Biological Assembly 1  

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: 199.46 kDa 
• Atom Count: 13,822 
• Modelled Residue Count: 1,529 
• Deposited Residue Count: 1,830 
• Unique protein chains: 1

 2NV1

Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis

• PDB DOI:  https://doi.org/10.2210/pdb2NV1/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-10 Released: 2006-12-05 
• Deposition Author(s): Strohmeier, M., Tews, I., Sinning, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.191 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

Literature

Structure of a bacterial pyridoxal 5'-phosphate synthase complex

Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B., Tews, I.

(2006) Proc Natl Acad Sci U S A 103: 19284-19289

• PubMed: 17159152 
• DOI: https://doi.org/10.1073/pnas.0604950103
• Primary Citation of Related Structures:  
  2NV0, 2NV1, 2NV2


• PubMed Abstract: 
  

Vitamin B6 is an essential metabolic cofactor that has more functions in humans than any other single nutrient. Its de novo biosynthesis occurs through two mutually exclusive pathways that are absent in animals. The predominant pathway found in most prokaryotes, fungi, and plants has only recently been discovered. It is distinguished by a glutamine amidotransferase, which is remarkable in that it alone can synthesize the cofactor form, pyridoxal 5'-phosphate (PLP), directly from a triose and a pentose saccharide and glutamine. Here we report the 3D structure of the PLP synthase complex with substrate glutamine bound as well as those of the individual synthase and glutaminase subunits Pdx1 and Pdx2, respectively. The complex is made up of 24 protein units assembled like a cogwheel, a dodecameric Pdx1 to which 12 Pdx2 subunits attach. In contrast to the architecture of previously determined glutamine amidotransferases, macromolecular assembly is directed by an N-terminal alpha-helix on the synthase. Interaction with the synthase subunit leads to glutaminase activation, resulting in formation of an oxyanion hole, a prerequisite for catalysis. Mutagenesis permitted identification of the remote glutaminase and synthase catalytic centers and led us to propose a mechanism whereby ammonia shuttles between these active sites through a methionine-rich hydrophobic tunnel.

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Organizational Affiliation: 

Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal biosynthesis lyase pdxS	A, B, C, D, E, F	305	Bacillus subtilis	Mutation(s): 0  EC: 4 (PDB Primary Data), 4.3.3.6 (UniProt)
UniProt
Find proteins for P37527 (Bacillus subtilis (strain 168)) Explore P37527  Go to UniProtKB:  P37527

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	EA [auth D], JA [auth E], L [auth A], M [auth A], NA [auth F], OA [auth F], Q [auth B], R [auth B], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth D], BA [auth D], FA [auth E], G [auth A], GA [auth E], H [auth A], KA [auth F], LA [auth F], N [auth B], O [auth B], S [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	CA [auth D], DA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], MA [auth F], P [auth B], U [auth C], V [auth C], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.191 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.055	α = 90
b = 106.202	β = 90
c = 182.332	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Strohmeier, M., Tews, I., Sinning, I.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance