1QHM

ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1QHM/pdb

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


• Deposited: 1999-05-19 Released: 2000-05-24 
• Deposition Author(s): Leppanen, V.-M., Merckel, M.C., Ollis, D.L., Wong, K.K., Kozarich, J.W., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 

Literature

Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase.

Leppanen, V.M., Merckel, M.C., Ollis, D.L., Wong, K.K., Kozarich, J.W., Goldman, A.

(1999) Structure 7: 733-744

• PubMed: 10425676 
• DOI: https://doi.org/10.1016/S0969-2126(99)80098-7
• Primary Citation of Related Structures:  
  1QHM


• PubMed Abstract: 
  

  Pyruvate formate lyase (PFL) catalyses a key step in Escherichia coli anaerobic glycolysis by converting pyruvate and CoA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate, involving an essential C alpha radical of Gly734 and two cysteine residues, Cys418 and Cys419, which may form thiyl radicals required for catalysis. We undertook this study to understand the structural basis for catalysis.

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Organizational Affiliation: 

Centre for Biotechnology, University of Turku, Finland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.08 kDa 
• Atom Count: 9,810 
• Modelled Residue Count: 1,224 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE FORMATE-LYASE	A, B	624	Escherichia coli	Mutation(s): 0  Gene Names: PFL EC: 2.3.1.54
UniProt
Find proteins for P09373 (Escherichia coli (strain K12)) Explore P09373  Go to UniProtKB:  P09373

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.8	α = 90
b = 140.8	β = 90
c = 215.9	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-24 
Deposition Author(s): Leppanen, V.-M., Merckel, M.C., Ollis, D.L., Wong, K.K., Kozarich, J.W., Goldman, A.

Revision History  

• Version 1.0: 2000-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references