Adenylate kinase from Methanococcus voltae

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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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

  • DOI: https://doi.org/10.1016/s0022-2836(03)00655-7
  • Primary Citation of Related Structures:  
    1KHT, 1KI9

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
adenylate kinase
A, B, C
192Methanococcus voltaeMutation(s): 0 
Gene Names: adk
Find proteins for P43411 (Methanococcus voltae)
Explore P43411 
Go to UniProtKB:  P43411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43411
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.5α = 90
b = 200.5β = 90
c = 200.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-09-28
    Changes: Other
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description