1BXN

THE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.7 ANGSTROMS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.

Hansen, S.Vollan, V.B.Hough, E.Andersen, K.

(1999) J.Mol.Biol. 288: 609-621

  • DOI: 10.1006/jmbi.1999.2701

  • PubMed Abstract: 
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is involved in photosynthesis where it catalyzes the initial step in the fixation of carbon dioxide. The enzyme also catalyzes a competing oxygenation reaction leading to loss of fixed carbon ...

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is involved in photosynthesis where it catalyzes the initial step in the fixation of carbon dioxide. The enzyme also catalyzes a competing oxygenation reaction leading to loss of fixed carbon dioxide, thus reducing the net efficiency of photosynthesis significantly. Rubisco has therefore been studied extensively, and a challenging goal is the engineering of a more photosynthetically efficient enzyme. Hexadecameric rubiscos fall in two distinct groups, "green-like" and "red-like". The ability to discriminate between CO2 and O2 as substrates varies significantly, and some algae have red-like rubisco with even higher specificity for CO2 than the plant enzyme. The structure of unactivated rubisco from Alcaligenes eutrophus has been determined to 2.7 A resolution by molecular replacement and refined to R and Rfree values of 26.6 and 32.2 %, respectively. The overall fold of the protein is very similar to the rubisco structures solved previously for green-like hexadecameric enzymes, except for the extended C-terminal domains of the small subunits which together form an eight-stranded beta-barrel which sits as a plug in the entrance to the central solvent channel in the molecule. The present structure is the first which has been solved for a red-like rubisco and is likely to represent a fold which is common for this group. The small subunits in general are believed to have a stabilizing effect, and the new quaternary structure in the oligomer of the present structure is likely to contribute even more to this stabilization of the assembled rubisco protein.


    Related Citations: 
    • Purification, Crystallization and Preliminary X-Ray Studies of Two Isoforms of Rubisco from Alcaligenes Eutrophus
      Hansen, S.,Hough, E.,Andersen, K.
      (1999) Acta Crystallogr.,Sect.D 55: 310


    Organizational Affiliation

    Department of Chemistry, University of Tromso, Tromso, N-9037, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
A, C, E, G
485Cupriavidus necatorGene Names: cbbL1 (cbbL, cbxLC, cfxLC)
EC: 4.1.1.39
Find proteins for P0C2C2 (Cupriavidus necator)
Go to UniProtKB:  P0C2C2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
I, J, K, L
139Cupriavidus necatorGene Names: cbxSC (cbbS, cfxSC, rbcS)
EC: 4.1.1.39
Find proteins for P09658 (Cupriavidus necator)
Go to UniProtKB:  P09658
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.266 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.000α = 90.00
b = 112.000β = 90.00
c = 402.700γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description