2CDN

Crystal structure of Mycobacterium tuberculosis adenylate kinase complexed with two molecules of ADP and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of Mycobacterium Tuberculosis Adenylate Kinase in Complex with Two Molecules of Adp and Mg2+ Supports an Associative Mechanism for Phosphoryl Transfer.

Bellinzoni, M.Haouz, A.Grana, M.Munier-Lehmann, H.Shepard, W.Alzari, P.M.

(2006) Protein Sci 15: 1489

  • DOI: https://doi.org/10.1110/ps.062163406
  • Primary Citation of Related Structures:  
    2CDN

  • PubMed Abstract: 

    The crystal structure of Mycobacterium tuberculosis adenylate kinase (MtAK) in complex with two ADP molecules and Mg2+ has been determined at 1.9 A resolution. Comparison with the solution structure of the enzyme, obtained in the absence of substrates, shows significant conformational changes of the LID and NMP-binding domains upon substrate binding. The ternary complex represents the state of the enzyme at the start of the backward reaction (ATP synthesis). The structure is consistent with a direct nucleophilic attack of a terminal oxygen from the acceptor ADP molecule on the beta-phosphate from the donor substrate, and both the geometry and the distribution of positive charge in the active site support the hypothesis of an associative mechanism for phosphoryl transfer.


  • Organizational Affiliation

    Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, F-75724 Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADENYLATE KINASE201Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 2.7.4.3
UniProt
Find proteins for P9WKF5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKF5 
Go to UniProtKB:  P9WKF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKF5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.544α = 90
b = 64.91β = 110.12
c = 39.773γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description