1H16

Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate and CoA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical for Pyruvate Cleavage

Becker, A., Kabsch, W.

(2002) J Biol Chem 277: 40036

  • DOI: 10.1074/jbc.M205821200
  • Primary Citation of Related Structures:  
    1H18, 1H17, 1H16

  • PubMed Abstract: 

    • The glycyl radical enzyme pyruvate formate-lyase (PFL) synthesizes acetyl-CoA and formate from pyruvate and CoA. With the crystal structure of the non-radical form of PFL in complex with its two substrates, we have trapped the moment prior to pyruvate cleavage ...

    The glycyl radical enzyme pyruvate formate-lyase (PFL) synthesizes acetyl-CoA and formate from pyruvate and CoA. With the crystal structure of the non-radical form of PFL in complex with its two substrates, we have trapped the moment prior to pyruvate cleavage. The structure reveals how the active site aligns the scissile bond of pyruvate for radical attack, prevents non-radical side reactions of the pyruvate, and confines radical migration. The structure shows CoA in a syn conformation awaiting pyruvate cleavage. By changing to an anti conformation, without affecting the adenine binding mode of CoA, the thiol of CoA could pick up the acetyl group resulting from pyruvate cleavage.

    Organizational Affiliation: 

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FORMATE ACETYLTRANSFERASE 1 A759Escherichia coliMutation(s): 0 
EC: 2.3.1.54
Find proteins for P09373 (Escherichia coli (strain K12))
Explore P09373 
Go to UniProtKB:  P09373
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA
Download Ideal Coordinates CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
DTL
Query on DTL
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A
L-TREITOL
C4 H10 O4
UNXHWFMMPAWVPI-IMJSIDKUSA-N		 Ligand Interaction
PYR
Query on PYR
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A
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.9α = 90
b = 153.05β = 90
c = 205.95γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2002-07-03 
  • Released Date: 2002-11-01 
    • Deposition Author(s): Becker, A., Kabsch, W.

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-01
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection