3SR0

Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: ADP/AlF4/AMP in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.565 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 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, 4JKY, 4JL5, 4JL6, 4JL8, 4JLA, 4JLB, 4JLD, 4JLO, 4JLP

  • 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, includi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate kinase
A, B
206Aquifex aeolicus (strain VF5)Gene Names: adk
EC: 2.7.4.3
Find proteins for O66490 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66490
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ALF
Query on ALF

Download SDF File 
Download CCD File 
A, B
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.565 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.950α = 90.00
b = 69.580β = 90.00
c = 85.670γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-06 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Cho, Y.-J., Kern, D.

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-28
    Type: Database references
  • Version 1.3: 2015-02-18
    Type: Database references