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Topic: Ribulose-1,5-bisphosphate

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RuBP

Robert Hill (British biophysicist)

Photosynthesis

NADP

RUBISCO

PGA

Calvin cycle

Transmembrane ATPase

ATP synthase

Marxian

Adenosine triphosphate

Glycolysis

Citric acid cycle

List of biomolecules

Enzyme

homework5ans Ribulose bisphosphate carboxylase (Rubisco) is the enzyme responsible for catalyzing the addition of carbon dioxide to ribulose bisphosphate, forming two molecules of phosphoglycerate. In turn, ATP and NADPH are used in the dark reactions (light-independent reactions) of photosynthesis to convert phosphoglycerate to glyceraldehydes phosphate in the second stage of the Calvin-Benson cycle, and ATP is used to convert ribulose phosphate to ribulose bisphosphate in the third stage of the cycle. For this reason Rubisco is often referred to as ribulose bisphosphate carboxylase/oxygenase. www.lclark.edu /~lycan/Bio200/homework/answers52.html

PDB Molecule of the Month: Rubisco (Ribulose Bisphosphate Carboxylase/Oxygenase) Inside plant cells, the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco) forms the bridge between life and the lifeless, creating organic carbon from the inorganic carbon dioxide in the air. Most of the phosphoglycerate made by rubisco is recycled to build more ribulose bisphosphate, which is needed to feed the carbon-fixing cycle. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate, a short sugar chain with five carbon atoms. www.rcsb.org /pdb/molecules/pdb11_1.html

Michael W. Finn 2004 6360 Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) is one of the two unique enzymes of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway, along with phosphoribulokinase (PRK), the enzyme responsible for generating RuBP, the substrate for RubisCO. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure. www.bionewsonline.com /z/v/michael_w_finn_2004_6360.htm

Photosynthesis Research Unit : Archie Portis Lab Rubisco is an enzyme that initiates photosynthetic carbon metabolism by combining atmospheric carbon dioxide with a sugar phosphate -- ribulose bisphosphate -- in a reaction called carboxylation. Also, rubisco cannot prevent oxygen from reacting with some of the ribulose bisphosphate, allowing oxygenation to occur instead of carboxylation. For example, plants use about 25 percent of the nitrogen present in their leaves for the synthesis of rubisco because the carboxylation rate is slow compared to most other metabolic processes. www.ars.usda.gov /Research/docs.htm?docid=3346

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms -- Elsaied and Naganuma 67 (4): 1751 -- Applied and Environmental Microbiology Ribulose 1,5-bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. Nucleotide sequence of the ribulose bisphosphate carboxylase gene from Rhodospirillum rubrum. aem.asm.org /cgi/content/full/67/4/1751

PLB 308 Rubisco catalyzes a carboxylation reaction with ribulose bisphosphate that leads to the fixation on one carbon dioxide and the formation of two moleculesof phosphogyceric acid (PGA). Rubisco catalyzes an oxygenation reaction in which ribulose bisphosphate is split into one, three carbon molecule (PGA) and one, two carbon molecule--phosphogylcolate. Ribulose bisphosphate carboxylase oxygenase (rubisco) has two activities. lsvl.la.asu.edu /plb308/Text/wherewewerebeforespringbreak.html

DARK REACTIONS Ribulose bisphosphate carboxylase (Rubisco) catalyzes the reaction between CO2 and the five carbon sugar ribulose bisphosphate. Ribulose bisphosphate carboxylase is not a very efficient enzyme in comparison to other enzyme substrate-enzyme interactions (in terms of Km and Vmax); but realize carbon dioxide is small with no charges so what is there for an active site to grab onto? Eventually the ribulose bisphosphate is regenerated so that it may again bind to another CO2 molecule. www.mrs.umn.edu /~goochv/CellBio/lectures/darkrxn/darkrxn.html

Expression of glnB and a glnB-Like Gene (glnK) in a Ribulose Bisphosphate Carboxylase/Oxygenase-Deficient Mutant of Rhodobacter sphaeroides -- Qian and Tabita 180 (17): 4644 -- The Journal of Bacteriology In a ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deficient mutant of Rhodobacter sphaeroides, strain 16PHC, Expression of endogenous and foreign ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) genes in a RubisCO deletion mutant of Rhodobacter sphaeroides. Strain 16 of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides, a ribulose bisphosphate carboxylase/oxygenase jb.asm.org /cgi/content/full/180/17/4644

