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PDBsum entry 1ir2

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1ir2
Jmol
Contents
Protein chains
(+ 10 more) 468 a.a. *
(+ 10 more) 140 a.a. *
Ligands
CAP ×16
GOL ×40
Metals
_MG ×16
Waters ×9999
* Residue conservation analysis
PDB id:
1ir2
Name: Lyase
Title: Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from green alga, chlamydomo reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosp cabp)
Structure: Large subunit of rubisco. Chain: a, b, c, d, e, f, g, h, s, t, u, v, w, x, y, z. Synonym: ribulose bisphosphate carboxylase large chain. Small subunit of rubisco. Chain: i, j, k, l, m, n, o, p, 1, 2, 3, 4, 5, 6, 7, 8. Synonym: ribulose bisphosphate carboxylase small chain 2. Ec: 4.1.1.39
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: 137c mt+. Strain: 137c mt+
Biol. unit: 16mer (from PQS)
Resolution:
1.84Å     R-factor:   0.152     R-free:   0.181
Authors: E.Mizohata,H.Matsumura,Y.Okano,M.Kumei,H.Takuma,J.Onodera,K. N.Shibata,T.Inoue,A.Yokota,Y.Kai
Key ref:
E.Mizohata et al. (2002). Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. J Mol Biol, 316, 679-691. PubMed id: 11866526 DOI: 10.1006/jmbi.2001.5381
Date:
03-Sep-01     Release date:   20-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
468 a.a.*
Protein chains
Pfam   ArchSchema ?
P08475  (RBS2_CHLRE) -  Ribulose bisphosphate carboxylase small chain 2, chloroplastic
Seq:
Struc:
185 a.a.
140 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, I, B, J, C, K, D, L, E, M, F, N, G, O, H, P, S, 1, T, 2, U, 3, V, 4, W, 5, X, 6, Y, 7, Z, 8: 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 85.71% 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: 10.1006/jmbi.2001.5381 J Mol Biol 316:679-691 (2002)
PubMed id: 11866526  
 
 
Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
E.Mizohata, H.Matsumura, Y.Okano, M.Kumei, H.Takuma, J.Onodera, K.Kato, N.Shibata, T.Inoue, A.Yokota, Y.Kai.
 
  ABSTRACT  
 
Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyzes the initial steps of photosynthetic carbon reduction and photorespiratory carbon oxidation cycles by combining CO(2) and O(2), respectively, with ribulose-1,5-bisphosphate. Many photosynthetic organisms have form I rubiscos comprised of eight large (L) and eight small (S) subunits. The crystal structure of the complex of activated rubisco from the green alga Chlamydomonas reinhardtii and the reaction intermediate analogue 2-carboxyarabinitol-1,5-bisphosphate (2-CABP) has been solved at 1.84 A resolution (R(cryst) of 15.2 % and R(free) of 18.1 %). The subunit arrangement of Chlamydomonas rubisco is the same as those of the previously solved form I rubiscos. Especially, the present structure is very similar to the activated spinach structure complexed with 2-CABP in the L-subunit folding and active-site conformation, but differs in S-subunit folding. The central insertion of the Chlamydomonas S-subunit forms the longer betaA-betaB loop that protrudes deeper into the solvent channel of rubisco than higher plant, cyanobacterial, and red algal (red-like) betaA-betaB loops. The C-terminal extension of the Chlamydomonas S-subunit does not protrude into the solvent channel, unlike that of the red algal S-subunit, but lies on the protein surface anchored by interactions with the N-terminal region of the S-subunit. Further, the present high-resolution structure has revealed novel post-translational modifications. Residue 1 of the S-subunit is N(alpha)-methylmethionine, residues 104 and 151 of the L-subunit are 4-hydroxyproline, and residues 256 and 369 of the L-subunit are S(gamma)-methylcysteine. Furthermore, the unusual electron density of residue 471 of the L-subunit, which has been deduced to be threonine from the genomic DNA sequence, suggests that the residue is isoleucine produced by RNA editing or O(gamma)-methylthreonine.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Electron-density map (2F[o] -F[c], contoured at 1s) at the active site in the Chlamydomonas L-subunit. In the stick model, C, N, O, and P atoms are colored in yellow, blue, red, and orange, respectively. 2-CABP, Mg2+, and active-site residues including carbamate LysL-201 (KcxL-201) are clearly seen in the map. The Figure was prepared using the program TURBO-FRODO.
Figure 8.
Figure 8. The omit maps (F[o] -F[c], contoured at 3.5s) of unusual residues of Chlamydomonas rubisco. Each map is calculated without a contribution of the coordinates of the unusual residue. In the stick model, C, N, O, and S atoms are colored in yellow, blue, red, and green, respectively. The stick models fitted in the electron-density maps are (a) Na-methyl-MetS-1, (b) 4-hydroxy-ProL-104, (c) 4-hydroxy-ProL-151, (d) Sg-methyl-CysL-256, (e) Sg-methyl-CysL-369, and (f) ThrL-471. The electron-density map in (f) is probably that of Og-methyl-Thr or Ile, as described in the text. The white arrows show the additional electron densities resulting from modifications or amino acid conversion. The Figure was prepared using the program TURBO-FRODO.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 679-691) copyright 2002.  
  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
18077893 V.O.Popov, R.A.Zvyagilskaya, and A.N.Bach (2007).
A.N.Bach--a revolutionary in politics and science. Commemorating 150th anniversary of academician A.N. Bach.
  Biochemistry (Mosc), 72, 1029-1038.  
14679208 I.Yosef, V.Irihimovitch, J.A.Knopf, I.Cohen, I.Orr-Dahan, E.Nahum, C.Keasar, and M.Shapira (2004).
RNA binding activity of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit from Chlamydomonas reinhardtii.
  J Biol Chem, 279, 10148-10156.  
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.  
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.