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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.aah3717
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE KINSE
A
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.917α = 90.00
b = 63.341β = 90.00
c = 70.457γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2019-05-08
    Type: Data collection, Experimental preparation