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PDBsum entry 1aus

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protein ligands metals Protein-protein interface(s) links
Lyase (carbon-carbon) PDB id
1aus
Jmol
Contents
Protein chains
439 a.a.
123 a.a. *
Ligands
FMT ×4
Metals
_MG ×4
Waters ×241
* Residue conservation analysis
PDB id:
1aus
Name: Lyase (carbon-carbon)
Title: Activated unliganded spinach rubisco
Structure: Ribulose bisphosphate carboxylase/oxygenase. Chain: l, m, n, o. Synonym: rubisco. Ribulose bisphosphate carboxylase/oxygenase. Chain: s, t, u, v. Synonym: rubisco. Ec: 4.1.1.39
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: 60mer (from PQS)
Resolution:
2.20Å     R-factor:   0.217     R-free:   0.239
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
Date:
21-Jun-95     Release date:   15-Oct-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
439 a.a.
Protein chains
Pfam   ArchSchema ?
Q43832  (RBS2_SPIOL) -  Ribulose bisphosphate carboxylase small chain 2, chloroplastic
Seq:
Struc:
180 a.a.
123 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains L, S, M, T, N, U, O, V: E.C.4.1.1.39  - 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
+ 2 × H(+)
= D-ribulose 1,5-bisphosphate
+
CO(2)
Bound ligand (Het Group name = FMT)
corresponds exactly
+ 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  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.