,301 
• Modeled Residue Count: 149 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MepB	A	160	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: MepB, SAV0335
UniProt
Find proteins for A0A0H3JPI4 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JPI4  Go to UniProtKB:  A0A0H3JPI4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.279 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.645	α = 90
b = 91.139	β = 90
c = 100.004	γ = 90

Software Package:

Software Name	Purpose
CRANK	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Faham, S., Agah, S.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-05-07
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary