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

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal biosynthesis lyase pdxS
A, B, C, D, E
A, B, C, D, E, F
305Bacillus subtilisMutation(s): 0 
EC: 4
Find proteins for P37527 (Bacillus subtilis (strain 168))
Explore P37527 
Go to UniProtKB:  P37527
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37527
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth D]
JA [auth E]
L [auth A]
M [auth A]
NA [auth F]
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]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
G [auth A]
GA [auth E]
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]
Query on MG

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
HA [auth E]
I [auth A]
IA [auth E]
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]
Experimental Data & Validation

Experimental Data

  • 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 = 101.055α = 90
b = 106.202β = 90
c = 182.332γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description