1ZUI

Structural Basis for Shikimate-binding Specificity of Helicobacter pylori Shikimate Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase

Cheng, W.C.Chang, Y.N.Wang, W.C.

(2005) J.Bacteriol. 187: 8156-8163

  • DOI: 10.1128/JB.187.23.8156-8163.2005
  • Primary Citation of Related Structures:  1ZUH
  • Also Cited By: 3HR7

  • PubMed Abstract: 
  • Shikimate kinase (EC 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP. As the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, ...

    Shikimate kinase (EC 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP. As the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, but not mammals, shikimate kinase represents an attractive target for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here, we report the 1.8-Angstroms crystal structure of Helicobacter pylori shikimate kinase (HpSK). The crystal structure shows a three-layer alpha/beta fold consisting of a central sheet of five parallel beta-strands flanked by seven alpha-helices. An HpSK-shikimate-PO(4) complex was also determined and refined to 2.3 Angstroms, revealing induced-fit movement from an open to a closed form on substrate binding. Shikimate is located above a short 3(10) helix formed by a strictly conserved motif (GGGXV) after beta(3). Moreover, several highly conserved charged residues including Asp33 (in a conserved DT/SD motif), Arg57, and Arg132 (interacting with shikimate) are identified, guiding the development of novel inhibitors of shikimate kinase.


    Organizational Affiliation

    Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shikimate kinase
A
168Helicobacter pylori (strain ATCC 700392 / 26695)Gene Names: aroK
EC: 2.7.1.71
Find proteins for P56073 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56073
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.203 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 97.286α = 90.00
b = 97.286β = 90.00
c = 46.909γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description