5LNU

Crystal structure of Arabidopsis thaliana Pdx1-I320 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 4.3.3.6
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KIK
Query on KIK

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
(4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one
C5 H9 N O2
UCJPATVGPSMUQX-BYPYZUCNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.117α = 90
b = 178.117β = 90
c = 115.963γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Diamond Light SourceUnited KingdomFunding for PhD of M. Rodrigues

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