PDBsum entry 1aa1

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
438 a.a.
123 a.a. *
3PG ×8
_MG ×4
Waters ×1008
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Activated spinach rubisco in complex with the product 3- phosphoglycerate
Structure: Ribulose bisphosphate carboxylase (large chain). Chain: l, b, e, h. Synonym: rubisco. Ribulose bisphosphate carboxylase (small chain). Chain: s, c, f, i. Synonym: rubisco. Ec:
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: Octamer (from PDB file)
2.20Å     R-factor:   0.207     R-free:   0.224
Authors: T.C.Taylor,I.Andersson
Key ref:
T.C.Taylor and I.Andersson (1997). Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry, 36, 4041-4046. PubMed id: 9092835 DOI: 10.1021/bi962818w
20-Jan-97     Release date:   07-Jul-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain
475 a.a.
438 a.a.*
Protein chains
Pfam   ArchSchema ?
Q43832  (RBS2_SPIOL) -  Ribulose bisphosphate carboxylase small chain 2, chloroplastic
180 a.a.
123 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains L, S, B, C, E, F, H, I: E.C.  - Ribulose-bisphosphate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
2 × 3-phospho-D-glycerate
Bound ligand (Het Group name = 3PG)
corresponds exactly
+ 2 × H(+)
= D-ribulose 1,5-bisphosphate
+ CO(2)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plastid   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  


DOI no: 10.1021/bi962818w Biochemistry 36:4041-4046 (1997)
PubMed id: 9092835  
Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.
T.C.Taylor, I.Andersson.
The crystal structure of an activated complex of ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach and its product 3-phosphoglycerate has been determined to 2.2 A resolution. The structure is of the open form with the active site accessible to the solvent as observed in the structures of the activated ligand-free enzyme and the complex of the activated enzyme with the substrate ribulose-1,5-bisphosphate. Two molecules of 3-phosphoglycerate are bound per active site. The phosphates of both molecules bind approximately at the same position as the phosphates of ribulose-1,5-bisphosphate or the six-carbon intermediate analogue 2-carboxyarabinitol-1,5-bisphosphate, but one product molecule is swung out from the active site with its carboxylate group pointing toward solution. The present structure points to direct participation of the active site side chain of lysine 175 in later stages of catalysis. This possibility is discussed in the light of mutagenesis studies.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19690372 H.Tamura, Y.Saito, H.Ashida, Y.Kai, T.Inoue, A.Yokota, and H.Matsumura (2009).
Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 65, 942-951.
PDB code: 2zvi
15613396 B.Pierce, W.Tong, and Z.Weng (2005).
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking.
  Bioinformatics, 21, 1472-1478.  
15893668 H.Li, M.R.Sawaya, F.R.Tabita, and D.Eisenberg (2005).
Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.
  Structure, 13, 779-789.
PDB code: 1ykw
12221984 R.J.Spreitzer, and M.E.Salvucci (2002).
Rubisco: structure, regulatory interactions, and possibilities for a better enzyme.
  Annu Rev Plant Biol, 53, 449-475.  
11435112 K.Kitano, N.Maeda, T.Fukui, H.Atomi, T.Imanaka, and K.Miki (2001).
Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.
  Structure, 9, 473-481.
PDB code: 1geh
11553771 K.Motohashi, A.Kondoh, M.T.Stumpp, and T.Hisabori (2001).
Comprehensive survey of proteins targeted by chloroplast thioredoxin.
  Proc Natl Acad Sci U S A, 98, 11224-11229.  
  11641402 T.C.Taylor, A.Backlund, K.Bjorhall, R.J.Spreitzer, and I.Andersson (2001).
First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.
  J Biol Chem, 276, 48159-48164.
PDB code: 1gk8
10542276 C.Dabney-Smith, P.W.van Den Wijngaard, Y.Treece, W.J.Vredenberg, and B.D.Bruce (1999).
The C terminus of a chloroplast precursor modulates its interaction with the translocation apparatus and PIRAC.
  J Biol Chem, 274, 32351-32359.  
9988772 H.Ishida, A.Makino, and T.Mae (1999).
Fragmentation of the large subunit of ribulose-1,5-bisphosphate carboxylase by reactive oxygen species occurs near Gly-329.
  J Biol Chem, 274, 5222-5226.  
10336462 H.Sugawara, H.Yamamoto, N.Shibata, T.Inoue, S.Okada, C.Miyake, A.Yokota, and Y.Kai (1999).
Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.
  J Biol Chem, 274, 15655-15661.
PDB code: 1bwv
  9541405 M.R.Harpel, F.W.Larimer, and F.C.Hartman (1998).
Multiple catalytic roles of His 287 of Rhodospirillum rubrum ribulose 1,5-bisphosphate carboxylase/oxygenase.
  Protein Sci, 7, 730-738.  
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