4RYV

Crystal structure of yellow lupin LLPR-10.1A protein in complex with trans-zeatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 55-66

  • DOI: 10.1016/j.jsb.2015.11.008
  • Primary Citation of Related Structures:  
  • Also Cited By: 5I8F, 5MXW, 5MXB

  • PubMed Abstract: 
  • Plant pathogenesis-related class 10 (PR-10) proteins are a family of abundant proteins initially identified as elements of the plant defense system. The key structural feature suggesting PR-10 functionality is a huge hydrophobic cavity created in the ...

    Plant pathogenesis-related class 10 (PR-10) proteins are a family of abundant proteins initially identified as elements of the plant defense system. The key structural feature suggesting PR-10 functionality is a huge hydrophobic cavity created in the protein interior by a scaffold composed of an extended β-sheet wrapped around a long and flexible C-terminal α-helix. Several crystallographic and NMR studies have shown that the cavity can accommodate a variety of small molecule ligands, including phytohormones. The article describes ∼1.3 Å resolution crystal structures of a Lupinus luteus PR-10 isoform LlPR-10.1A, in its free form and in complex with trans-zeatin, a naturally occurring plant hormone belonging to the cytokinin group. Moreover we present the structure of the same protein where the saturation with zeatin is not complete. This set of three crystal structures allows us to track the structural adaptation of the protein upon trans-zeatin docking, as well as the sequence of the ligand-binding events, step-by-step. In addition, titration of LlPR-10.1A with trans-zeatin monitored in solution by CD spectra, confirmed the pattern of structural adaptations deduced from the crystallographic studies. The ligand-biding mode shows no similarity to other zeatin complexes of PR-10 proteins. The present work, which describes the first atomic models of the same PR-10 protein with and without a physiological ligand, reveals that the conformation of LlPR-10.1A undergoes a significant structural rearrangement upon trans-zeatin binding.


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein LLPR-10.1A
A
155Lupinus luteusMutation(s): 0 
Gene Names: LLR18A
EC: 3.1.27.-
Find proteins for P52778 (Lupinus luteus)
Go to UniProtKB:  P52778
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZEA
Query on ZEA

Download SDF File 
Download CCD File 
A
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
TRANS-ZEATIN
C10 H13 N5 O
UZKQTCBAMSWPJD-FARCUNLSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.970α = 90.00
b = 63.910β = 126.68
c = 47.560γ = 90.00
Software Package:
Software NamePurpose
IS4CCDIdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Database references
  • Version 1.2: 2016-01-13
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection