2G1K

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate at 1.75 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Mycobacterium tuberculosis Shikimate Kinase in Complex with Shikimic Acid and an ATP Analogue.

Gan, J.Gu, Y.Li, Y.Yan, H.Ji, X.

(2006) Biochemistry 45: 8539-8545

  • DOI: https://doi.org/10.1021/bi0606290
  • Primary Citation of Related Structures:  
    1ZYU, 2G1J, 2G1K

  • PubMed Abstract: 

    Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs, because the pathway is essential in microorganisms, plants, and parasites but absent from mammals. SK catalyzes the reaction of phosphoryl transfer from ATP to shikimic acid (SA). Since 2002, a total of 11 SK structures have been reported, but none contains either the two substrate (SA and ATP) or the two product (SA-phosphate and ADP) molecules. Here, we present three crystal structures of SK from Mycobacterium tuberculosis (MtSK), including apo-MtSK, a binary complex MtSK x SA, and the ternary complex of MtSK with SA and an ATP analogue, AMPPCP. The structures of apo-MtSK and MtSK x AMPPCP x SA make it possible to elucidate the conformational changes of MtSK upon the binding of both substrates; the structure of MtSK x AMPPCP x SA reveals interactions between the protein and gamma-phosphate which indicate dynamic roles of catalytic residues Lys15 and Arg117.


  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Shikimate kinase176Mycobacterium tuberculosisMutation(s): 0 
Gene Names: aroK
EC: 2.7.1.71
UniProt
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY3 
Go to UniProtKB:  P9WPY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.309α = 90
b = 59.309β = 90
c = 102.537γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary