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PDBsum entry 1rcx

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protein ligands Protein-protein interface(s) links
Lyase (carbon-carbon) PDB id
1rcx
Jmol
Contents
Protein chains
(+ 2 more) 467 a.a.
(+ 2 more) 123 a.a. *
Ligands
RUB ×8
Waters ×1768
* Residue conservation analysis
PDB id:
1rcx
Name: Lyase (carbon-carbon)
Title: Non-activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate
Structure: Ribulose bisphosphate carboxylase/oxygenase. Chain: l, b, e, h, k, o, r, v. Synonym: rubisco. Ribulose bisphosphate carboxylase/oxygenase. Chain: s, c, f, i, m, p, t, w. Synonym: rubisco. Ec: 4.1.1.39
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: 60mer (from PQS)
Resolution:
2.40Å     R-factor:   0.224     R-free:   0.237
Authors: T.C.Taylor,I.Andersson
Key ref:
T.C.Taylor and I.Andersson (1997). The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. J Mol Biol, 265, 432-444. PubMed id: 9034362 DOI: 10.1006/jmbi.1996.0738
Date:
06-Dec-96     Release date:   16-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
467 a.a.*
Protein chains
Pfam   ArchSchema ?
P00870  (RBS1_SPIOL) -  Ribulose bisphosphate carboxylase small chain
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 L, S, B, C, E, F, H, I, K, M, O, P, R, T, V, W: 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 = RUB)
corresponds exactly
+ 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.1996.0738 J Mol Biol 265:432-444 (1997)
PubMed id: 9034362  
 
 
The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate.
T.C.Taylor, I.Andersson.
 
  ABSTRACT  
 
The three-dimensional structure of the complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco; EC 4.1.1.39) from spinach with its natural substrate ribulose 1,5-bisphosphate (RuBP) has been determined both under activating and non-activating conditions by X-ray crystallography to a resolution of 2.1 A and 2.4 A, respectively. Under activating conditions, the use of calcium instead of magnesium as the activator metal ion enabled us to trap the substrate in a stable complex for crystallographic analysis. Comparison of the structure of the activated and the non-activated RuBP complexes shows a tighter binding for the substrate in the non-activated form of the enzyme, in line with previous solution studies. In the non-activated complex, the substrate triggers isolation of the active site by inducing movements of flexible loop regions of the catalytic subunits. In contrast, in the activated complex the active site remains partly open, probably awaiting the binding of the gaseous substrate. By inspection of the structures and by comparison with other complexes of the enzyme we were able to identify a network of hydrogen bonds that stabilise a closed active site structure during crucial steps in the reaction. The present structure underlines the central role of the carbamylated lysine 201 in both activation and catalysis, and completes available structural information for our proposal on the mechanism of the enzyme.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Comparison of the active-site structures in the activated RuBP complex (magenta), the non-activated RuBP complex (blue) and the 2CABP complex (atoms coloured according to atom type). In the open form of the enzyme (activated RuBP complex, magenta), loop 6 of the a/b-barrel is swung away from the active site, and lies outside the image frame of the Figure. In the closed structures, the loop is folded over the active site with Lys334 at its tip, interacting with the substrate. Further differences between the open and closed forms are seen in the N-terminal loops, one beginning with Glu60 and the other centred at Asn123. Coordinates for the 2CABP complex of spinach rubisco are from the 1.6 Å resolution refined structure (8RUC, Andersson, 1996). Superposition of the structures was carried out using O (Jones et al., 1991). The picture was produced with MOLSCRIPT (Kraulis, 1991), modified by Robert Esnouf (Oxford University, unpublished). For the sake of simplicity, only key residues are labelled. See the bottom stereo pair of Figure 5 (same orientation) for further residue numbering.
Figure 7.
Figure 7. The reaction mechanism for carboxylation by rubisco based on the present structure.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 265, 432-444) copyright 1997.  
  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
19238429 K.Lohrig, B.Müller, J.Davydova, D.Leister, and D.A.Wolters (2009).
Phosphorylation site mapping of soluble proteins: bioinformatical filtering reveals potential plastidic phosphoproteins in Arabidopsis thaliana.
  Planta, 229, 1123-1134.  
18849407 R.G.Coleman, and K.A.Sharp (2009).
Finding and characterizing tunnels in macromolecules with application to ion channels and pores.
  Biophys J, 96, 632-645.  
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.  
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.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
17669419 C.V.Iancu, H.J.Ding, D.M.Morris, D.P.Dias, A.D.Gonzales, A.Martino, and G.J.Jensen (2007).
The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography.
  J Mol Biol, 372, 764-773.  
17498284 M.V.Kapralov, and D.A.Filatov (2007).
Widespread positive selection in the photosynthetic Rubisco enzyme.
  BMC Evol Biol, 7, 73.  
17150955 S.M.Whitney, and R.E.Sharwood (2007).
Linked Rubisco subunits can assemble into functional oligomers without impeding catalytic performance.
  J Biol Chem, 282, 3809-3818.  
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
15766539 S.Dutta, and H.M.Berman (2005).
Large macromolecular complexes in the Protein Data Bank: a status report.
  Structure, 13, 381-388.  
16228002 Y.Zhai, F.Sun, X.Li, H.Pang, X.Xu, M.Bartlam, and Z.Rao (2005).
Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer.
  Nat Struct Mol Biol, 12, 980-986.
PDB code: 2ahm
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.  
12524213 S.A.Ensign, and J.R.Allen (2003).
Aliphatic epoxide carboxylation.
  Annu Rev Biochem, 72, 55-76.  
12529884 S.Chakrabarti, S.Bhattacharya, and S.K.Bhattacharya (2003).
Immobilization of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a step toward carbon dioxide fixation bioprocess.
  Biotechnol Bioeng, 81, 705-711.  
12904291 S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, and M.Fischer (2003).
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.
  J Biol Chem, 278, 42256-42265.
PDB codes: 1pvw 1pvy
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.  
11821404 S.Luo, H.Ishida, A.Makino, and T.Mae (2002).
Fe2+-catalyzed site-specific cleavage of the large subunit of ribulose 1,5-bisphosphate carboxylase close to the active site.
  J Biol Chem, 277, 12382-12387.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
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
10903941 N.M.Okeley, and W.A.van der Donk (2000).
Novel cofactors via post-translational modifications of enzyme active sites.
  Chem Biol, 7, R159-R171.  
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
10375564 R.Douce, and M.Neuburger (1999).
Biochemical dissection of photorespiration.
  Curr Opin Plant Biol, 2, 214-222.  
  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.  
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
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.