3ADK

REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution.

Dreusicke, D.Karplus, P.A.Schulz, G.E.

(1988) J Mol Biol 199: 359-371

  • DOI: 10.1016/0022-2836(88)90319-1
  • Primary Citation of Related Structures:  
    3ADK

  • PubMed Abstract: 
  • The crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0 ...

    The crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0.026 A in bond lengths and 3.3 degrees in bond angles. In comparison with the previous structure at 3 A resolution, there is a significant improvement. The high resolution structure has been used to rationalize the strictly conserved residues in the adenylate kinase family. Among these is the glycine-rich loop, which forms a giant anion hole accommodating a sulfate ion which mimics a phosphoryl group of a substrate. Such a structure seems to occur in a large group of mononucleotide binding proteins. Moreover, a conserved cis-proline has been detected in the active center. A structural comparison with the complex between adenylate kinase from yeast and a substrate-analog at medium resolution indicates that this kinase performs appreciable mechanical movements during a catalytic cycle. The reported structure presumably represents an open form of the enzyme, similar to that in solution in the absence of substrates. However, since there are large intermolecular contacts in the crystal, some deviation from the solution structure has to be expected.


    Related Citations: 
    • Structural Relationships in the Adenylate Kinase Family
      Schulz, G.E., Schiltz, E., Tomasselli, A.G., Frank, R., Brune, M., Wittinghofer, A., Schirmer, R.H.
      (1986) Eur J Biochem 161: 127
    • The Glycine-Rich Loop of Adenylate Kinase Forms a Giant Anion Hole
      Dreusicke, D., Schulz, G.E.
      (1986) FEBS Lett 208: 301
    • Two Conformations of Crystalline Adenylate Kinase
      Sachsenheimer, W., Schulz, G.E.
      (1977) J Mol Biol 114: 23
    • Substrate Positions and Induced-Fit in Crystalline Adenylate Kinase
      Pai, E.F., Sachsenheimer, W., Schirmer, R.H., Schulz, G.E.
      (1977) J Mol Biol 114: 37
    • Three-Dimensional Structure of Adenylate Kinase
      Schulz, G.E., Elzinga, M., Marx, F., Schirmer, R.H.
      (1974) Nature 250: 120
    • Topological Comparison of Adenylate Kinase with Other Proteins
      Schulz, G.E., Schirmer, R.H.
      (1974) Nature 250: 142
    • Comparison of Predicted and Experimentally Determined Secondary Structure of Adenylate Kinase
      Schulz, G.E., Barry, C.D., Friedman, J., Chou, P.Y., Fasman, G.D., Finkelstein, A.V., Lim, V.I., Ptitsyn, O.B., Kabat, E.A., Wu, T.T., Levitt, M., Robson, B., Nagano, K.
      (1974) Nature 250: 140
    • The Amino-Acid Sequence of Porcine Adenylate Kinase from Skeletal Muscle
      Heil, A., Mueller, G., Noda, L., Pinder, T., Schirmer, H., Schirmer, I., Vonzabern, I.
      (1974) Eur J Biochem 43: 131
    • Low Resolution Structure of Adenylate Kinase
      Schulz, G.E., Biedermann, K., Kabsch, W., Schirmer, R.H.
      (1973) J Mol Biol 80: 857

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie der Universität, Freiburg i.Br., Federal Republic of Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENYLATE KINASEA195Sus scrofaMutation(s): 0 
Gene Names: AK1
EC: 2.7.4.3 (PDB Primary Data), 2.7.4.6 (UniProt)
UniProt
Find proteins for P00571 (Sus scrofa)
Explore P00571 
Go to UniProtKB:  P00571
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.5α = 90
b = 48.5β = 90
c = 141γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1987-11-19 
  • Released Date: 1988-01-16 
  • Deposition Author(s): Schulz, G.E.
  • This entry supersedes: 2ADK

Revision History  (Full details and data files)

  • Version 1.0: 1988-01-16
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance