3AKY

STABILITY, ACTIVITY AND STRUCTURE OF ADENYLATE KINASE MUTANTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

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Literature

Stability, activity and structure of adenylate kinase mutants.

Spuergin, P.Abele, U.Schulz, G.E.

(1995) Eur J Biochem 231: 405-413

  • DOI: 10.1111/j.1432-1033.1995.tb20713.x
  • Primary Citation of Related Structures:  
    3AKY

  • PubMed Abstract: 
  • Sequence/structure relationships have been explored by site-directed mutagenesis using a structurally known adenylate kinase. In particular the effects of helix capping and nonpolar core expansion on thermodynamic stability have been analyzed. Six point mutations were produced and characterized by SDS/PAGE, native PAGE, isoelectric focussing, electrophoretic titration, enzyme kinetics, and X-ray structure analysis ...

    Sequence/structure relationships have been explored by site-directed mutagenesis using a structurally known adenylate kinase. In particular the effects of helix capping and nonpolar core expansion on thermodynamic stability have been analyzed. Six point mutations were produced and characterized by SDS/PAGE, native PAGE, isoelectric focussing, electrophoretic titration, enzyme kinetics, and X-ray structure analysis. Heat-denaturation experiments yielded melting temperatures Tm and melting enthalpy changes delta Hm. The heat capacity change delta Cp of the wild-type enzyme was determined by guanidine hydrochloride denaturation in conjunction with Tm and delta Hm. Using the wild-type delta Cp value, Gibbs free energy changes delta G at room temperature were calculated for all mutants. Four mutants were designed for helix capping stabilization, but only one of them showed such an effect. Because of electrostatic interference with the induced-fit motion, one mutant decreased the catalytic activity strongly. Two mutants expanded nonpolar cores causing destabilization. The mutant with the lower stability could be crystallized and subjected to an X-ray analysis at 223-pm resolution which showed the structural changes. The enzyme was stabilized by adding a -Pro-His-His tail to the C-terminal alpha-helix for nickel-chelate chromatography. This addition constitutes a helix cap. Taken together, the results demonstrate that stabilization by helix capping is difficult to achieve because the small positive effect is drowned by adverse mutational disruption. Further addition of atoms to nonpolar cores destabilized the protein, although the involved geometry changes were very small, demonstrating the importance of efficient packing.


    Related Citations: 
    • High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
      Abele, U., Schulz, G.E.
      (1995) Protein Sci 4: 1262
    • The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae)
      Proba, K., Tomasselli, A.G., Nielsen, P., Schulz, G.E.
      (1987) Nucleic Acids Res 15: 7187
    • Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution
      Egner, U., Tomasselli, A.G., Schulz, G.E.
      (1987) J Mol Biol 195: 649
    • The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast
      Tomasselli, A.G., Mast, E., Janes, W., Schiltz, E.
      (1986) Eur J Biochem 155: 111

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENYLATE KINASEA220Saccharomyces cerevisiaeMutation(s): 1 
EC: 2.7.4.3
UniProt
Find proteins for P07170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07170 
Go to UniProtKB:  P07170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07170
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP5
Query on AP5

Download Ideal Coordinates CCD File 
B [auth A]BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36α = 111.7
b = 40.4β = 109
c = 45.3γ = 63.3
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other