1QPG

3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate.

McPhillips, T.M.Hsu, B.T.Sherman, M.A.Mas, M.T.Rees, D.C.

(1996) Biochemistry 35: 4118-4127

  • DOI: 10.1021/bi952500o

  • PubMed Abstract: 
  • The structure of a ternary complex of the R65Q mutant of yeast 3-phosphoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate (Mg-AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-ray crystallography to 2.4 angstrom resol ...

    The structure of a ternary complex of the R65Q mutant of yeast 3-phosphoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate (Mg-AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-ray crystallography to 2.4 angstrom resolution. The structure was solved by single isomorphous replacement, anamalous scattering, and solvent flattening and has been refined to an R-factor of 0.185, with rms deviations from ideal bond distance and angles of 0.009 angstrom and 1.78 degrees, respectively. PGK consists of two domains, with the 3-PG bound to a "basic patch" of residues from the N-terminal domain and the Mg-AMP-PNP interacting with residues from the C-terminal domain. The two ligands are separated by approximately 11 angstrom across the interdomain cleft. The model of the R65Q mutant of yeast PGK is very similar to the structures of PGK isolated from horse, pig, and Bacillus stearothermophilus (rms deviations between equivalent alpha-carbons in the individual domains < 1.0 angstrom) but exhibits substantial variations with a previously reported yeast structure (rms deviations between equivalent alpha-carbons in the individual domains of 2.9-3.2 angstrom). The most significant tertiary structural differences among the yeast R65Q, equine, porcine, and B. stearothermophilus PGK structures occur in the relative orientations of the two domains. However, the relationships between the observed conformations of PGK are inconsistent with a "hinge-bending" behavior that would close the interdomain cleft. It is proposed that the available structural and biochemical data on PGK may indicate that the basic patch primarily represents the site of anion activation and not the catalytically active binding site for 3-PG.


    Related Citations: 
    • Site-Directed Mutations of Arginine 65 at the Periphery of the Active Site Cleft of Yeast 3-Phosphoglycerate Kinase Enhance the Catalytic Activity and Eliminate Anion-Dependent Activation
      Sherman, M.A.,Dean, S.A.,Mathiowetz, A.M.,Mas, M.T.
      (1991) Protein Eng. 4: 935
    • Characterization of the Structure and Properties of the His 62-->Ala and Arg 38-->Ala Mutants of Yeast Phosphoglycerate Kinase: An Investigation of the Catalytic and Activatory Sites by Site-Directed Mutagenesis and NMR
      Sherman, M.A.,Fairbrother, W.J.,Mas, M.T.
      (1992) Protein Sci. 1: 752
    • Probing the Role of Arginines and Histidines in the Catalytic Function and Activation of Yeast 3-Phosphoglycerate Kinase by Site-Directed Mutagenesis
      Sherman, M.A.,Szpikowska, B.K.,Dean, S.A.,Mathiowetz, A.M.,Mcqueen, N.L.,Mas, M.T.
      (1990) J.Biol.Chem. 265: 10659


    Organizational Affiliation

    Division of Chemistry, California Institute of Technology, Pasadena, 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-PHOSPHOGLYCERATE KINASE
A
415Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PGK1
EC: 2.7.2.3
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PGK1
Go to UniProtKB:  P00560
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
MAP
Query on MAP

Download SDF File 
Download CCD File 
A
MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE
C10 H16 Mg N6 O12 P3
QTQJEIANUKJRTB-RSYYIFEXDO
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MP3Kd: 110000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.000α = 90.00
b = 70.100β = 122.20
c = 82.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
TNTrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance