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PDBsum entry 1bxn

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1bxn
Jmol
Contents
Protein chains
445 a.a. *
129 a.a. *
Ligands
PO4 ×8
* Residue conservation analysis
PDB id:
1bxn
Name: Lyase
Title: The crystal structure of rubisco from alcaligenes eutrophus angstroms.
Structure: Protein (ribulose bisphosphate carboxylase large chain: a, c, e, g. Synonym: rubisco. Engineered: yes. Protein (ribulose bisphosphate carboxylase small chain: i, j, k, l. Synonym: rubisco. Engineered: yes
Source: Cupriavidus necator. Organism_taxid: 106590. Organism_taxid: 106590
Biol. unit: 60mer (from PDB file)
Resolution:
2.70Å     R-factor:   0.266     R-free:   0.322
Authors: S.Hansen,V.B.Vollan,E.Hough,K.Andersen
Key ref:
S.Hansen et al. (1999). The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits. J Mol Biol, 288, 609-621. PubMed id: 10329167 DOI: 10.1006/jmbi.1999.2701
Date:
06-Oct-98     Release date:   06-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C2C2  (RBL1C_CUPNE) -  Ribulose bisphosphate carboxylase large chain, chromosomal
Seq:
Struc:
486 a.a.
445 a.a.*
Protein chains
Pfam   ArchSchema ?
P09658  (RBSC_CUPNE) -  Ribulose bisphosphate carboxylase small chain, chromosomal
Seq:
Struc:
139 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, I, C, J, E, K, G, L: 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
Bound ligand (Het Group name = PO4)
matches with 45.45% similarity
+ 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!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2701 J Mol Biol 288:609-621 (1999)
PubMed id: 10329167  
 
 
The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.
S.Hansen, V.B.Vollan, E.Hough, K.Andersen.
 
  ABSTRACT  
 
Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is involved in photosynthesis where it catalyzes the initial step in the fixation of carbon dioxide. The enzyme also catalyzes a competing oxygenation reaction leading to loss of fixed carbon dioxide, thus reducing the net efficiency of photosynthesis significantly. Rubisco has therefore been studied extensively, and a challenging goal is the engineering of a more photosynthetically efficient enzyme. Hexadecameric rubiscos fall in two distinct groups, "green-like" and "red-like". The ability to discriminate between CO2 and O2 as substrates varies significantly, and some algae have red-like rubisco with even higher specificity for CO2 than the plant enzyme. The structure of unactivated rubisco from Alcaligenes eutrophus has been determined to 2.7 A resolution by molecular replacement and refined to R and Rfree values of 26.6 and 32.2 %, respectively. The overall fold of the protein is very similar to the rubisco structures solved previously for green-like hexadecameric enzymes, except for the extended C-terminal domains of the small subunits which together form an eight-stranded beta-barrel which sits as a plug in the entrance to the central solvent channel in the molecule. The present structure is the first which has been solved for a red-like rubisco and is likely to represent a fold which is common for this group. The small subunits in general are believed to have a stabilizing effect, and the new quaternary structure in the oligomer of the present structure is likely to contribute even more to this stabilization of the assembled rubisco protein.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Two dimer-related large subunits viewed down the crystallographic 2-fold axis. The backbone in one subunit is colored according to temperature factors (from dark blue for low, to red for high temperature fac- tors) and shows that the regions around the active sites are the most flexible. The essential lysine residue (Lys204) is shown in yellow. The flexible Glu207 to Met215 loop is emphasised in green. The Figure was produced with MOLSCRIPT/BOBSCRIPT (Kraulis, 1991).
Figure 10.
Figure 10. Superimposition (in stereo) of small sub- unit I of the spinach enzyme (red) on the A. eutrophus enzyme (green). The neighboring subunit J of the A. eutrophus enzyme is shown in blue. The Figure was produced with O (Jones et al., 1991).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 609-621) copyright 1999.  
  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
19734149 T.Genkov, and R.J.Spreitzer (2009).
Highly conserved small subunit residues influence rubisco large subunit catalysis.
  J Biol Chem, 284, 30105-30112.  
17922215 B.Gubernator, R.Bartoszewski, J.Kroliczewski, G.Wildner, and A.Szczepaniak (2008).
Ribulose-1,5-bisphosphate carboxylase/oxygenase from thermophilic cyanobacterium Thermosynechococcus elongatus.
  Photosynth Res, 95, 101-109.  
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
14734540 S.Satagopan, and R.J.Spreitzer (2004).
Substitutions at the Asp-473 latch residue of chlamydomonas ribulosebisphosphate carboxylase/oxygenase cause decreases in carboxylation efficiency and CO(2)/O(2) specificity.
  J Biol Chem, 279, 14240-14244.  
  16233341 H.Atomi (2002).
Microbial enzymes involved in carbon dioxide fixation.
  J Biosci Bioeng, 94, 497-505.  
11751824 J.B.Utåker, K.Andersen, A.Aakra, B.Moen, and I.F.Nes (2002).
Phylogeny and functional expression of ribulose 1,5-bisphosphate carboxylase/oxygenase from the autotrophic ammonia-oxidizing bacterium Nitrosospira sp. isolate 40KI.
  J Bacteriol, 184, 468-478.  
12070156 N.Maeda, T.Kanai, H.Atomi, and T.Imanaka (2002).
The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability.
  J Biol Chem, 277, 31656-31662.  
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
11439139 S.M.Whitney, P.Baldet, G.S.Hudson, and T.J.Andrews (2001).
Form I Rubiscos from non-green algae are expressed abundantly but not assembled in tobacco chloroplasts.
  Plant J, 26, 535-547.  
  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
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.