3E4F

Crystal structure of BA2930- a putative aminoglycoside N3-acetyltransferase from Bacillus anthracis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.

Klimecka, M.M.Chruszcz, M.Font, J.Skarina, T.Shumilin, I.Onopryienko, O.Porebski, P.J.Cymborowski, M.Zimmerman, M.D.Hasseman, J.Glomski, I.J.Lebioda, L.Savchenko, A.Edwards, A.Minor, W.

(2011) J.Mol.Biol. 410: 411-423

  • DOI: 10.1016/j.jmb.2011.04.076
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. Th ...

    For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. The most popular are antibiotics such as tetracyclines and fluoroquinolones. While aminoglycosides appear to be less effective antimicrobial agents than other antibiotics, synthetic aminoglycosides have been shown to act as potent inhibitors of anthrax lethal factor and may have potential application as antitoxins. Here, we present a structural analysis of the BA2930 protein, a putative aminoglycoside acetyltransferase, which may be a component of the bacterium's aminoglycoside resistance mechanism. The determined structures revealed details of a fold characteristic only for one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis. Both BA2930 and YokD are members of the Antibiotic_NAT superfamily (PF02522). Sequential and structural analyses showed that residues conserved throughout the Antibiotic_NAT superfamily are responsible for the binding of the cofactor acetyl coenzyme A. The interaction of BA2930 with cofactors was characterized by both crystallographic and binding studies.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside N3-acetyltransferase
A, B
265Bacillus anthracisMutation(s): 0 
Gene Names: yokD
EC: 2.3.1.81
Find proteins for A0A1J9VPY4 (Bacillus anthracis)
Go to UniProtKB:  A0A1J9VPY4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 36.313α = 90.00
b = 108.046β = 90.00
c = 132.809γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
HKL-2000data scaling
RESOLVEphasing
HKL-2000data collection
DMphasing
REFMACrefinement
SOLVEphasing
SHELXEmodel building
HKL-2000data reduction
MLPHAREphasing
SHELXDphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Type: Database references