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PDBsum entry 1rco

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1rco
Jmol
Contents
Protein chains
(+ 2 more) 467 a.a.
(+ 2 more) 123 a.a. *
Ligands
XDP ×8
Waters ×1904
* Residue conservation analysis
PDB id:
1rco
Name: Lyase
Title: Spinach rubisco in complex with the inhibitor d-xylulose-2, 2-diol-1,5-bisphosphate
Structure: Ribulose bisphosphate carboxylase/oxygenase. Chain: l, b, e, h, k, o, r, v. Synonym: rubisco. Ribulose bisphosphate carboxylase/oxygenase. Chain: s, c, f, i, m, p, t, w. Synonym: rubisco. Ec: 4.1.1.39
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: Hetero-60mer (from PDB file)
Resolution:
2.30Å     R-factor:   0.239     R-free:   0.246
Authors: T.C.Taylor,I.Andersson
Key ref:
T.C.Taylor et al. (1996). A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate. J Biol Chem, 271, 32894-32899. PubMed id: 8955130 DOI: 10.1074/jbc.271.51.32894
Date:
31-Oct-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
467 a.a.*
Protein chains
Pfam   ArchSchema ?
P00870  (RBS1_SPIOL) -  Ribulose bisphosphate carboxylase small chain
Seq:
Struc:
123 a.a.
123 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 31 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains L, S, B, C, E, F, H, I, K, M, O, P, R, T, V, W: 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
Bound ligand (Het Group name = XDP)
matches with 94.00% similarity
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.271.51.32894 J Biol Chem 271:32894-32899 (1996)
PubMed id: 8955130  
 
 
A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate.
T.C.Taylor, M.D.Fothergill, I.Andersson.
 
  ABSTRACT  
 
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the carboxylation of ribulose 1,5-bisphosphate. The reaction catalyzed by Rubisco involves several steps, some of which can occur as partial reactions, forming intermediates that can be isolated. Analogues of these intermediates are potent inhibitors of the enzyme. We have studied the interactions with the enzyme of two inhibitors, xylulose 1,5-bisphosphate and 4-carboxyarabinitol 1,5-bisphosphate, by x-ray crystallography. Crystals of the complexes were formed by cocrystallization under activating conditions. In addition, 4-carboxyarabinitol 1,5-bisphosphate was soaked into preformed activated crystals of the enzyme. The result of these experiments was the release of the activating CO2 molecule as well as the metal ion from the active site when the inhibitors bound to the enzyme. Comparison with the structure of an activated complex of the enzyme indicates that the structural basis for the release of the activator groups is a distortion of the metal binding site due to the different geometry of the C-3 hydroxyl of the inhibitors. Both inhibitors induce closure of active site loops despite the inactivated state of the enzyme. Xylulose 1,5-bisphosphate binds in a hydrated form at the active site.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The reactions catalyzed by Rubisco.
Figure 4.
Fig. 4. Stereochemistry of the substrate RuBP and various inhibitors of Rubisco.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 32894-32899) copyright 1996.  
  Figures were selected by an automated process.  

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
  20461160 O.Mourad, K.Abdelkrim, B.Messaoud, K.Khaled, and R.Nouredine (2009).
Binding of 2CA1P (nocturnal inhibitor) to the active site of RubisCO using genetic algorithm (GA).
  Bioinformation, 4, 206-209.  
17498284 M.V.Kapralov, and D.A.Filatov (2007).
Widespread positive selection in the photosynthetic Rubisco enzyme.
  BMC Evol Biol, 7, 73.  
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
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.