1AKY

HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1262-1271

  • DOI: 10.1002/pro.5560040702
  • Primary Citation of Related Structures:  2AKY

  • PubMed Abstract: 
  • The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ ...

    The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified.


    Related Citations: 
    • 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
    • Stability, Activity and Structure of Adenylate Kinase Mutants
      Spuergin, P.,Abele, U.,Schulz, G.E.
      (1995) Eur.J.Biochem. 231: 405
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE KINASE
A
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ADK1 (AKY, AKY1, AKY2)
EC: 2.7.4.3
Find proteins for P07170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07170
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
AP5
Query on AP5

Download SDF File 
Download CCD File 
A
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Work: 0.194 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.300α = 110.80
b = 40.500β = 109.00
c = 45.700γ = 63.30
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
SYNDUCdata reduction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance