2W93 | pdb_00002w93

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide

• PDB DOI: https://doi.org/10.2210/pdb2W93/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-21 Released: 2009-02-03 
• Deposition Author(s): Kutter, S., Weiss, M.S., Konig, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story.

Konig, S., Spinka, M., Kutter, S.

(2014) J Mol Catal B Enzym 61: 100

• DOI: https://doi.org/10.1016/J.MOLCATB.2009.02.010

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 248.93 kDa 
• Atom Count: 18,690 
• Modeled Residue Count: 2,225 
• Deposited Residue Count: 2,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DECARBOXYLASE ISOZYME 1	A, B, C, D	563	Saccharomyces cerevisiae	Mutation(s): 1  EC: 4.1.1.1 (PDB Primary Data), 4.1.1.74 (UniProt), 4.1.1.72 (UniProt), 4.1.1.43 (UniProt), 4.1.1 (UniProt)
UniProt
Find proteins for P06169 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06169  Go to UniProtKB:  P06169

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	E [auth A], I [auth B], M [auth C], Q [auth D]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
PY0	G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate C3 H8 N O3 ISJWJWXATCJUBY-STHAYSLISA-N
MG	F [auth A], J [auth B], N [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.05	α = 89.23
b = 79.22	β = 73.32
c = 109.09	γ = 62.43

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Kutter, S., Weiss, M.S., Konig, S.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-07-10
  Changes: Data collection, Derived calculations
• Version 1.5: 2019-07-24
  Changes: Data collection
• Version 1.6: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary