3FEM | pdb_00003fem

Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3FEM/pdb

• Classification: BIOSYNTHETIC PROTEIN, TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-30 Released: 2009-06-16 
• Deposition Author(s): Strohmeier, M., Windeisen, V., Sinning, I., Tews, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.181 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases.

Neuwirth, M., Strohmeier, M., Windeisen, V., Wallner, S., Deller, S., Rippe, K., Sinning, I., Macheroux, P., Tews, I.

(2009) FEBS Lett 583: 2179-2186

• PubMed: 19523954 
• DOI: https://doi.org/10.1016/j.febslet.2009.06.009
• Primary Citation Related Structures: 
  3FEM


• PubMed Abstract: 
  

  The universal enzymatic cofactor vitamin B6 can be synthesized as pyridoxal 5-phosphate (PLP) by the glutamine amidotransferase Pdx1. We show that Saccharomyces cerevisiae Pdx1 is hexameric by analytical ultracentrifugation and by crystallographic 3D structure determination. Bacterial homologues were previously reported to exist in hexamer:dodecamer equilibrium. A small sequence insertion found in yeast Pdx1 elevates the dodecamer dissociation constant when introduced into Bacillus subtilis Pdx1. Further, we demonstrate that the yeast Pdx1 C-terminus contacts an adjacent subunit, and deletion of this segment decreases enzymatic activity 3.5-fold, suggesting a role in catalysis.

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Organizational Affiliation: 
• Technische Universität Graz, Institut für Biochemie, Graz, Austria.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 191.15 kDa 
• Atom Count: 12,600 
• Modeled Residue Count: 1,686 
• Deposited Residue Count: 1,782 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine biosynthesis protein SNZ1	A, B, C, D, E, F	297	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SNZ1, Snz1p, YM6543.03, YMR096W EC: 4.3.3.6
UniProt
Find proteins for Q03148 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03148  Go to UniProtKB:  Q03148

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.181 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.073	α = 90
b = 154.218	β = 90
c = 154.868	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Strohmeier, M., Windeisen, V., Sinning, I., Tews, I.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description