3KZL

Crystal structure of BA2930 mutant (H183G) in complex with AcCoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.jmb.2011.04.076
  • Primary Citation of Related Structures:  
    3E4F, 3IJW, 3KZL, 3N0M, 3N0S

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N3-acetyltransferaseA,
B [auth D],
C,
D [auth B]
268Bacillus anthracisMutation(s): 1 
Gene Names: aacC7BA_2930GBAA2930GBAA_2930
UniProt
Find proteins for A0A1J9VPY4 (Bacillus anthracis)
Explore A0A1J9VPY4 
Go to UniProtKB:  A0A1J9VPY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J9VPY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth D],
L [auth C],
Q [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
R [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
H [auth D]
I [auth D]
J [auth D]
M [auth C]
F [auth A],
H [auth D],
I [auth D],
J [auth D],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
S [auth B],
U [auth B],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth D],
T [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth D],
C,
D [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
ACO Binding MOAD:  3KZL Kd: 6100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.831α = 90
b = 109.182β = 111.91
c = 73.721γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2022-04-13
    Changes: Database references, Structure summary