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 

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:  

  • 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 pyruvat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMATE ACETYLTRANSFERASE 1
A
759Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pflB (pfl)
EC: 2.3.1.54
Find proteins for P09373 (Escherichia coli (strain K12))
Go to UniProtKB:  P09373
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTL
Query on DTL
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A
L-TREITOL
C4 H10 O4
UNXHWFMMPAWVPI-IMJSIDKUSA-N
 Ligand Interaction
NA
Query on NA
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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR
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A
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA
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A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
PG4
Query on PG4
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A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 54.900α = 90.00
b = 153.050β = 90.00
c = 205.950γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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