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PDBsum entry 1gk8

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1gk8
Jmol
Contents
Protein chains
469 a.a. *
126 a.a. *
Ligands
CAP ×4
EDO ×33
Metals
_MG ×4
Waters ×2556
* Residue conservation analysis
PDB id:
1gk8
Name: Lyase
Title: Rubisco from chlamydomonas reinhardtii
Structure: Ribulose-1,5 bisphosphate carboxylase large chain. Chain: a, c, e, g. Synonym: rubisco large subunit. Ribulose bisphosphate carboxylase small chain 1. Chain: i, k, m, o. Synonym: rubisco small subunit 1. Ec: 4.1.1.39
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055. Organism_taxid: 3055
Biol. unit: 60mer (from PDB file)
Resolution:
1.4Å     R-factor:   0.149     R-free:   0.162
Authors: T.C.Taylor,R.J.Spreitzer,I.Andersson
Key ref:
T.C.Taylor et al. (2001). First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii. J Biol Chem, 276, 48159-48164. PubMed id: 11641402 DOI: 10.1074/jbc.M107765200
Date:
09-Aug-01     Release date:   24-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
469 a.a.*
Protein chains
Pfam   ArchSchema ?
P00873  (RBS1_CHLRE) -  Ribulose bisphosphate carboxylase small chain 1, chloroplastic
Seq:
Struc:
185 a.a.
126 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 A, C, E, G, I, K, M, O: 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 = CAP)
matches with 85.00% similarity
+
CO(2)
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ 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.M107765200 J Biol Chem 276:48159-48164 (2001)
PubMed id: 11641402  
 
 
First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.
T.C.Taylor, A.Backlund, K.Bjorhall, R.J.Spreitzer, I.Andersson.
 
  ABSTRACT  
 
The crystal structure of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) from the unicellular green alga Chlamydomonas reinhardtii has been determined to 1.4 A resolution. Overall, the structure shows high similarity to the previously determined structures of L8S8 Rubisco enzymes. The largest difference is found in the loop between beta strands A and B of the small subunit (betaA-betaB loop), which is longer by six amino acid residues than the corresponding region in Rubisco from Spinacia. Mutations of residues in the betaA-betaB loop have been shown to affect holoenzyme stability and catalytic properties. The information contained in the Chlamydomonas structure enables a more reliable analysis of the effect of these mutations. No electron density was observed for the last 13 residues of the small subunit, which are assumed to be disordered in the crystal. Because of the high resolution of the data, some posttranslational modifications are unambiguously apparent in the structure. These include cysteine and N-terminal methylations and proline 4-hydroxylations.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Electron density ( 2mF[o] DF[c] contoured at 1 ) for the A- B loop of the S subunit. Alternate conformations for the O of Ser-64 and S of Cys-65 are shown in dark red and green, respectively.
Figure 5.
Fig. 5. Representative electron density for modified residues. A, S-methylcysteine; B, 4-hydroxyproline; and C, N-methylmethionine.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 48159-48164) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20067527 F.Witzel, J.Götze, and O.Ebenhöh (2010).
Slow deactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase elucidated by mathematical models.
  FEBS J, 277, 931-950.  
20700376 L.Bohlin, U.Göransson, C.Alsmark, C.Wedén, and A.Backlund (2010).
Natural products in modern life science.
  Phytochem Rev, 9, 279-301.  
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
19323825 M.Muto, R.E.Henry, and S.P.Mayfield (2009).
Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast.
  BMC Biotechnol, 9, 26.  
19734149 T.Genkov, and R.J.Spreitzer (2009).
Highly conserved small subunit residues influence rubisco large subunit catalysis.
  J Biol Chem, 284, 30105-30112.  
18713375 K.L.Liu, L.Shen, J.Q.Wang, and J.P.Sheng (2008).
Rapid inactivation of chloroplastic ascorbate peroxidase is responsible for oxidative modification to Rubisco in tomato (Lycopersicon esculentum) under cadmium stress.
  J Integr Plant Biol, 50, 415-426.  
18664299 S.Satagopan, and R.J.Spreitzer (2008).
Plant-like substitutions in the large-subunit carboxy terminus of Chlamydomonas Rubisco increase CO2/O2 Specificity.
  BMC Plant Biol, 8, 85.  
18063718 F.R.Tabita, T.E.Hanson, H.Li, S.Satagopan, J.Singh, and S.Chan (2007).
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
  Microbiol Mol Biol Rev, 71, 576-599.
PDB code: 2qyg
17955341 T.Wydrzynski, W.Hillier, and B.Conlan (2007).
Engineering model proteins for Photosystem II function.
  Photosynth Res, 94, 225-233.  
17087473 J.Marín-Navarro, and J.Moreno (2006).
Cysteines 449 and 459 modulate the reduction-oxidation conformational changes of ribulose 1.5-bisphosphate carboxylase/oxygenase and the translocation of the enzyme to membranes during stress.
  Plant Cell Environ, 29, 898-908.  
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
16282373 R.J.Spreitzer, S.R.Peddi, and S.Satagopan (2005).
Phylogenetic engineering at an interface between large and small subunits imparts land-plant kinetic properties to algal Rubisco.
  Proc Natl Acad Sci U S A, 102, 17225-17230.  
14674769 J.Marín-Navarro, and J.Moreno (2003).
Modification of the proteolytic fragmentation pattern upon oxidation of cysteines from ribulose 1,5-bisphosphate carboxylase/oxygenase.
  Biochemistry, 42, 14930-14938.  
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.  
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.