2EU8

Crystal structure of a thermostable mutant of Bacillus subtilis Adenylate Kinase (Q199R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

In vivo molecular evolution reveals biophysical origins of organismal fitness.

Counago, R.Chen, S.Shamoo, Y.

(2006) Mol.Cell 22: 441-449

  • DOI: 10.1016/j.molcel.2006.04.012

  • PubMed Abstract: 
  • In nature, evolution occurs through the continuous adaptation of a population to its environment. At the molecular level, adaptive changes in protein sequence and expression impact organismal fitness and, consequently, dictate population dynamics. He ...

    In nature, evolution occurs through the continuous adaptation of a population to its environment. At the molecular level, adaptive changes in protein sequence and expression impact organismal fitness and, consequently, dictate population dynamics. Here, we have used a "weak link" method to favor variations in one gene, allowing adaptation to thermostability to be studied in molecular detail as bacteria were grown continuously for approximately 1500 generations. Surprisingly, only six mutant alleles, representing less than 1% of the possible missense mutations, were observed, suggesting a highly constrained molecular landscape during protein evolution. The changes in organismal fitness were linked directly to incremental increases in enzyme stability and activity maxima and corresponded to the narrow temperature ranges where each mutant enjoyed success within the overall population. Thus, continuous evolution of a single gene permits a quantitative approach that extends from the phenotypes of the microbial populations to their underlying biophysical basis.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate kinase
A, B
216Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: adk
EC: 2.7.4.3
Find proteins for P16304 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P16304
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AP5
Query on AP5

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A, B
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.690α = 90.00
b = 75.140β = 98.13
c = 77.350γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
d*TREKdata scaling
CNSrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-10-28 
  • Released Date: 2006-06-27 
  • Deposition Author(s): Chen, S., Shamoo, Y.

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance