1KI9

Adenylate kinase from Methanococcus thermolithotrophicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus

Criswell, A.R.Bae, E.Stec, B.Konisky, J.Phillips Jr., G.N.

(2003) J.Mol.Biol. 330: 1087-1099

  • Primary Citation of Related Structures:  1KHT

  • PubMed Abstract: 
  • The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8A and 2.5A, respectively. The structures of the enzymes are similar to th ...

    The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8A and 2.5A, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central beta-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M.voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the "invariant" Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S.acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S.acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
adenylate kinase
A, B, C
192Methanothermococcus thermolithotrophicusGene Names: adkA (adk)
EC: 2.7.4.3
Find proteins for P43410 (Methanothermococcus thermolithotrophicus)
Go to UniProtKB:  P43410
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.204 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.500α = 90.00
b = 128.500β = 90.00
c = 88.500γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
Crystaldata collection
d*TREKdata reduction
CrystalCleardata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance