1EJ7

CRYSTAL STRUCTURE OF UNACTIVATED TOBACCO RUBISCO WITH BOUND PHOSPHATE IONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate.

Duff, A.P.Andrews, T.J.Curmi, P.M.G.

(2000) J.Mol.Biol. 298: 903-916

  • DOI: 10.1006/jmbi.2000.3724

  • PubMed Abstract: 
  • d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products h ...

    d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products have been determined by X-ray crystallography. The structures fall into two well-defined and distinct states. The active site is either "open" or "closed". The timing and mechanism of the transition between these two states have been uncertain. We solved the crystal structure of unactivated (metal-free) rubisco from tobacco with only inorganic phosphate bound and conclude that phosphate binding per se does not trigger closure, as it does in the similarly structured enzyme, triosephosphate isomerase. Comparison of all available rubisco structures suggests that, instead, the distance between the terminal phosphates (P1 and P2) of the bisphosphate ligand is the trigger: if that distance is less than 9.1 A, then the active site closes; if it is greater than 9.4 A then the enzyme remains open. Shortening of the inter-phosphate distance results from the ligand binding in a more curved conformation when O atoms of the ligand's sugar backbone interact either with the metal, if it is present, or with charged groups in the metal-binding site, if the metal is absent. This shortening brings the P1 phosphate into hydrogen bonding contact with Thr65. Thr65 exists in two discrete states related by a rotation of the backbone psi torsion angle. This rotation is coupled to domain rotation and hence to active site closure. Rotation of the side-chain of Thr65 also affects the C-terminal strand of large subunit which packs against Loop 6 after closure. The position of the C-terminal strand in the closed state is stabilised by multiple polar interactions with a distinctive highly-charged latch site involving the side-chain of Asp473. In the open state, this latch site may be occupied instead by phosphorylated anions.


    Organizational Affiliation

    Initiative in Biomolecular Structure, School of Physics University of New South Wales, Sydney, NSW 2052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBISCO (LARGE SUBUNIT)
L
475Nicotiana tabacumMutation(s): 0 
Gene Names: rbcL (rbcA)
EC: 4.1.1.39
Find proteins for P00876 (Nicotiana tabacum)
Go to UniProtKB:  P00876
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RUBISCO (SMALL SUBUNIT)
S
123Nicotiana tabacumMutation(s): 0 
Gene Names: RBCS
EC: 4.1.1.39
Find proteins for P69249 (Nicotiana tabacum)
Go to UniProtKB:  P69249
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.149 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.180α = 90.00
b = 149.180β = 90.00
c = 138.340γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-15
    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