5MXB

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

PR-10 proteins as potential mediators of melatonin-cytokinin cross-talk in plants: crystallographic studies of LlPR-10.2B isoform from yellow lupine.

Sliwiak, J.Sikorski, M.Jaskolski, M.

(2018) FEBS J 285: 1907-1922

  • DOI: 10.1111/febs.14455
  • Primary Citation of Related Structures:  
    5MXW, 5MXB

  • PubMed Abstract: 
  • LlPR-10.2B, a Pathogenesis-related class 10 (PR-10) protein from yellow lupine (Lupinus luteus) was crystallized in complex with melatonin, an emerging important plant regulator and antioxidant. The structure reveals two molecules of melatonin bound ...

    LlPR-10.2B, a Pathogenesis-related class 10 (PR-10) protein from yellow lupine (Lupinus luteus) was crystallized in complex with melatonin, an emerging important plant regulator and antioxidant. The structure reveals two molecules of melatonin bound in the internal cavity of the protein, plus a very well-defined electron density near the cavity entrance, corresponding to an unknown ligand molecule comprised of two flat rings, which is most likely a product of melatonin transformation. In a separate LlPR-10.2B co-crystallization experiment with an equimolar mixture of melatonin and trans-zeatin, which is a cytokinin phytohormone well recognized as a PR-10-binding partner, a quaternary 1 : 1 : 1 : 1 complex was formed, in which one of the melatonin-binding sites has been substituted with trans-zeatin, whereas the binding of melatonin at the second binding site and binding of the unknown ligand are undisturbed. This unusual complex, when compared with the previously described PR-10/trans-zeatin complexes and with the emerging structural information about melatonin binding by PR-10 proteins, provides intriguing insights into the role of PR-10 proteins in phytohormone regulation in plants, especially with the involvement of melatonin, and implicates the PR-10 proteins as low-affinity melatonin binders under the conditions of elevated melatonin concentration.


    Related Citations: 
    • Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.
      Sliwiak, J., Dauter, Z., Jaskolski, M.
      (2016) Front Plant Sci 7: 668
    • Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.
      Sliwiak, J., Dolot, R., Michalska, K., Szpotkowski, K., Bujacz, G., Sikorski, M., Jaskolski, M.
      (2016) J Struct Biol 193: 55
    • Specific binding of gibberellic acid by cytokinin-specific binding proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold.
      Ruszkowski, M., Sliwiak, J., Ciesielska, A., Barciszewski, J., Sikorski, M., Jaskolski, M.
      (2014) Acta Crystallogr D Biol Crystallogr 70: 2032
    • ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.
      Sliwiak, J., Dauter, Z., Kowiel, M., McCoy, A.J., Read, R.J., Jaskolski, M.
      (2015) Acta Crystallogr D Biol Crystallogr 71: 829
    • Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.
      Fernandes, H., Bujacz, A., Bujacz, G., Jelen, F., Jasinski, M., Kachlicki, P., Otlewski, J., Sikorski, M.M., Jaskolski, M.
      (2009) FEBS J 276: 1596
    • Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.
      Fernandes, H., Pasternak, O., Bujacz, G., Bujacz, A., Sikorski, M.M., Jaskolski, M.
      (2008) J Mol Biol 378: 1040
    • Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.
      Pasternak, O., Biesiadka, J., Dolot, R., Handschuh, L., Bujacz, G., Sikorski, M.M., Jaskolski, M.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 99
    • Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
      Biesiadka, J., Bujacz, G., Sikorski, M.M., Jaskolski, M.
      (2002) J Mol Biol 319: 1223
    • Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin.
      Pasternak, O., Bujacz, G.D., Fujimoto, Y., Hashimoto, Y., Jelen, F., Otlewski, J., Sikorski, M.M., Jaskolski, M.
      (2006) Plant Cell 18: 2622
    • The landscape of cytokinin binding by a plant nodulin.
      Ruszkowski, M., Szpotkowski, K., Sikorski, M., Jaskolski, M.
      (2013) Acta Crystallogr D Biol Crystallogr 69: 2365

    Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Class 10 plant pathogenesis-related proteinA155Lupinus luteusMutation(s): 0 
Gene Names: PR10.2BYpr10.2b
EC: 3.1.27
Find proteins for Q9LLQ2 (Lupinus luteus)
Explore Q9LLQ2 
Go to UniProtKB:  Q9LLQ2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ML1
Query on ML1

Download CCD File 
A
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide
C13 H16 N2 O2
DRLFMBDRBRZALE-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A
Unknown ligand
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.469α = 90
b = 74.469β = 90
c = 67.11γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BioStruct-X283570
European UnionFP7/2007-20013

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references