4JL5

A high resolution structure of Aquifex Adenylate kinase with 2 ADP's


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The energy landscape of adenylate kinase during catalysis.

Kerns, S.J.Agafonov, R.V.Cho, Y.J.Pontiggia, F.Otten, R.Pachov, D.V.Kutter, S.Phung, L.A.Murphy, P.N.Thai, V.Alber, T.Hagan, M.F.Kern, D.

(2015) Nat Struct Mol Biol 22: 124-131

  • DOI: 10.1038/nsmb.2941
  • Primary Citation of Related Structures:  
    4CF7, 4JL5, 4JLO, 4JLP, 4JLA, 4JLB, 4JLD, 4JL6, 4JL8, 4JKY

  • PubMed Abstract: 
  • Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking ...

    Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylate kinaseA, B203Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: adkaq_078
EC: 2.7.4.3
Find proteins for O66490 (Aquifex aeolicus (strain VF5))
Explore O66490 
Go to UniProtKB:  O66490
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth B], F [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.17α = 90
b = 69.56β = 90
c = 85.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-03-12 
  • Released Date: 2014-06-25 
  • Deposition Author(s): Cho, Y.-J., Kern, D.

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2015-02-18
    Changes: Database references