Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 212012.92 
• Atom Count: 11142 
• Residue Count: 1950 
• Unique protein chains: 1

1ZNN

Structure of the synthase subunit of PLP synthase

• DOI: 10.2210/pdb1ZNN/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Geobacillus kaustophilus (strain HTA426)


• Deposited: 2005-05-11 Released: 2005-05-24 
• Deposition Author(s): Zhu, J., Burgner, J.W., Harms, E., Belitsky, B.R., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.198 
• R-Value Work: 0.159 

Literature

A New Arrangement of (beta/alpha)8 Barrels in the Synthase Subunit of PLP Synthase.

Zhu, J., Burgner, J.W., Harms, E., Belitsky, B.R., Smith, J.L.

(2005) J.Biol.Chem. 280: 27914-27923

• PubMed: 15911615 
• DOI: 10.1074/jbc.M503642200


• PubMed Abstract: 
  

Pyridoxal 5'-phosphate (PLP, vitamin B6), a cofactor in many enzymatic reactions, has two distinct biosynthetic routes, which do not coexist in any organism. Two proteins, known as PdxS and PdxT, together form a PLP synthase in plants, fungi, archaea, and some eubacteria. PLP synthase is a heteromeric glutamine amidotransferase in which PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. In the 2.2-A crystal structure, PdxS is a cylindrical dodecamer of subunits having the classic (beta/alpha)8 barrel fold. PdxS subunits form two hexameric rings with the active sites positioned on the inside. The hexamer and dodecamer forms coexist in solution. A novel phosphate-binding site is suggested by bound sulfate. The sulfate and another bound molecule, methyl pentanediol, were used to model the substrate ribulose 5-phosphate, and to propose catalytic roles for residues in the active site. The distribution of conserved surfaces in the PdxS dodecamer was used to predict a docking site for the glutaminase partner, PdxT.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PLP SYNTHASE	A, B, C, D, E, F	325	Geobacillus kaustophilus (strain HTA426)	Mutation(s): 0  Gene Names: pdxS EC: 4.3.3.6
Find proteins for Q5L3Y2 (Geobacillus kaustophilus (strain HTA426)) Go to UniProtKB:  Q5L3Y2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D, E, F	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MRD	A, B, C, D, E, F	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.198 
• R-Value Work: 0.159 
• Space Group: C 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 162.531	α = 90.00
b = 163.917	β = 90.00
c = 186.804	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SHELXS	phasing
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-11 
• Released Date: 2005-05-24 
• Deposition Author(s): Zhu, J., Burgner, J.W., Harms, E., Belitsky, B.R., Smith, J.L.

Revision History 

• Version 1.0: 2005-05-24
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance