1GKY

REFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS SUBSTRATE GMP AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution.

Stehle, T.Schulz, G.E.

(1992) J.Mol.Biol. 224: 1127-1141


  • PubMed Abstract: 
  • The crystal structure of guanylate kinase from Saccharomyces cerevisiae complexed with its substrate GMP has been refined at a resolution of 2.0 A. The final crystallographic R-factor is 17.3% in the resolution range 7.0 A to 2.0 A for all reflection ...

    The crystal structure of guanylate kinase from Saccharomyces cerevisiae complexed with its substrate GMP has been refined at a resolution of 2.0 A. The final crystallographic R-factor is 17.3% in the resolution range 7.0 A to 2.0 A for all reflections of the 100% complete data set. The final model has standard geometry with root-mean-square deviations of 0.016 A in bond lengths and 3.0 in bond angles. It consists of all 186 amino acid residues, the N-terminal acetyl group, the substrate GMP, one sulfate ion and 174 water molecules. Guanylate kinase is structurally related to adenylate kinases and G-proteins with respect to its central beta-sheet with connecting helices and the giant anion hole that binds nucleoside triphosphates. These nucleotides are ATP and GTP for the kinases and GTP for the G-proteins. The chain segment binding the substrate GMP of guanylate kinase differs grossly from the respective part of the adenylate kinases; it has no counterpart in the G-proteins. The binding mode of GMP is described in detail. Probably, the observed structure represents one of several structurally quite different intermediate states of the catalytic cycle.


    Related Citations: 
    • Guanylate Kinase from Saccharomyces Cerevisiae. Isolation and Characterization, Crystallization and Preliminary X-Ray Analysis, Amino Acid Sequence and Comparison with Adenylate Kinases
      Berger, A.,Schiltz, E.,Schulz, G.E.
      (1989) Eur.J.Biochem. 184: 433
    • Three-Dimensional Structure of the Complex of Guanylate Kinase from Yeast with its Substrate Gmp
      Stehle, T.,Schulz, G.E.
      (1990) J.Mol.Biol. 211: 249


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GUANYLATE KINASE
A
187Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GUK1
EC: 2.7.4.8
Find proteins for P15454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: GUK1
Go to UniProtKB:  P15454
Small Molecules
Ligands 2 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
5GP
Query on 5GP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 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 Å
  • R-Value Work: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.800α = 90.00
b = 50.800β = 90.00
c = 155.300γ = 90.00
Software Package:
Software NamePurpose
SIMULATEDrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance