6F7U

Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Molecular mechanism of ATP versus GTP selectivity of adenylate kinase.

Rogne, P.Rosselin, M.Grundstrom, C.Hedberg, C.Sauer, U.H.Wolf-Watz, M.

(2018) Proc Natl Acad Sci U S A 115: 3012-3017

  • DOI: https://doi.org/10.1073/pnas.1721508115
  • Primary Citation of Related Structures:  
    6F7U

  • PubMed Abstract: 

    Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure-function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate kinase214Escherichia coli K-12Mutation(s): 0 
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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP (Subject of Investigation/LOI)
Query on GCP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.88α = 90
b = 31.779β = 112.35
c = 54.205γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2013.0187
Swedish Research CouncilSweden--
Kempe FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 2.0: 2023-10-25
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.1: 2024-05-01
    Changes: Refinement description