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PDBsum entry 8ruc
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protein ligands metals Protein-protein interface(s) links
Lyase (carbon-carbon) PDB id
8ruc

 

 

 

 

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Contents
Protein chains
467 a.a.
123 a.a. *
Ligands
CAP ×4
Metals
_MG ×4
Waters ×1520
* Residue conservation analysis
PDB id:
8ruc
Name: Lyase (carbon-carbon)
Title: Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate
Structure: Ribulose-1,5-bisphosphate carboxylase/oxygenase. Chain: a, c, e, g. Synonym: rubisco. Ribulose-1,5-bisphosphate carboxylase/oxygenase. Chain: i, j, k, l. Synonym: rubisco. Ec: 4.1.1.39
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: 60mer (from PDB file)
Resolution:
1.60Å     R-factor:   0.211    
Authors: I.Andersson,S.Knight,C.-I.Branden
Key ref:
I.Andersson (1996). Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate. J Mol Biol, 259, 160-174. PubMed id: 8648644 DOI: 10.1006/jmbi.1996.0310
Date:
22-Feb-96     Release date:   01-Aug-96    
Supersedes: 8rub
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain from Spinacia oleracea
Seq:
Struc: 		475 a.a.
467 a.a.*
Protein chains
Pfam   ArchSchema ?
P00870  (RBS1_SPIOL) -  Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 from Spinacia oleracea
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 A, C, E, G, I, J, K, L: E.C.4.1.1.39  - ribulose-bisphosphate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 (2R)-3-phosphoglycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
2 × (2R)-3-phosphoglycerate
 + 2 × H(+)
 = D-ribulose 1,5-bisphosphate
 +
CO2
Bound ligand (Het Group name = CAP)
matches with 85.71% similarity 		+ H2O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1996.0310 J Mol Biol 259:160-174 (1996)
PubMed id: 8648644  
 
 
Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.
I.Andersson.
 
