13PK

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.

Bernstein, B.E.Michels, P.A.Hol, W.G.

(1997) Nature 385: 275-278

  • DOI: 10.1038/385275a0

  • PubMed Abstract: 
  • Phosphoglycerate kinase (PGK), a key enzyme in glycolysis, catalyses the transfer of a phosphoryl-group from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP. Despite extensive kinetic and structural investigations over more than two ...

    Phosphoglycerate kinase (PGK), a key enzyme in glycolysis, catalyses the transfer of a phosphoryl-group from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP. Despite extensive kinetic and structural investigations over more than two decades, the conformation assumed by this enzyme during catalysis remained unknown. Here we present the 2.8 A crystal structure of a ternary complex of PGK from Trypanosoma brucei, the causative agent of sleeping sickness. This structure determination relied on a procedure in which fragments containing less than 10% of the scattering mass were successively positioned in the unit cell to obtain phases. The PGK ternary complex exhibits a dramatic closing of the large cleft between the two domains seen in all previous studies, thereby bringing the two ligands, 3-phosphoglycerate and ADP into close proximity. Our results demonstrate that PGK is a hinge-bending enzyme, reveal a novel mechanism in which substrate-induced effects combine synergistically to induce major conformational changes and, to our knowledge, afford the first observation of the PGK active site in a catalytic conformation.


    Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-PHOSPHOGLYCERATE KINASE
A, B, C, D
415Trypanosoma brucei bruceiEC: 2.7.2.3
Find proteins for P07378 (Trypanosoma brucei brucei)
Go to UniProtKB:  P07378
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A, B
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.213α = 90.00
b = 115.959β = 90.00
c = 171.327γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance