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PDBsum entry 8rub

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protein ligands metals Protein-protein interface(s) links
Lyase(carbon-carbon) PDB id
8rub
Jmol
Contents
Protein chains
123 a.a.
467 a.a.
Ligands
CAP
Metals
_MG
Superseded by: 8ruc 8ruc
PDB id:
8rub
Name: Lyase(carbon-carbon)
Structure: Ribulose 1,5-bisphosphate carboxylase(slash)oxygenase complex with co=2=,mg==++== and 2-carboxyarabinitol-1,5-bisphosphate
Source: Spinach (spinacia oleracea)
Authors: S.Knight,I.Andersson,C.- I.Branden
Key ref: S.Knight et al. (1990). Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site. J Mol Biol, 215, 113-160. PubMed id: 2118958 DOI: 10.1016/S0022-2836(05)80100-7
Date:
13-Nov-90     Release date:   15-Jul-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 123 a.a.
Protein chain
No UniProt id for this chain
Struc: 468 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0022-2836(05)80100-7 J Mol Biol 215:113-160 (1990)
PubMed id: 2118958  
 
 
Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site.
S.Knight, I.Andersson, C.I.Brändén.
 
  ABSTRACT  
 
The X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2.4 A resolution. Cyclic non-crystallographic symmetry averaging around the molecular 4-fold axis and phase combination were used to improve the initial multiple isomorphous replacement phases. A model composed of one large subunit and one small subunit was built in the resulting electron density map, which was of excellent quality. Application of the local symmetry gave an initial model of the L8S8 molecule with a crystallographic R-value of 0.43. Refinement of this initial model was performed by a combination of conventional least-squares energy refinement and molecular dynamics simulation using the XPLOR program. Three rounds of refinement, interspersed with manual rebuilding at the graphics display, resulted in a model containing all of the 123 amino acid residues in the small subunit, and 467 of the 475 residues in the large subunit. The R-value for this model is 0.24, with relatively small deviations from ideal stereochemistry. Subunit interactions in the L8S8 molecule have been analysed and are described. The interface areas between the subunits are extensive, and bury almost half of the accessible surface areas of both the large and the small subunit. A number of conserved interaction areas that may be of functional significance have been identified and are described, and biochemical and mutagenesis data are discussed in the structural framework of the model.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21172830 M.V.Kapralov, D.S.Kubien, I.Andersson, and D.A.Filatov (2011).
Changes in Rubisco kinetics during the evolution of C4 photosynthesis in Flaveria (Asteraceae) are associated with positive selection on genes encoding the enzyme.
  Mol Biol Evol, 28, 1491-1503.  
19661266 H.Eichelmann, E.Talts, V.Oja, E.Padu, and A.Laisk (2009).
Rubisco in planta kcat is regulated in balance with photosynthetic electron transport.
  J Exp Bot, 60, 4077-4088.  
19247501 S.Iida, A.Miyagi, S.Aoki, M.Ito, Y.Kadono, and K.Kosuge (2009).
Molecular adaptation of rbcL in the heterophyllous aquatic plant Potamogeton.
  PLoS ONE, 4, e4633.  
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.  
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
17498284 M.V.Kapralov, and D.A.Filatov (2007).
Widespread positive selection in the photosynthetic Rubisco enzyme.
  BMC Evol Biol, 7, 73.  
17661753 R.Sulpice, H.Tschoep, M.VON Korff, D.Büssis, B.Usadel, M.Höhne, H.Witucka-Wall, T.Altmann, M.Stitt, and Y.Gibon (2007).
Description and applications of a rapid and sensitive non-radioactive microplate-based assay for maximum and initial activity of D-ribulose-1,5-bisphosphate carboxylase/oxygenase.
  Plant Cell Environ, 30, 1163-1175.  
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.  
17183712 M.V.Kapralov, and D.A.Filatov (2006).
Molecular adaptation during adaptive radiation in the Hawaiian endemic genus Schiedea.
  PLoS ONE, 1, e8.  
16898026 W.Yamori, K.Suzuki, K.Noguchi, M.Nakai, and I.Terashima (2006).
Effects of Rubisco kinetics and Rubisco activation state on the temperature dependence of the photosynthetic rate in spinach leaves from contrasting growth temperatures.
