Crystal structure of Arabidopsis thaliana Pdx1-PLP complex

Experimental Data Snapshot

  • Resolution: 1.61 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

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Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.

Rodrigues, M.J.Windeisen, V.Zhang, Y.Guedez, G.Weber, S.Strohmeier, M.Hanes, J.W.Royant, A.Evans, G.Sinning, I.Ealick, S.E.Begley, T.P.Tews, I.

(2017) Nat Chem Biol 13: 290-294

  • DOI: https://doi.org/10.1038/nchembio.2273
  • Primary Citation of Related Structures:  
    5LNR, 5LNS, 5LNT, 5LNU, 5LNV, 5LNW

  • PubMed Abstract: 

    Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in the transfer of carbonyl-group-containing intermediates, despite their wideuse in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I 320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand β6 of the Pdx1 (βα) 8 -barrel. The dual-specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions that follow a path of over 20 Å between substrate- and product-binding sites.

  • Organizational Affiliation

    Biological Sciences, University of Southampton, Southampton, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal 5'-phosphate synthase subunit PDX1.3
A, B, C, D
316Arabidopsis thalianaMutation(s): 0 
Gene Names: PDX13GIP2PDX1L3RSR4At5g01410T10O8.120
Find proteins for Q8L940 (Arabidopsis thaliana)
Explore Q8L940 
Go to UniProtKB:  Q8L940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L940
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
C8 H10 N O6 P
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.61 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.56α = 90
b = 178.56β = 90
c = 116.881γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references