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 
  • R-Value Observed: 0.191 

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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
  • Primary Citation of Related Structures:  
    1DVR

  • 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 known structures display only the states "both domains open", "both closed" and "NMP bind closed" ...

    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
    • 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
    • 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
    • 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 Albertstr. Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENYLATE KINASEA, B220Saccharomyces cerevisiaeMutation(s): 2 
EC: 2.7.4.3
UniProt
Find proteins for P07170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07170 
Go to UniProtKB:  P07170
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATF (Subject of Investigation/LOI)
Query on ATF

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.8α = 90
b = 73.4β = 90
c = 118.8γ = 90
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: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection, Other