  Plant Cell Environ, 29, 1659-1670.  
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
15822007 J.H.Venema, P.Linger, A.W.van Heusden, P.R.van Hasselt, and W.Brüggemann (2005).
The inheritance of chilling tolerance in tomato (Lycopersicon spp.).
  Plant Biol (Stuttg), 7, 118-130.  
15316720 J.Schwedock, T.L.Harmer, K.M.Scott, H.J.Hektor, A.P.Seitz, M.C.Fontana, D.L.Distel, and C.M.Cavanaugh (2004).
Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO.
  Arch Microbiol, 182, 18-29.  
15067012 S.A.Smith, and F.R.Tabita (2004).
Glycine 176 affects catalytic properties and stability of the Synechococcus sp. strain PCC6301 ribulose-1,5-bisphosphate carboxylase/oxygenase.
  J Biol Chem, 279, 25632-25637.  
14573957 A.C.Terwisscha van Scheltinga, K.Valegård, J.Hajdu, and I.Andersson (2003).
MIR phasing using merohedrally twinned crystals.
  Acta Crystallogr D Biol Crystallogr, 59, 2017-2022.  
12783874 F.G.Pearce, and T.J.Andrews (2003).
The relationship between side reactions and slow inhibition of ribulose-bisphosphate carboxylase revealed by a loop 6 mutant of the tobacco enzyme.
  J Biol Chem, 278, 32526-32536.  
12147471 B.Wawrik, J.H.Paul, and F.R.Tabita (2002).
Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes.
  Appl Environ Microbiol, 68, 3771-3779.  
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.  
11717489 A.C.Terwisscha van Scheltinga, K.Valegård, S.Ramaswamy, J.Hajdu, and I.Andersson (2001).
Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase.
  Acta Crystallogr D Biol Crystallogr, 57, 1776-1785.  
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
10666625 S.D.Knight (2000).
RSPS version 4.0: a semi-interactive vector-search program for solving heavy-atom derivatives.
  Acta Crystallogr D Biol Crystallogr, 56, 42-47.  
10446051 D.Choudhury, A.Thompson, V.Stojanoff, S.Langermann, J.Pinkner, S.J.Hultgren, and S.D.Knight (1999).
X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli.
  Science, 285, 1061-1066.
PDB code: 1qun
9988772 H.Ishida, A.Makino, and T.Mae (1999).
Fragmentation of the large subunit of ribulose-1,5-bisphosphate carboxylase by reactive oxygen species occurs near Gly-329.
  J Biol Chem, 274, 5222-5226.  
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
  10383960 K.M.Horken, and F.R.Tabita (1999).
The "green" form I ribulose 1,5-bisphosphate carboxylase/oxygenase from the nonsulfur purple bacterium Rhodobacter capsulatus.
  J Bacteriol, 181, 3935-3941.  
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.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
  J Biol Chem, 272, 3190-3194.  
9038145 M.K.Morell, J.M.Wilkin, H.J.Kane, and T.J.Andrews (1997).
Side reactions catalyzed by ribulose-bisphosphate carboxylase in the presence and absence of small subunits.
  J Biol Chem, 272, 5445-5451.  
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
8702495 G.Zhu, and R.J.Spreitzer (1996).
Directed mutagenesis of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Loop 6 substitutions complement for structural stability but decrease catalytic efficiency.
  J Biol Chem, 271, 18494-18498.  
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
7784428 D.W.Deerfield, D.J.Fox, M.Head-Gordon, R.G.Hiskey, and L.G.Pedersen (1995).
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.
  Proteins, 21, 244-255.  
  7663348 M.Gondry, K.H.Diêp Lê, F.D.Manson, S.K.Chapman, F.S.Mathews, G.A.Reid, and F.Lederer (1995).
On the lack of coordination between protein folding and flavin insertion in Escherichia coli for flavocytochrome b2 mutant forms Y254L and D282N.
  Protein Sci, 4, 925-935.  
  8563629 P.Dunten, and S.L.Mowbray (1995).
Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis.
  Protein Sci, 4, 2327-2334.
PDB code: 1dpp
8592705 T.Sandalova, and Y.Lindqvist (1995).
Three-dimensional model of the alpha-subunit of bacterial luciferase.
  Proteins, 23, 241-255.  
7744819 Y.R.Chen, and F.C.Hartman (1995).
A signature of the oxygenase intermediate in catalysis by ribulose-bisphosphate carboxylase/oxygenase as provided by a site-directed mutant.
  J Biol Chem, 270, 11741-11744.  
7813491 B.Gontero, M.T.Giudici-Orticoni, and J.Ricard (1994).
The modulation of enzyme reaction rates within multi-enzyme complexes. 2. Information transfer within a chloroplast multi-enzyme complex containing ribulose bisphosphate carboxylase-oxygenase.
  Eur J Biochem, 226, 999.  
7922027 J.Newman, and S.Gutteridge (1994).
Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate.
  Structure, 2, 495-502.
PDB code: 1rsc
7813490 J.Ricard, M.T.Giudici-Orticoni, and B.Gontero (1994).
The modulation of enzyme reaction rates within multi-enzyme complexes. 1. Statistical thermodynamics of information transfer through multi-enzyme complexes.
  Eur J Biochem, 226, 993-998.  
  8491708 G.D.Price, S.M.Howitt, K.Harrison, and M.R.Badger (1993).
Analysis of a genomic DNA region from the cyanobacterium Synechococcus sp. strain PCC7942 involved in carboxysome assembly and function.
  J Bacteriol, 175, 2871-2879.  
  8358297 G.J.Lee, K.A.McDonald, and B.A.McFadden (1993).
Leucine 332 influences the CO2/O2 specificity factor of ribulose-1,5-bisphosphate carboxylase/oxygenase from Anacystis nidulans.
  Protein Sci, 2, 1147-1154.  
8234342 H.A.Schreuder, S.Knight, P.M.Curmi, I.Andersson, D.Cascio, C.I.Brändén, and D.Eisenberg (1993).
Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form.
  Proc Natl Acad Sci U S A, 90, 9968-9972.  
  8358296 H.A.Schreuder, S.Knight, P.M.Curmi, I.Andersson, D.Cascio, R.M.Sweet, C.I.Brändén, and D.Eisenberg (1993).
Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.
  Protein Sci, 2, 1136-1146.  
8223630 M.Rault, M.T.Giudici-Orticoni, B.Gontero, and J.Ricard (1993).
Structural and functional properties of a multi-enzyme complex from spinach chloroplasts. 1. Stoichiometry of the polypeptide chains.
  Eur J Biochem, 217, 1065-1073.  
8433995 M.Wilmanns, and D.Eisenberg (1993).
Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.
  Proc Natl Acad Sci U S A, 90, 1379-1383.  
  8514750 R.B.Bourret, S.K.Drake, S.A.Chervitz, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. II. Analysis of activated mutants by 19F NMR and protein engineering.
  J Biol Chem, 268, 13089-13096.  
  8514749 S.K.Drake, R.B.Bourret, L.A.Luck, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering.
  J Biol Chem, 268, 13081-13088.  
1396677 A.Yokota, M.Higashioka, and A.Wadano (1992).
Regulation of the activity of ribulose-1,5-bisphosphate carboxylase/oxygenase through cooperative binding of 6-phosphogluconate to its regulatory sites.
  Eur J Biochem, 208, 721-727.  
1606957 E.Söderlind, G.Schneider, and S.Gutteridge (1992).
Substitution of ASP193 to ASN at the active site of ribulose-1,5-bisphosphate carboxylase results in conformational changes.
  Eur J Biochem, 206, 729-735.
PDB code: 1rba
1603801 G.G.Lu, Y.Lindqvist, and G.Schneider (1992).
Electrostatic fields at the active site of ribulose-1,5-bisphosphate carboxylase.
  Proteins, 12, 117-127.  
1889404 B.Ranty, G.Lorimer, and S.Gutteridge (1991).
An intra-dimeric crosslink of large subunits of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase is formed by oxidation of cysteine 247.
  Eur J Biochem, 200, 353-358.  
1904095 C.W.Morden, and S.S.Golden (1991).
Sequence analysis and phylogenetic reconstruction of the genes encoding the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase from the chlorophyll b-containing prokaryote Prochlorothrix hollandica.
  J Mol Evol, 32, 379-395.  
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.