Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41804.90 
• Atom Count: 2949 
• Residue Count: 390 
• Unique protein chains: 1

2IE8

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

• DOI: 10.2210/pdb2IE8/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus caldophilus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-09-18 Released: 2006-11-07 
• Deposition Author(s): Lee, J.H., Im, Y.J., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.273 
• R-Value Work: 0.201 

Literature

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

Lee, J.H., Im, Y.J., Bae, J., Kim, D., Kim, M.K., Kang, G.B., Lee, D.S., Eom, S.H.

(2006) Biochem.Biophys.Res.Commun. 350: 1044-1049

• PubMed: 17045964 
• DOI: 10.1016/j.bbrc.2006.09.151


• PubMed Abstract: 
  

Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational change occurs that brings the N- and C-domains of PGK closer together. Here we present the 1.8A crystal structure of unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK (closed conformation) revealed that the conformational change reflects a change in the interaction between the domains. We identified Arg148 as a key residue involved in open-to-closed transition. The open conformation of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation.

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Organizational Affiliation: 

Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
phosphoglycerate kinase	A	390	Thermus caldophilus	Mutation(s): 0  Gene Names: pgk EC: 2.7.2.3
Find proteins for Q08GC7 (Thermus caldophilus) Go to UniProtKB:  Q08GC7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.273 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 65.100	α = 90.00
b = 71.300	β = 90.00
c = 80.200	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing
ADSC	data collection
SCALEPACK	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-18 
• Released Date: 2006-11-07 
• Deposition Author(s): Lee, J.H., Im, Y.J., Eom, S.H.

Revision History 

• Version 1.0: 2006-11-07
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance