1H16

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

• PDB DOI: https://doi.org/10.2210/pdb1H16/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Mutation(s): No 


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

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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 

Starting Model: experimental

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

• PubMed: 12163496 
• DOI: https://doi.org/10.1074/jbc.M205821200
• Primary Citation of Related Structures:  
  1H16, 1H17, 1H18


• 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 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.

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Organizational Affiliation: 

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

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 87.2 kDa 
• Atom Count: 7,593 
• Modelled Residue Count: 759 
• Deposited Residue Count: 759 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE ACETYLTRANSFERASE 1	A	759	Escherichia coli	Mutation(s): 0  EC: 2.3.1.54
UniProt
Find proteins for P09373 (Escherichia coli (strain K12)) Explore P09373  Go to UniProtKB:  P09373

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PG4	N [auth A], O [auth A], P [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
DTL	L [auth A], M [auth A]	L-TREITOL C4 H10 O4 UNXHWFMMPAWVPI-IMJSIDKUSA-N
PYR	C [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
MG	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 54.9	α = 90
b = 153.05	β = 90
c = 205.95	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-12-13
  Changes: Refinement description