3AXM

Structure of rice Rubisco in complex with 6PG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate

Matsumura, H.Mizohata, E.Ishida, H.Kogami, A.Ueno, T.Makino, A.Inoue, T.Yokota, A.Mae, T.Kai, Y.

(2012) J.Mol.Biol. 422: 75-86

  • DOI: 10.1016/j.jmb.2012.05.014
  • Primary Citation of Related Structures:  1WDD, 3AXK

  • PubMed Abstract: 
  • The key enzyme of plant photosynthesis, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coord ...

    The key enzyme of plant photosynthesis, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coordination. Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate (NADPH) and 6-phosphogluconate (6PG) function as positive effectors to promote activation. However, the structural mechanism remains unknown. Here, we have determined the crystal structures of activated rice Rubisco in complex with NADPH, 6PG, or 2-carboxy-D-arabinitol 1,5-bisphosphate (2CABP). The structures of the NADPH and 6PG complexes adopt open-state conformations, in which loop 6 at the catalytic site and some other loops are disordered. The structure of the 2CABP complex is in a closed state, similar to the previous 2CABP-bound activated structures from other sources. The catalytic sites of the NADPH and 6PG complexes are fully activated, despite the fact that bicarbonate (NaHCO(3)) was not added into the crystallization solution. In the catalytic site, NADPH does not interact with Mg(2+) directly but interacts with Mg(2+)-coordinated water molecules, while 6PG interacts with Mg(2+) directly. These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg(2+) and the carbamylated Lys201 with unique interactions and preventing its dissociation. The structure also reveals that the relaxed complex of the effectors (NADPH or 6PG), distinct from the tight-binding mode of 2CABP, would allow rapid exchange of the effectors in the catalytic sites by substrate D-ribulose 1,5-bisphosphate for catalysis in physiological conditions.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan. matsumura@chem.eng.osaka-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chain
A, B, C, D, E, F, G, H
477Oryza sativa subsp. japonicaGene Names: rbcL
EC: 4.1.1.39
Find proteins for P0C512 (Oryza sativa subsp. japonica)
Go to UniProtKB:  P0C512
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase small chain, chloroplastic
S, T, U, V, W, X, Y, Z
129Oryza sativa subsp. japonicaGene Names: RBCS (RBCS-C)
EC: 4.1.1.39
Find proteins for Q0INY7 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q0INY7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
6PG
Query on 6PG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
6-PHOSPHOGLUCONIC ACID
C6 H13 O10 P
BIRSGZKFKXLSJQ-SQOUGZDYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
NME
Query on NME
S, T, U, V, W, X, Y, Z
NON-POLYMERC H5 N

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6PGKi: 8500 nM BINDINGMOAD
6PGKi: 8500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 110.408α = 90.00
b = 199.624β = 91.45
c = 111.169γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-06-13
    Type: Database references
  • Version 1.2: 2013-06-05
    Type: Database references