3O07

Crystal structure of yeast pyridoxal 5-phosphate synthase Snz1 complexed with substrate G3P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1

Zhang, X.Teng, Y.B.Liu, J.P.He, Y.X.Zhou, K.Chen, Y.Zhou, C.Z.

(2010) Biochem.J. 432: 445-450

  • DOI: 10.1042/BJ20101241
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydro ...

    In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydrolysed from glutamine by a complexed glutaminase. Of the three active sites of DXP (deoxyxylulose 5-phosphate)independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. In the present study, we present the crystal structures of yeast Pdx1/Snz1, in apo-, G3P (glyceraldehyde 3-phosphate)- and PLP-bound forms, at 2.3, 1.8 and 2.2 Å (1 Å=0.1 nm) respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxine biosynthesis protein SNZ1
A, B, C
291Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNZ1
EC: 4.3.3.6
Find proteins for Q03148 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03148
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3H
Query on G3H

Download SDF File 
Download CCD File 
A, B, C
GLYCERALDEHYDE-3-PHOSPHATE
C3 H7 O6 P
LXJXRIRHZLFYRP-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.474α = 90.00
b = 111.972β = 90.00
c = 158.744γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-26
    Type: Database references
  • Version 1.3: 2014-10-22
    Type: Non-polymer description