1DVR

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.

Schlauderer, G.J.Proba, K.Schulz, G.E.

(1996) J.Mol.Biol. 256: 223-227

  • DOI: 10.1006/jmbi.1996.0080

  • PubMed Abstract: 
  • Structural studies on unligated and ligated adenylate kinases have shown that two domains, LID and NMPbind, close over the bound substrates, ATP and AMP, respectively. These motions can be, but need not be independent from each other. Up to now, the ...

    Structural studies on unligated and ligated adenylate kinases have shown that two domains, LID and NMPbind, close over the bound substrates, ATP and AMP, respectively. These motions can be, but need not be independent from each other. Up to now, the known structures display only the states "both domains open", "both closed" and "NMP bind closed". In spite of numerous cocrystallization attempts with ATP, a crystalline state "LID closed" has not yet been produced. These experiences suggested that LID closure depends on a bound AMP molecule, in contrast to enzyme kinetic studies indicating a random-bi-bi mechanism. Using an inactive mutant of yeast adenylate kinase together with the ATP analogue AMPPCF2P, however, we have now crystallized an adenylate kinase in the LID closed state. The structure was established at 2.36 A resolution; it indicates that the domain motions occur largely independent from each other in agreement with the kinetic studies. As a side-result, we report the protein environment of the fluorine atoms of the bound ATP analogue.


    Related Citations: 
    • Stability, Activity and Structure of Adenylate Kinase Mutants
      Spuergin, P.,Abele, U.,Schulz, G.E.
      (1995) Eur.J.Biochem. 231: 405
    • 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
    • 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 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
    • Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
      Vonrhein, C.,Schlauderer, G.J.,Schulz, G.E.
      (1995) Structure 3: 483


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie Albertstr. Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE KINASE
A, B
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATF
Query on ATF

Download SDF File 
Download CCD File 
A, B
PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER
C11 H16 F2 N5 O12 P3
ODWAWOIUPXBZKQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.800α = 90.00
b = 73.400β = 90.00
c = 118.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
XDSdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Advisory, Data collection, Other