1QJO | pdb_00001qjo

INNERMOST LIPOYL DOMAIN OF THE PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb1QJO/pdb

• Classification: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-06-29 Released: 1999-06-30 
• Deposition Author(s): Jones, D.D., Howard, M.J., Perham, R.N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 30 

Literature

Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli.

Jones, D.D., Stott, K.M., Howard, M.J., Perham, R.N.

(2000) Biochemistry 39: 8448-8459

• PubMed: 10913250 
• DOI: https://doi.org/10.1021/bi992978i
• Primary Citation Related Structures: 
  1QJO


• PubMed Abstract: 
  

  The three lipoyl (E2plip) domains of the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase (PDH) complex of Escherichia coli house the lipoyl-lysine side chain essential for active-site coupling and substrate channelling within the complex. The structure of the unlipoylated form of the innermost domain (E2plip(apo)) was determined by multidimensional NMR spectroscopy and found to resemble closely that of a nonfunctional hybrid domain determined previously [Green et al. (1995) J. Mol. Biol. 248, 328-343]. The domain comprises two four-stranded beta-sheets, with the target lysine residue residing at the tip of a type-I beta-turn in one of the sheets; the N- and C-termini lie close together at the opposite end of the molecule in the other beta-sheet. Measurement of (15)N NMR relaxation parameters and backbone hydrogen/deuterium (H/D) exchange rates reveals that the residues in and surrounding the lipoyl-lysine beta-turn in the E2plip(apo) form of the domain become less flexible after lipoylation of the lysine residue. This implies that the lipoyl-lysine side chain may not sample the full range of conformational space once thought. Moreover, reductive acetylation of the lipoylated domain (E2plip(holo) --> E2plip(redac)) was accompanied by large changes in chemical shift between the two forms, and multiple resonances were observed for several residues. This implies a change in conformation and the existence of multiple conformations of the domain on reductive acetylation, which may be important in stabilizing this catalytic intermediate.

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Organizational Affiliation: 
• Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.38 kDa 
• Atom Count: 584 
• Modeled Residue Count: 80 
• Deposited Residue Count: 80 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROLIPOAMIDE ACETYLTRANSFERASE	A	80	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: E2P_ECOLI EC: 2.3.1.12
UniProt
Find proteins for P06959 (Escherichia coli (strain K12)) Explore P06959  Go to UniProtKB:  P06959

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 30 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-30 
Deposition Author(s): Jones, D.D., Howard, M.J., Perham, R.N.

Revision History  

• Version 1.0: 1999-06-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references