4Y0A

Shikimate kinase from Acinetobacter baumannii in complex with shikimate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.911 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate.

Sutton, K.A.Breen, J.MacDonald, U.Beanan, J.M.Olson, R.Russo, T.A.Schultz, L.W.Umland, T.C.

(2015) Acta Crystallogr.,Sect.D 71: 1736-1744

  • DOI: 10.1107/S139900471501189X

  • PubMed Abstract: 
  • Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. ba ...

    Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii strains are increasingly being observed. Compounding this concern is the dearth of new antibacterial agents in late-stage development that are effective against MDR and XDR A. baumannii. As part of an effort to address these concerns, two genes (aroA and aroC) of the shikimate pathway have previously been determined to be essential for the growth and survival of A. baumannii during host infection (i.e. to be essential in vivo). This study expands upon these results by demonstrating that the A. baumannii aroK gene, encoding shikimate kinase (SK), is also essential in vivo in a rat soft-tissue infection model. The crystal structure of A. baumannii SK in complex with the substrate shikimate and a sulfate ion that mimics the binding interactions expected for the β-phosphate of ATP was then determined to 1.91 Å resolution and the enzyme kinetics were characterized. The flexible shikimate-binding domain and LID region are compared with the analogous regions in other SK crystal structures. The impact of structural differences and sequence divergence between SKs from pathogenic bacteria that may influence antibiotic-development efforts is discussed.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shikimate kinase
A
179Acinetobacter baumannii (strain AB307-0294)Mutation(s): 0 
Gene Names: aroK
EC: 2.7.1.71
Find proteins for A0A0M3KL09 (Acinetobacter baumannii (strain AB307-0294))
Go to UniProtKB:  A0A0M3KL09
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SKM
Query on SKM

Download SDF File 
Download CCD File 
A
(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
SHIKIMATE
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.911 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.980α = 90.00
b = 85.810β = 90.00
c = 112.720γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (United States)United States--

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Data collection
  • Version 1.2: 2019-04-10
    Type: Author supporting evidence, Data collection, Derived calculations