2IYX

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and SO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 

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 4 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
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SKM
Query on SKM

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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: 1.49 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.245α = 90.00
b = 59.245β = 90.00
c = 102.797γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing
DENZOdata reduction

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