1WDD

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.4 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, 3AXM

  • 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+) coordination ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chainA, C [auth E]477Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: rbcLLOC_Osp1g00420Nip064
EC: 4.1.1.39
UniProt
Find proteins for P0C512 (Oryza sativa subsp. japonica)
Explore P0C512 
Go to UniProtKB:  P0C512
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chain CB [auth S], D [auth W]128Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: RBCSRBCS-COs12g0274700LOC_Os12g17600OsJ_016909OsJ_17688
EC: 4.1.1.39
UniProt
Find proteins for Q0INY7 (Oryza sativa subsp. japonica)
Explore Q0INY7 
Go to UniProtKB:  Q0INY7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP (Subject of Investigation/LOI)
Query on CAP

Download Ideal Coordinates CCD File 
F [auth A], O [auth E]2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , P [auth E] , 
G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth E], Q [auth E], R [auth E], S [auth E], T [auth E], U [auth E], V [auth E], W [auth E], X [auth W], Y [auth W]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], N [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, C [auth E]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
MME
Query on MME
B [auth S], D [auth W]L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.713α = 90
b = 111.713β = 90
c = 196.78γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-06-13
    Changes: Database references
  • Version 1.4: 2013-06-05
    Changes: Database references