3ADK

REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 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


  • 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% ...

    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: 
    • 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
    • The Glycine-Rich Loop of Adenylate Kinase Forms a Giant Anion Hole
      Dreusicke, D.,Schulz, G.E.
      (1986) FEBS Lett. 208: 301
    • Topological Comparison of Adenylate Kinase with Other Proteins
      Schulz, G.E.,Schirmer, R.H.
      (1974) Nature 250: 142
    • 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
    • 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
    • Three-Dimensional Structure of Adenylate Kinase
      Schulz, G.E.,Elzinga, M.,Marx, F.,Schirmer, R.H.
      (1974) Nature 250: 120
    • Two Conformations of Crystalline Adenylate Kinase
      Sachsenheimer, W.,Schulz, G.E.
      (1977) J.Mol.Biol. 114: 23
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE KINASE
A
195Sus scrofaMutation(s): 0 
Gene Names: AK1
EC: 2.7.4.3, 2.7.4.6
Find proteins for P00571 (Sus scrofa)
Go to Gene View: AK1
Go to UniProtKB:  P00571
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.500α = 90.00
b = 48.500β = 90.00
c = 141.000γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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