Illustration of the Calvin Cycle The enzyme for this reaction is ribulose bisphosphate carboxylase or Rubisco. To begin the Calvin cycle, a molecule of CO reacts with a five-carbon compound called ribulose bisphosphate (RuBP) producing an unstable six-carbon intermediate which immediately breaks down into two molecules of the three-carbon compound phosphoglycerate (PGA). Each molecule of RP then becomes phosphorylated by the hydrolysis of ATP to produce ribulose bisphosphate (RuBP), the starting compound for the Calvin cycle. www.cat.cc.md.us /courses/bio141/lecguide/unit4/metabolism/photosyn/fg7.html

Ferreira Lab Ferreira, R.B. and Davies, D.D. (1987) Protein degradation in Lemna with particular reference to ribulose bisphosphate carboxylase II. Ferreira, R.B. and Davies, D.D. (1987) Protein degradation in Lemna with particular reference to ribulose bisphosphate carboxylase I. Ferreira, R.M.B., Franco, E. and Teixeira, A.R.N. Covalent dimerization of ribulose bisphosphate carboxylase subunits by UV radiation. www.mobot.org /jwcross/duckweed/Ferreira-lab.htm

Gready_u53_98 King, J. Gready and T. Andrews, Quantum Chemical Analysis of the Enolization of Ribulose Bisphosphate: The First Hurdle in the Fixation of CO2 by Rubisco, Biochemistry, 37, 1998, 15414-15422. We have examined the first step in the reaction catalysed by Rubisco, the enolisation of ribulose bisphosphate. What is the essential base that initiates the reaction by removing a proton from Rubisco's substrate, ribulose bisphosphate? anusf.anu.edu.au /annual_reports/annual_report98/Appendix_A/I_Gready_u53_98.html

g.pl?D00-355xp D00/355 1bwvY 204.2.1.1.1.1 ribulose bisphosphate carboxylase (rubisco) biological_ 1bwvY 1bwvW 1bwvU 204.2.1.1.1.1 ribulose bisphosphate carboxylase (rubisco) biological_ 1bwvY 204.2.1.1.1.1 ribulose bisphosphate carboxylase (rubisco) biological_ 1bwvW 204.2.1.1.1.1 ribulose bisphosphate carboxylase (rubisco) biological_ 1bwvU 204.2.1.1.1.1 ribulose bisphosphate carboxylase (rubisco) biological_ 1bwvS bioinformatics.ljcrf.edu /FFAS/cgi-bin/g.pl?D00-355xp

Botanik online: rubisco The enzyme from spinach was crystallized together with the substrate ribulose bisphosphate (blue in the above figure). The X-ray diffraction data of this complex gave clues to the reaction mechanism and it's stereo chemistry. To the right there is a side view, below is shown a view along the four-fold symmetry axis. www.biologie.uni-hamburg.de /b-online/fo24_1/e1rxoe.htm

References - rubisco - HORT640 - Metabolic Plant Physiology - Department of Horticulture and Landscape Architecture - Purdue University Qian Y, Tabita FR 1998 Expression of glnB and a glnB-like gene (glnK) in a ribulose bisphosphate carboxylase/oxygenase-deficient mutant of Rhodobacter sphaeroides. Hubbs AE, Roy H 1993 Assembly of in vitro-synthesized large subunits into ribulose bisphosphate carboxylase/oxygenase is sensitive to Cl-, requires ATP, and does not proceed when large subunits are synthesized at temperatures greater than or equal to 32 C. Plant Physiol. Li LA, Zianni MR, Tabita FR 1999 Inactivation of the monocistronic rca gene in Anabaena variabilis suggests a physiological ribulose bisphosphate carboxylase/oxygenase activase-like function in heterocystous cyanobacteria. www.hort.purdue.edu /rhodcv/hort640c/referen/rubisco.htm

