2IYZ

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate-3-phosphate and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium Tuberculosis.

Hartmann, M.D.Bourenkov, G.P.Oberschall, A.Strizhov, N.Bartunik, H.D.

(2006) J.Mol.Biol. 364: 411

  • DOI: 10.1016/j.jmb.2006.09.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The ...

    The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The catalytic turnover of shikimate and ATP into the products shikimate-3-phosphate and ADP, followed by release of ADP, was studied in the crystalline environment. Based on a comparison of the structural states before initiation of the reaction and immediately after the catalytic step, we derived a structural model of the transition state that suggests that phosphoryl transfer proceeds with inversion by an in-line associative mechanism. The random sequential binding of shikimate and nucleotides is associated with domain movements. We identified a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.


    Organizational Affiliation

    Max Planck Unit for Structural Molecular Biology, MPG-ASMB c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SHIKIMATE KINASE
A
184Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: aroK
EC: 2.7.1.71
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPY3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S3P
Query on S3P

Download SDF File 
Download CCD File 
A
SHIKIMATE-3-PHOSPHATE
C7 H11 O8 P
QYOJSKGCWNAKGW-PBXRRBTRSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.610α = 90.00
b = 59.610β = 90.00
c = 102.911γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance