PDBsum entry 1geh

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Lyase PDB id
Jmol PyMol
Protein chains
427 a.a.
SO4 ×10
PDB id:
Name: Lyase
Title: Crystal structure of archaeal rubisco (ribulose 1,5-bisphosp carboxylase/oxygenase)
Structure: Ribulose-1,5-bisphosphate carboxylase/oxygenase. Chain: a, b, c, d, e. Engineered: yes
Source: Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Decamer (from PDB file)
2.80Å     R-factor:   0.224     R-free:   0.254
Authors: K.Kitano,N.Maeda,T.Fukui,H.Atomi,T.Imanaka,K.Miki
Key ref:
K.Kitano et al. (2001). Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Structure, 9, 473-481. PubMed id: 11435112 DOI: 10.1016/S0969-2126(01)00608-6
13-Nov-00     Release date:   19-Dec-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O93627  (RBL_PYRKO) -  Ribulose bisphosphate carboxylase
444 a.a.
427 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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)
+ 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   2 terms 
  Biochemical function     oxidoreductase activity     5 terms  


DOI no: 10.1016/S0969-2126(01)00608-6 Structure 9:473-481 (2001)
PubMed id: 11435112  
Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.
K.Kitano, N.Maeda, T.Fukui, H.Atomi, T.Imanaka, K.Miki.
BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.
  Selected figure(s)  
Figure 4.
Figure 4. Oligomeric Structures of Rubiscos(a) Decamer structure of Tk-Rubisco, with ribbon diagram from top view. Each monomer is shown in different colors and labeled from "A" to "J." Plausible structures of RuBP molecules and magnesium ions are marked in ellipses.(b) Side view of Tk-Rubisco by -90 rotation from (a), with the AB dimer at the center.(c) The (L[2])[4] core of type I Rubisco, with ribbon diagram from top view, where only L subunits in the L[8]S[8] structure [11] are shown. Each monomer is shown in different colors. RuBP molecules and magnesium ions are marked in ellipses.(d) Side view of the (L[2])[4] core of type I Rubisco by -90 rotation from (c)

  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 473-481) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19837658 H.Alonso, M.J.Blayney, J.L.Beck, and S.M.Whitney (2009).
Substrate-induced assembly of Methanococcoides burtonii D-ribulose-1,5-bisphosphate carboxylase/oxygenase dimers into decamers.
  J Biol Chem, 284, 33876-33882.  
19705820 S.Satagopan, S.S.Scott, T.G.Smith, and F.R.Tabita (2009).
A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.
  Biochemistry, 48, 9076-9083.  
18487131 F.R.Tabita, T.E.Hanson, S.Satagopan, B.H.Witte, and N.E.Kreel (2008).
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms.
  Philos Trans R Soc Lond B Biol Sci, 363, 2629-2640.  
17665149 A.R.Portis, and M.A.Parry (2007).
Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective.
  Photosynth Res, 94, 121-143.  
17024516 H.E.Elsaied, H.Kimura, and T.Naganuma (2007).
Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems.
  Extremophiles, 11, 191-202.  
17621634 O.Mueller-Cajar, and M.R.Badger (2007).
New roads lead to Rubisco in archaebacteria.
  Bioessays, 29, 722-724.  
17675435 S.Yoshida, H.Atomi, and T.Imanaka (2007).
Engineering of a type III rubisco from a hyperthermophilic archaeon in order to enhance catalytic performance in mesophilic host cells.
  Appl Environ Microbiol, 73, 6254-6261.  
17303759 T.Sato, H.Atomi, and T.Imanaka (2007).
Archaeal type III RuBisCOs function in a pathway for AMP metabolism.
  Science, 315, 1003-1006.  
16737967 A.Carré-Mlouka, A.Méjean, P.Quillardet, H.Ashida, Y.Saito, A.Yokota, I.Callebaut, A.Sekowska, E.Dittmann, C.Bouchier, and Marsac (2006).
A new rubisco-like protein coexists with a photosynthetic rubisco in the planktonic cyanobacteria Microcystis.
  J Biol Chem, 281, 24462-24471.  
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
12730164 M.W.Finn, and F.R.Tabita (2003).
Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea.
  J Bacteriol, 185, 3049-3059.  
  16233341 H.Atomi (2002).
Microbial enzymes involved in carbon dioxide fixation.
  J Biosci Bioeng, 94, 497-505.  
16233297 H.Imanaka, T.Fukui, H.Atomi, and T.Imanaka (2002).
Gene cloning and characterization of fructose-1,6-bisphosphate aldolase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  J Biosci Bioeng, 94, 237-243.  
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.  
12057965 T.Fukui, T.Eguchi, H.Atomi, and T.Imanaka (2002).
A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins.
  J Bacteriol, 184, 3689-3698.  
12112867 T.Imanaka, and H.Atomi (2002).
Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.
  Chem Rec, 2, 149-163.  
  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.