4X8M

Crystal structure of E. coli Adenylate kinase Y171W mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/ncomms8644
  • Primary Citation of Related Structures:  

  • 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 stru ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate kinase
A
214Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: adk (dnaW, plsA)
EC: 2.7.4.3
Find proteins for P69441 (Escherichia coli (strain K12))
Go to UniProtKB:  P69441
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.566α = 90.00
b = 31.618β = 114.42
c = 63.080γ = 90.00
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references