Crystal structure of pyruvate formate-lyase with pyruvate

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Structure of Escherichia coli pyruvate formate-lyase with pyruvate.

Lehtio, L.Leppanen, V.M.Kozarich, J.W.Goldman, A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 2209-2212

  • DOI: https://doi.org/10.1107/s0907444902016402
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of inactive pyruvate formate-lyase in complex with a natural substrate, pyruvate, was solved at 2.7 A resolution. Both active sites of the homodimeric enzyme are occupied by pyruvate; additional binding sites were not found. Pyruvate was found in a cleft close to the active-site cysteines 418 and 419, with the carboxyl group in contact with arginines 176 and 435 and the methyl group within van der Waals distance of Phe327. It is believed that the binding site of pyruvate is not the position of pyruvate as the reaction initiates, as conformational changes occur during activation of the enzyme.

  • Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, PO Box 65, FIN-00014, Helsinki, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate formate-lyase
A, B
759Escherichia coliMutation(s): 0 
Find proteins for P09373 (Escherichia coli (strain K12))
Explore P09373 
Go to UniProtKB:  P09373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09373
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.355α = 90
b = 158.355β = 90
c = 159.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    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, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection