4X8O

Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.

Kovermann, M.Aden, J.Grundstrom, C.Elisabeth Sauer-Eriksson, A.Sauer, U.H.Wolf-Watz, M.

(2015) Nat Commun 6: 7644-7644

  • DOI: https://doi.org/10.1038/ncomms8644
  • Primary Citation of Related Structures:  
    4X8H, 4X8L, 4X8M, 4X8O

  • PubMed Abstract: 

    An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or 'invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power--a key aspect in rational design of enzymes catalysing novel reactions.


  • Organizational Affiliation

    Department of Chemistry, Chemical Biological Centre, Umeå University, Umeå 90187, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate kinase
A, B
214Escherichia coliMutation(s): 1 
Gene Names: adkdnaWplsAb0474JW0463
EC: 2.7.4.3
UniProt
Find proteins for P69441 (Escherichia coli (strain K12))
Explore P69441 
Go to UniProtKB:  P69441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69441
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.257α = 90
b = 72.654β = 90
c = 79.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description