5LNT

Crystal structure of Arabidopsis thaliana Pdx1K166R-preI320 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

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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

    Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal 5'-phosphate synthase subunit PDX1.1
A, B, C, D
316Arabidopsis thalianaMutation(s): 0 
Gene Names: PDX11PDX1L1At2g38230F16M14.16
EC: 4.3.3.6
UniProt
Find proteins for O80448 (Arabidopsis thaliana)
Explore O80448 
Go to UniProtKB:  O80448
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO80448
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.9α = 90
b = 177.9β = 90
c = 115.02γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyTE 368

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