  ABSTRACT  
 
Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with large unit cells is not a trivial task due to the effect of radiation damage and the large number of overlapping reflections when conventional data collection methods are used. In order to minimise these effects, data on rubisco were collected with a giant Weissenberg camera at long crystal to image-plate distances at the synchrotron of the Photon Factory, Japan. Relative to conventional data sets, this experimental arrangement allowed a 20 to 30-fold reduction of the X-ray dose/exposure time for data collection. This paper describes the refined 1.6 A crystal structure of activated rubisco complexed with a transition state analogue, 2-carboxyarabinitol-bisphosphate. The crystallographic asymmetric unit contains an L4S4 unit, representing half of the molecule. The structure presented here is currently the highest resolution structure for any protein of comparable size. Refinement of the model was carried out by restrained least squares techniques without non-crystallographic symmetry averaging. The results show that all L and S subunits have identical three-dimensional structures, and their arrangement within the hexadecamer has no intrinsic asymmetry. A detailed analysis of the high-resolution maps identified 30 differences in the sequence of the small subunit, indicating a larger than usual heterogeneity for this nuclear encoded protein in spinach. No such differences were found in the sequence of the chloroplast encoded large subunit. The transition state analogue is in the cis conformation at the active site suggesting a key role for the carbamate of Lys201 in catalysis. Analysis of the active site around the catalytically essential magnesium ion further indicates that residues in the second liganding sphere of the metal play a role in fine-tuning the acid-base character and the position of the residues directly liganded to the metal.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Reactions catalysed by rubisco. 		Figure 7.
Figure 7. Overview of the active site of spinach rubisco showing 2-CABP, Mg 2+ and residues within hydrogen-bonding distance to these ligands. The hydroxyl groups at C2 and C3 of 2-CABP are in cis conformation. The two views in (a) and (b) are related by 180° with respect to the vertical axis.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 160-174) 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
19208805 S.Raunser, R.Magnani, Z.Huang, R.L.Houtz, R.C.Trievel, P.A.Penczek, and T.Walz (2009).
Rubisco in complex with Rubisco large subunit methyltransferase.
  Proc Natl Acad Sci U S A, 106, 3160-3165.  
19734149 T.Genkov, and R.J.Spreitzer (2009).
Highly conserved small subunit residues influence rubisco large subunit catalysis.
  J Biol Chem, 284, 30105-30112.  
19279009 Y.Saito, H.Ashida, T.Sakiyama, N.T.de Marsac, A.Danchin, A.Sekowska, and A.Yokota (2009).
Structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Bacillus subtilis and photosynthetic RuBisCO.
  J Biol Chem, 284, 13256-13264.  
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
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.  
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.  
14506244 Y.C.Du, S.R.Peddi, and R.J.Spreitzer (2003).
Assessment of structural and functional divergence far from the large subunit active site of ribulose-1,5-bisphosphate carboxylase/oxygenase.
  J Biol Chem, 278, 49401-49405.  
12591867 Y.Marcus, H.Altman-Gueta, A.Finkler, and M.Gurevitz (2003).
Dual role of cysteine 172 in redox regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase activity and degradation.
  J Bacteriol, 185, 1509-1517.  
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
  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
11114203 Y.C.Du, S.Hong, and R.J.Spreitzer (2000).
RbcS suppressor mutations improve the thermal stability and CO2/O2 specificity of rbcL- mutant ribulose-1,5-bisphosphate carboxylase/oxygenase.
  Proc Natl Acad Sci U S A, 97, 14206-14211.  
10425677 A.Mattevi, G.Tedeschi, L.Bacchella, A.Coda, A.Negri, and S.Ronchi (1999).
Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.
  Structure, 7, 745-756.
PDB code: 1chu
10600135 E.L.Hegg, A.K.Whiting, R.E.Saari, J.McCracken, R.P.Hausinger, and L.Que (1999).
Herbicide-degrading alpha-keto acid-dependent enzyme TfdA: metal coordination environment and mechanistic insights.
  Biochemistry, 38, 16714-16726.  
10336462 H.Sugawara, H.Yamamoto, N.Shibata, T.Inoue, S.Okada, C.Miyake, A.Yokota, and Y.Kai (1999).
Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.
  J Biol Chem, 274, 15655-15661.
PDB code: 1bwv
10480884 J.Moreno, and R.J.Spreitzer (1999).
C172S substitution in the chloroplast-encoded large subunit affects stability and stress-induced turnover of ribulose-1,5-bisphosphate carboxylase/oxygenase.
  J Biol Chem, 274, 26789-26793.  
10375564 R.Douce, and M.Neuburger (1999).
Biochemical dissection of photorespiration.
  Curr Opin Plant Biol, 2, 214-222.  
10583377 S.Khan, P.J.Andralojc, P.J.Lea, and M.A.Parry (1999).
2'-carboxy-D-arabitinol 1-phosphate protects ribulose 1, 5-bisphosphate carboxylase/oxygenase against proteolytic breakdown.
  Eur J Biochem, 266, 840-847.  
9784589 M.Hippler, K.Redding, and J.D.Rochaix (1998).
Chlamydomonas genetics, a tool for the study of bioenergetic pathways.
  Biochim Biophys Acta, 1367, 1.  
  9541405 M.R.Harpel, F.W.Larimer, and F.C.Hartman (1998).
Multiple catalytic roles of His 287 of Rhodospirillum rubrum ribulose 1,5-bisphosphate carboxylase/oxygenase.
  Protein Sci, 7, 730-738.  
9799503 W.A.King, J.E.Gready, and T.J.Andrews (1998).
Quantum chemical analysis of the enolization of ribulose bisphosphate: the first hurdle in the fixation of CO2 by Rubisco.
  Biochemistry, 37, 15414-15422.  
9111007 S.Hong, and R.J.Spreitzer (1997).
Complementing substitutions at the bottom of the barrel influence catalysis and stability of ribulose-bisphosphate carboxylase/oxygenase.
  J Biol Chem, 272, 11114-11117.  
9092835 T.C.Taylor, and I.Andersson (1997).
Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.
  Biochemistry, 36, 4041-4046.
PDB codes: 1aa1 1aus
8909282 M.R.Harpel, and F.C.Hartman (1996).
Facilitation of the terminal proton transfer reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase by active-site Lys166.
  Biochemistry, 35, 13865-13870.  
8900108 N.Shibata, T.Inoue, K.Fukuhara, Y.Nagara, R.Kitagawa, S.Harada, N.Kasai, K.Uemura, K.Kato, A.Yokota, and Y.Kai (1996).
Orderly disposition of heterogeneous small subunits in D-ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach.
  J Biol Chem, 271, 26449-26452.
PDB code: 1bur
8955130 T.C.Taylor, M.D.Fothergill, and I.Andersson (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.
PDB codes: 1rbo 1rco
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.

 

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