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: 1.56 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/nsmb.2941
  • Primary Citation of Related Structures:  
    3SR0, 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, 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate kinase
A, B
206Aquifex aeolicusMutation(s): 0 
Gene Names: adkAquifexaq_078
EC: 2.7.4.3
UniProt
Find proteins for O66490 (Aquifex aeolicus (strain VF5))
Explore O66490 
Go to UniProtKB:  O66490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66490
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
ALF
Query on ALF

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.95α = 90
b = 69.58β = 90
c = 85.67γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Database references
  • Version 1.3: 2015-02-18
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations