4MKV

Structure of Pisum sativum Rubisco with ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase.

Galka, M.M.Rajagopalan, N.Buhrow, L.M.Nelson, K.M.Switala, J.Cutler, A.J.Palmer, D.R.Loewen, P.C.Abrams, S.R.Loewen, M.C.

(2015) PLoS One 10: e0133033-e0133033

  • DOI: 10.1371/journal.pone.0133033
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorime ...

    Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a Kd of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (Ki of 2.1 mM), but more potent inhibition of Rubisco activation (Ki of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation.


    Organizational Affiliation

    National Research Council of Canada, Saskatoon, Saskatchewan, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chain
A, B, C, D
458Pisum sativumMutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
Find proteins for P04717 (Pisum sativum)
Go to UniProtKB:  P04717
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
S, T, U, V
123Pisum sativumMutation(s): 0 
Gene Names: RBCS-3A
EC: 4.1.1.39
Find proteins for P07689 (Pisum sativum)
Go to UniProtKB:  P07689
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUB
Query on RUB

Download CCD File 
A, B, C, D
RIBULOSE-1,5-DIPHOSPHATE
C5 H12 O11 P2
YAHZABJORDUQGO-NQXXGFSBSA-N
 Ligand Interaction
A8S
Query on A8S

Download CCD File 
B
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
C15 H20 O4
JLIDBLDQVAYHNE-YKALOCIXSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.44α = 90
b = 110.23β = 90
c = 203.16γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references