1MZO | pdb_00001mzo

Crystal structure of pyruvate formate-lyase with pyruvate

• PDB DOI: https://doi.org/10.2210/pdb1MZO/pdb

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


• Deposited: 2002-10-09 Released: 2002-12-11 
• Deposition Author(s): Lehtio, L., Leppanen, V.-M., Kozarich, J.W., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

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

• PubMed: 12454503 
• DOI: https://doi.org/10.1107/s0907444902016402
• Primary Citation Related Structures: 
  1MZO


• 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.

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Organizational Affiliation: 
• Institute of Biotechnology, University of Helsinki, PO Box 65, FIN-00014, Helsinki, 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: 170.98 kDa 
• Atom Count: 12,467 
• Modeled Residue Count: 1,512 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate formate-lyase	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PYR	D [auth A], E [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.191 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.355	α = 90
b = 158.355	β = 90
c = 159.3	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Lehtio, L., Leppanen, V.-M., Kozarich, J.W., Goldman, A.

Revision History  

• 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