9RUB

CRYSTAL STRUCTURE OF ACTIVATED RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE COMPLEXED WITH ITS SUBSTRATE, RIBULOSE-1,5-BISPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate.

Lundqvist, T.Schneider, G.

(1991) J.Biol.Chem. 266: 12604-12611


  • PubMed Abstract: 
  • The three-dimensional structure of the complex of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum, CO2, Mg2+, and ribulose bisphosphate has been determined with x-ray crystallographic methods to 2.6-A resolution. Ribulose-1,5-bisphos ...

    The three-dimensional structure of the complex of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum, CO2, Mg2+, and ribulose bisphosphate has been determined with x-ray crystallographic methods to 2.6-A resolution. Ribulose-1,5-bisphosphate binds across the active site with the two phosphate groups in the two phosphate binding sites of the beta/alpha barrel. The oxygen atoms of the carbamate and the side chain of Asp-193 provide the protein ligands to the bound Mg2+ ion. The C2 and the C3 or C4 oxygen atoms of the substrate are also within the first coordination sphere of the metal ion. At the present resolution of the electron density maps, two slightly different conformations of the substrate, with the C3 hydroxyl group "cis" or "trans" to the C2 oxygen, can be built into the observed electron density. The two different conformations suggest two different mechanisms of proton abstraction in the first step of catalysis, the enolization of the ribulose 1,5-bisphosphate. Two loop regions, which are disordered in the crystals of the nonactivated enzyme, could be built into their respective electron density. A comparison with the structure of the quaternary complex of the spinach enzyme shows that despite the different conformations of loop 6, the positions of the Mg2+ ion, and most atoms of the substrate are very similar when superimposed on each other. There are, however, some significant differences at the active site, especially in the metal coordination sphere.


    Related Citations: 
    • Comparison of the Crystal Structures of L2 and L8S8 Rubisco Suggests a Functional Role for the Small Subunit
      Schneider, G.,Knight, S.,Andersson, I.,Lindqvist, Y.,Lundqvist, T.,Branden, C.-I.
      (1990) Embo J. 9: 2045
    • Crystallographic Refinement and Structure of Ribulose-1,5-Bisphosphate Carboxylase from Rhodospirillum Rubrum at 1.7 Angstroms Resolution
      Schneider, G.,Lindqvist, Y.,Lundqvist, T.
      (1990) J.Mol.Biol. 211: 989
    • Crystal Structure of the Complex of Ribulose-1,5-Bisphosphate Carboxylase and a Transition State Analogue, 2-Carboxy-D-Arabinitol 1,5-Bisphosphate
      Lundqvist, T.,Schneider, G.
      (1989) J.Biol.Chem. 264: 7078
    • Three-Dimensional Structure of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase from Rhodospirillum Rubrum at 2.9 Angstroms Resolution
      Schneider, G.,Lindqvist, Y.,Branden, C.-I.,Lorimer, G.
      (1986) Embo J. 5: 3409
    • Crystal Structure of the Binary Complex of Ribulose-1,5-Bisphosphate Carboxylase and its Product, 3-Phospho-D-Glycerate
      Lundqvist, T.,Schneider, G.
      (1989) J.Biol.Chem. 264: 3643


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE
A, B
466Rhodospirillum rubrumGene Names: cbbM (cbbL2, rbpL)
EC: 4.1.1.39
Find proteins for P04718 (Rhodospirillum rubrum)
Go to UniProtKB:  P04718
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUB
Query on RUB

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

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.500α = 90.00
b = 70.600β = 92.10
c = 104.100γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-01-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other