2NV2

Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxal biosynthesis lyase pdxS
A, C, E, G, I, K, M, O
A, C, E, G, I, K, M, O, Q, S, U, W
294Bacillus subtilisMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamine amidotransferase subunit pdxT
B, D, F, H, J, L, N, P
B, D, F, H, J, L, N, P, R, T, V, X
204Bacillus subtilisMutation(s): 1 
EC: 2.6 (PDB Primary Data), 4.3.3.6 (UniProt), 3.5.1.2 (UniProt)
UniProt
Find proteins for P37528 (Bacillus subtilis (strain 168))
Explore P37528 
Go to UniProtKB:  P37528
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download Ideal Coordinates CCD File 
AB [auth P] , CA [auth B] , EB [auth R] , GA [auth D] , GB [auth T] , KA [auth F] , KB [auth V] , NA [auth H] , 
AB [auth P], CA [auth B], EB [auth R], GA [auth D], GB [auth T], KA [auth F], KB [auth V], NA [auth H], NB [auth X], SA [auth J], VA [auth L], YA [auth N]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A] , BA [auth A] , CB [auth Q] , DB [auth Q] , EA [auth C] , FA [auth C] , IA [auth E] , IB [auth U] , 
AA [auth A], BA [auth A], CB [auth Q], DB [auth Q], EA [auth C], FA [auth C], IA [auth E], IB [auth U], JA [auth E], JB [auth U], MA [auth G], MB [auth W], PA [auth I], QA [auth I], RA [auth I], UA [auth K], XA [auth M], Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth Q] , DA [auth C] , FB [auth S] , HA [auth E] , HB [auth U] , LA [auth G] , LB [auth W] , OA [auth I] , 
BB [auth Q], DA [auth C], FB [auth S], HA [auth E], HB [auth U], LA [auth G], LB [auth W], OA [auth I], TA [auth K], WA [auth M], Y [auth A], ZA [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.507α = 90
b = 259.009β = 92.13
c = 144.962γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

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, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations