1BWV

Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.

Sugawara, H.Yamamoto, H.Shibata, N.Inoue, T.Okada, S.Miyake, C.Yokota, A.Kai, Y.

(1999) J Biol Chem 274: 15655-15661

  • DOI: https://doi.org/10.1074/jbc.274.22.15655
  • Primary Citation of Related Structures:  
    1BWV

  • PubMed Abstract: 

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1. 39) obtained from a thermophilic red alga Galdieria partita has the highest specificity factor of 238 among the Rubiscos hitherto reported. Crystal structure of activated Rubisco from G. partita complexed with the reaction intermediate analogue, 2-carboxyarabinitol 1,5-bisphosphate (2-CABP) has been determined at 2.4-A resolution. Compared with other Rubiscos, different amino residues bring the structural differences in active site, which are marked around the binding sites of P-2 phosphate of 2-CABP. Especially, side chains of His-327 and Arg-295 show the significant differences from those of spinach Rubisco. Moreover, the side chains of Asn-123 and His-294 which are reported to bind the substrate, ribulose 1,5-bisphosphate, form hydrogen bonds characteristic of Galdieria Rubisco. Small subunits of Galdieria Rubisco have more than 30 extra amino acid residues on the C terminus, which make up a hairpin-loop structure to form many interactions with the neighboring small subunits. When the structures of Galdieria and spinach Rubiscos are superimposed, the hairpin region of the neighboring small subunit in Galdieria enzyme and apical portion of insertion residues 52-63 characteristic of small subunits in higher plant enzymes are almost overlapped to each other.


  • Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
A, C, E, G
493Galdieria partitaMutation(s): 1 
EC: 4.1.1.39
UniProt
Find proteins for O98949 (Galdieria partita)
Explore O98949 
Go to UniProtKB:  O98949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO98949
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)B [auth S],
D [auth U],
F [auth W],
H [auth Y]
138Galdieria partitaMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for O98950 (Galdieria partita)
Explore O98950 
Go to UniProtKB:  O98950
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO98950
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
J [auth A],
L [auth C],
N [auth E],
P [auth G]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth C],
M [auth E],
O [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, C, E, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.07α = 90
b = 117.07β = 90
c = 319.63γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-27
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection