1RBO

SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate.

Taylor, T.C.Fothergill, M.D.Andersson, I.

(1996) J Biol Chem 271: 32894-32899

  • DOI: 10.1074/jbc.271.51.32894
  • Primary Citation of Related Structures:  
    1RCO, 1RBO

  • PubMed Abstract: 
  • Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the carboxylation of ribulose 1,5-bisphosphate. The reaction catalyzed by Rubisco involves several steps, some of which can occur as partial reactions, forming intermediates that can ...

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the carboxylation of ribulose 1,5-bisphosphate. The reaction catalyzed by Rubisco involves several steps, some of which can occur as partial reactions, forming intermediates that can be isolated. Analogues of these intermediates are potent inhibitors of the enzyme. We have studied the interactions with the enzyme of two inhibitors, xylulose 1,5-bisphosphate and 4-carboxyarabinitol 1,5-bisphosphate, by x-ray crystallography. Crystals of the complexes were formed by cocrystallization under activating conditions. In addition, 4-carboxyarabinitol 1,5-bisphosphate was soaked into preformed activated crystals of the enzyme. The result of these experiments was the release of the activating CO2 molecule as well as the metal ion from the active site when the inhibitors bound to the enzyme. Comparison with the structure of an activated complex of the enzyme indicates that the structural basis for the release of the activator groups is a distortion of the metal binding site due to the different geometry of the C-3 hydroxyl of the inhibitors. Both inhibitors induce closure of active site loops despite the inactivated state of the enzyme. Xylulose 1,5-bisphosphate binds in a hydrated form at the active site.


    Related Citations: 
    • Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate
      Andersson, I.
      (1996) J Mol Biol 259: 160

    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, P. O. Box 590, S-751 24 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASEBEHL475Spinacia oleraceaMutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
Find proteins for P00875 (Spinacia oleracea)
Explore P00875 
Go to UniProtKB:  P00875
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASECFIS123Spinacia oleraceaMutation(s): 0 
Gene Names: RBCS
EC: 4.1.1.39
Find proteins for P00870 (Spinacia oleracea)
Explore P00870 
Go to UniProtKB:  P00870
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download CCD File 
B, E, H, L
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CAPKd:  0.0001900000061141327   nM  Binding MOAD
CAPKd :  0.0001900000061141327   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.2α = 90
b = 157.2β = 90
c = 201.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Data collection, Derived calculations