2IE8 | pdb_00002ie8

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

• PDB DOI: https://doi.org/10.2210/pdb2IE8/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus caldophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.80 Å
• R-Value Free: 
  0.273 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.bbrc.2006.09.151
• Primary Citation Related Structures: 
  2IE8


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.8 kDa 
• Atom Count: 3,101 
• Modeled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.273 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.1	α = 90
b = 71.3	β = 90
c = 80.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description