2RUS

CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE, MG(II), AND ACTIVATOR CO2 AT 2.3-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the ternary complex of ribulose-1,5-bisphosphate carboxylase, Mg(II), and activator CO2 at 2.3-A resolution.

Lundqvist, T.Schneider, G.

(1991) Biochemistry 30: 904-908


  • PubMed Abstract: 
  • The activated ternary complex, enzyme-CO2-Mg(II), of the dimeric ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum can be prepared in the same crystal form that was used for the crystallographic structure determination of the ...

    The activated ternary complex, enzyme-CO2-Mg(II), of the dimeric ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum can be prepared in the same crystal form that was used for the crystallographic structure determination of the native nonactivated enzyme (Schneider, G., Bränden, C.-I., & Lorimer, G. (1986) J. Mol. Biol. 187, 141-143). The three-dimensional structure of the activated enzyme has been determined to a nominal resolution of 2.3 A by protein crystallographic methods. The activator CO2 forms a carbamate with Lys191, located at the bottom of the funnel-shaped active site. In both subunits, this labile adduct is stabilized by a Mg(II) ion, bound to the carbamate and the side chains of Asp193 and Glu194. One solvent molecule was found within the first coordination sphere of the metal ion. The metal-binding site in ribulose-1,5-bisphosphate carboxylase consists thus of at least three protein ligands, all located on loop 2 of the beta/alpha barrel. One additional metal ligand, the side chain of the conserved Asn111, was observed close to the Mg(II) ion in the B-subunit. Other structural differences at the active site between the activated and nonactivated enzyme are limited to side-chain positions. Nevertheless, it is obvious that the hydrogen-bonding pattern in the vicinity of the activator site is completely altered.


    Related Citations: 
    • Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase
      Andersson, I.,Knight, S.,Schneider, G.,Lindqvist, Y.,Lundqvist, T.,Branden, C.-I.,Lorimer, G.H.
      (1989) Nature 337: 229
    • 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
    • Crystal Structure of the Binary Complex of Ribulose-1,5-Bisphosphate Carboxylase and its Product, 3-Phospho-D-Glycerate
      Lundqvist, T.,Schneider, G.
      (1988) J.Biol.Chem. 263: 3643
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)
A, B
490Rhodospirillum rubrumGene Names: cbbM (cbbL2, rbpL)
EC: 4.1.1.39
Find proteins for P04718 (Rhodospirillum rubrum)
Go to UniProtKB:  P04718
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FOR
Query on FOR

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Download CCD File 
A, B
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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: 1991-10-15
    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