1RUS

CRYSTAL STRUCTURE OF THE BINARY COMPLEX OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE AND ITS PRODUCT, 3-PHOSPHO-D-GLYCERATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 3643-3646


  • PubMed Abstract: 
  • The crystal structure of the binary complex of non-activated ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and its product 3-phospho-D-glycerate has been determined to 2.9-A resolution. This structure determination confir ...

    The crystal structure of the binary complex of non-activated ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and its product 3-phospho-D-glycerate has been determined to 2.9-A resolution. This structure determination confirms the proposed location of the active site (Schneider, G., Lindqvist, Y., Brändén, C.-I., and Lorimer, G. (1986) EMBO J. 5, 3409-3415) at the carboxyl end of the beta-strands of the alpha/beta-barrel in the carboxyl-terminal domain. One molecule of 3-phosphoglycerate is bound per active site. All oxygen atoms of 3-phosphoglycerate form hydrogen bonds to groups of the enzyme. The phosphate group interacts with the sidechains of residues Arg-288, His-321, and Ser-368, which are conserved between enzymes from different species as well as with the main chain nitrogens from residues Thr-322 and Gly-323. These amino acid residues constitute one of the two phosphate binding sites of the active site. The carboxyl group interacts with the side chains of His-287, Lys-191, and Asn-111. Implications of the activation process for the binding of 3-phosphoglycerate are discussed.


    Related Citations: 
    • 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 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
    • 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 Ternary Complex of Ribulose-1,5-Bisphosphate Carboxylase, Mg(II), and Activator Co2 at 2.3-Angstroms Resolution
      Lundqvist, T.,Schneider, G.
      (1991) Biochemistry 30: 904
    • 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


    Organizational Affiliation

    Swedish University of Agricultural Sciences, Department of Molecular Biology, Uppsala Biomedical Center, Sweden.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A, B
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 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: 2008-03-24
    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