5G3Y

Crystal structure of adenylate kinase ancestor 1 with Zn and ADP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 

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This is version 1.3 of the entry. See complete history


Literature

Evolutionary drivers of thermoadaptation in enzyme catalysis.

Nguyen, V.Wilson, C.Hoemberger, M.Stiller, J.B.Agafonov, R.V.Kutter, S.English, J.Theobald, D.L.Kern, D.

(2017) Science 355: 289-294

  • DOI: https://doi.org/10.1126/science.aah3717
  • Primary Citation of Related Structures:  
    5G3Y, 5G3Z, 5G40, 5G41

  • PubMed Abstract: 

    With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme's key kinetic obstacle-how to maintain catalytic speed on a cooler Earth-by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADENYLATE KINSE226synthetic constructMutation(s): 0 
EC: 2.7.4.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.917α = 90
b = 63.341β = 90
c = 70.457γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description