XXIII Through a sequence of reactions, 6 molecules of 3-P-Glycerate (produced from 3 molecules of Ribulose Diphosphate and 3 CO) are reduced and rearranged at the expense of 9 ATP and 6 NADPH to produce 1 molecule of glyceraldehyde-3-Phos. and regenerating the 3 molecules of Ribulose Diphosphate. Glyceraldehyde-3-Phosphate is used in the synthesis of carbohydrate or it can be reoxidized in the cytoplasm producing cytoplasmic ATP and NADPH for biosynthetic reactions. www.sci.sdsu.edu /class/bio202/TFrey/Photosynthesis.html

betaelim.html During catalytic turnover of ribulose bisphosphate by several mutants, substantial amounts of the substrate are diverted to 1-deoxy-D-glycero-2,3-pentodiulose 5-phosphate, reflecting To study the functional contributions of the residues implicated in ribulose bisphosphate binding and intermediate stabilization, we have replaced them individually with alanine, either to remove the H-bonding group (T53A, N54A) or to introduce bulk (G370A, G393A, G394A). Consequences of substitutions include diminution of carboxylase activity (with a lesser impact on enolization activity), increase of Km (ribulose bisphosphate), and decrease of carboxylation: oxygenation specificity. compbio.ornl.gov /~fwl/betaelim.html

Biological Sciences at Wright State University in Dayton, Ohio RubisCO is the enzyme of the Calvin-Benson-Bassham pathway that fixes CO2 onto ribulose 1,5-bisphosphate (RuBP). Our lab seeks to understand the molecular and structural determinants of ribulose 1,5-bisphosphate carboxylase/oxygenase RubisCO specificity. In a competing reaction, O2 is fixed onto RuBP, initiating a photorespiratory pathway which ultimately results in carbon and energy loss for the organism. biology.wright.edu /faculty/smith

Plant Gene Register PGR98-196 Holden PJ, Brown RW (1993) Amplification of ribulose bisphosphate carboxylase/oxygenase large subunit (RuBisCo LSU) gene fragments from Thiobacillus ferrooxidans and a moderate thermophile using the polymerase chain reaction. www.tarweed.com /pgr/PGR98-196.html

pubs.html Examination of the intersubunit interaction between Glutamate-48 and Lysine-168 of ribulose bisphosphate carboxylase/oxygenase by site-directed mutagenesis. A reconstruction of the gene for ribulose bisphosphate carboxylase from Rhodospirillum rubrum that expresses the authentic enzyme in Escherichia coli. Function of active-site residues of ribulose bisphosphate carboxylase/oxygenase. genome.ornl.gov /~fwl/pubs.html

Manipulation of Rubisco: the amount, activity, function and regulation -- Parry et al. 54 (386): 1321 -- Journal of Experimental Botany Release of the nocturnal inhibitor, carboxyarabinitol-1-phosphate, from ribulose bisphosphate carboxylase/oxygenase by Rubisco activase. Effect of mutation of lysine-128 of the large subunit of ribulose bisphosphate carboxylase/oxygenase from Anacystis nidulans. A hybrid ribulose bisphosphate carboxylase oxygenase enzyme exhibiting a substantial increase in substrate-specificity. jxb.oxfordjournals.org /cgi/content/full/54/386/1321

Photosynthetic carbon reduction A limited carboxylation capacity cannot be offset by a higher capacity for regeneration of the CO acceptor ribulose 1,5-bisphosphate (RuBP). Dietz, K.-J., Heber, U. (1986) Light and CO limitations of photosynthesis and states of the reactions regenerating ribulose 1,5-bisphosphate or reducing 3-phosphoglycerate. Sharkey, T.D. (1990) Feedback limitation of photosynthesis and the physiological role of ribulose bisphosphate carboxylase carbamylation. www.wisc.edu /biotron/Sharkey/Courses/Biochem621/CHAPTER.html

Plant Physiology carbon dioxide condenses with RuBP (ribulose bisphosphate; C5) to form 2 molecules of PGA (C3) The reaction catalyzed by ribulose bisphosphate carboxylase/ oxygenase. catalyzed by the enzyme ribulose bisphosphate carboxylase (rubisco). employees.csbsju.edu /SSAUPE/biol327/Lecture/photosyn-carbon.htm

