7NHF | pdb_00007nhf

Crystal structure of Arabidopsis thaliana Pdx1K166R

• PDB DOI: https://doi.org/10.2210/pdb7NHF/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-02-10 Released: 2021-12-22 
• Deposition Author(s): Rodrigues, M.J., Zhang, Y., Bolton, R., Evans, G., Giri, N., Royant, A., Begley, T., Ealick, S.E., Tews, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.249 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase.

Rodrigues, M.J., Giri, N., Royant, A., Zhang, Y., Bolton, R., Evans, G., Ealick, S.E., Begley, T., Tews, I.

(2022) RSC Chem Biol 3: 227-230

• PubMed: 35360887 
• DOI: https://doi.org/10.1039/d1cb00160d
• Primary Citation Related Structures: 
  7NHE, 7NHF


• PubMed Abstract: 
  

  The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I ₃₃₃ intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis.

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Organizational Affiliation: 
• Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK [e-mail].
Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK.
Department of Chemistry, Texas A&M University College Station TX 77843 USA.
Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), CS 10090 Grenoble Cedex 9 38044 France.
European Synchrotron Radiation Facility, CS 40220 Grenoble Cedex 9 38043 France.
Department of Chemistry and Chemical Biology, Cornell University Ithaca NY 14853 USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 125.22 kDa 
• Atom Count: 7,975 
• Modeled Residue Count: 1,072 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal 5'-phosphate synthase subunit PDX1.3	A, B, C, D	291	Arabidopsis thaliana	Mutation(s): 1  Gene Names: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 EC: 4.3.3.6
UniProt
Find proteins for Q8L940 (Arabidopsis thaliana) Explore Q8L940  Go to UniProtKB:  Q8L940

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth B], G [auth C], H [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.249 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.001	α = 90
b = 178.001	β = 90
c = 115.127	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Rodrigues, M.J., Zhang, Y., Bolton, R., Evans, G., Giri, N., Royant, A., Begley, T., Ealick, S.E., Tews, I.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description