DHS Data Page: DHSdata.2.0003.0030.0070.0150.html Activated ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) complexed with the reaction intermediate analogue 2-carboxyarabinitol 1,5-bisphosphate RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN 2 (EC 4.1.1.39) (RUBISCO LARGE SUBUNIT) RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (EC4.1.1.39) (RUBISCO LARGE SUBUNIT) www.biochem.ucl.ac.uk /bsm/dhs/class3/0003.0030.0070.0150/DHSdata.2.0003.0030.0070.0150.html

Yehouda Marcus 2003 1509 Alkylation and oxidation of cysteine residues significantly decrease the catalytic activity and stimulate the degradation of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Construction of a Synechocystis PCC 6803 mutant suitable for the study of variant hexadecameric ribulose bisphosphate carboxylase/oxygenase enzymes. Evidence for an in vivo conformational change in ribulose bisphosphate carboxylase-oxygenase from Puma rye during cold adaptation. www.bionewsonline.com /g/e/yehouda_marcus_2003_1509.htm

Rubisco Activity: Effects of Drought Stress -- PARRY et al. 89 (7): 833 -- Annals of Botany Inactive forms of wheat ribulose bisphosphate carboxylase – conversion from the slowly activating into the rapidly activating form. Elevated CO and water deficit effects on photosynthesis, ribulose bisphosphate carboxylase-oxygenase, and carbohydrate metabolism in rice. Formation of a carboxyarabinitol biphosphate complex with ribulose bisphosphate carboxylase/oxygenase and theoretical specific activity of the enzyme. aob.oxfordjournals.org /cgi/content/full/89/7/833

The Dictionary of Cell and Molecular Biology - Online! There were 4 hits for ribulose in 7070 records. RMP pathway (= ribulose monophosphate pathway; allulose phosphate pathway.) www.mblab.gla.ac.uk /~julian/dict2.cgi?ribulose

Blackwell Plant Sciences - Latest News - [Article Title] All three of these forms are capable of reacting 1,5-ribulose bisphosphate with carbon dioxide or it’s competitor, molecular oxygen — the key step in the Calvin cycle. In higher plants and algae and some photosynthetic bacteria, RuBisCO functions as a 16-subunit complex composed equal numbers of two unrelated polypeptides to catalyse the addition of CO to 1,5 ribulose bisphosphate. The RuBisCO reaction is effectively three separate reactions: enolization, carboxylation (or oxygenation) and the hydrolysis of the 1,5-ribulose bisphosphate (RuBP)-CO adjunct to make two molecules of 3-phosphoglycerate. www.blackwellpublishing.com /plantsci/latest/article.asp?id=31

OCA Atlas for 8RUC Rubisco catalyzes two reactions ribulose 1,5-bisphosphate, the primary event in photosynthetic carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate., Andersson I, J Mol Biol 1996 May 31;259(1):160-74. Both reactions occur simultaneously and in competition at the same active site. oca.ebi.ac.uk /oca-bin/ocashort?id=8ruc

ncbicites.txt (__3694826__)CCMP1665DEFINITION Pleurochloridella botrydiopsis ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, chloroplast gene encoding chloroplast protein, partial cds. (__3694820__)CCMP637DEFINITION Phaeothamnion confervicola ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, chloroplast gene encoding chloroplast protein, partial cds. (__3694824__)CCMP823DEFINITION Stichogloea doederleinii ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, chloroplast gene encoding chloroplast protein, partial cds. ccmp.bigelow.org /SD/ncbicites.txt

The transcription of the cbb operon in Nitrosomonas europaea -- Wei et al. 150 (6): 1869 -- Microbiology Hayashi, N. R., Terazono, K., Kodama, T. and Igarashi, Y. Structure of ribulose 1,5-bisphosphate carboxylase/oxygenase gene cluster from a thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus, and phylogeny of the fructose 1,6-bisphosphate aldolase encoded by cbbA in the cluster. Viale, A. M., Kobayashi, H., Akazawa, T. and Henikoff, S. rbcR [correction of rcbR], a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in the photosynthetic bacterium Chromatium vinosum. Lee, S. and Kim, Y. Cloning and characterization of ribulose bisphosphate carboxylase gene of a carboxydobacterium, Hydrogenophagea pseudoflava DSM 1084. mic.sgmjournals.org /cgi/content/full/150/6/1869

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