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Information on EC 4.1.1.39 - ribulose-bisphosphate carboxylase and Organism(s) Oryza sativa and UniProt Accession P0C512
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EC Tree
4.1.1.39 ribulose-bisphosphate carboxylaseIUBMB Comments
Will utilize O2 instead of CO2, forming 3-phospho-D-glycerate and 2-phosphoglycolate.
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Word Map
- 4.1.1.39
- co2
- chloroplast
- chlorophyll
-
stomatal
- plastid
- mesophyll
- activase
- photosystems
- spinach
- seedling
- dioxide
- thylakoids
- phosphoenolpyruvate
- wheat
-
photorespiration
-
atmospheric
- maize
-
acclimation
- chlamydomonas
- cyanobacteria
- drought
- reinhardtii
-
autotroph
-
photochemical
- anhydrase
-
photorespiratory
-
calvin
-
climate
-
light-harvesting
-
transpiration
-
nuclear-encoded
- rubrum
- aestivum
- triticum
- rhodospirillum
- 3-phosphoglycerate
-
canopy
- synechococcus
- phosphoribulokinase
-
photoautotrophic
-
photochemistry
- analysis
-
crassulacean
- molecular biology
- lhcii
- biotechnology
-
photoinhibition
-
non-photochemical
-
carbamylation
- carboxylases
-
nadp-malic
- dikinase
-
oxygen-evolving
- biofuel production
- agriculture
The taxonomic range for the selected organisms is: Oryza sativa
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
rubisco, ribulose-1,5-bisphosphate carboxylase/oxygenase, ribulose-1,5-bisphosphate carboxylase, rubpcase, ribulose bisphosphate carboxylase, ribulose 1,5-bisphosphate carboxylase/oxygenase, ribulose 1,5-bisphosphate carboxylase, ribulose bisphosphate carboxylase/oxygenase, rubp carboxylase, rubisco small subunit, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Carboxydismutase
-
-
-
-
D-ribulose 1,5-bisphosphate carboxylase/oxygenase
D-Ribulose 1,5-diphosphate carboxylase
D-Ribulose-1,5-bisphosphate carboxylase
-
-
-
-
Diphosphoribulose carboxylase
-
-
-
-
LESS17
-
-
-
-
PSS15
-
-
-
-
PSSU1
-
-
-
-
Ribulose 1,5-bisphosphate carboxylase
-
-
-
-
Ribulose 1,5-bisphosphate carboxylase-oxygenase
-
-
-
-
Ribulose 1,5-bisphosphate carboxylase/oxygenase
-
-
-
-
Ribulose 1,5-diphosphate carboxylase
-
-
-
-
Ribulose 1,5-diphosphate carboxylase/oxygenase
-
-
-
-
Ribulose bisphosphate carboxylase-oxygenase
-
-
-
-
Ribulose diphosphate carboxylase
-
-
-
-
Ribulose diphosphate carboxylase/oxygenase
-
-
-
-
ribulose-1,5-bisphosphate carboxylase/oxygenase
Rubisco
RuBP carboxylase
-
-
-
-
Water stress responsive proteins 1, 2 and 14
-
-
-
-
D-Ribulose 1,5-diphosphate carboxylase
-
-
-
-
Rubisco
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
D-ribulose 1,5-bisphosphate + CO2 = 2 3-phospho-D-glycerate, carboxylase reaction
-
2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
D-Ribulose 1,5-bisphosphate + O2 = D-3-phosphoglycerate + 2-phosphoglycolate, oxygenase reaction
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylation
oxygenation
carboxylation
-
-
-
-
oxygenation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
3-phospho-D-glycerate carboxy-lyase (dimerizing; D-ribulose-1,5-bisphosphate-forming)
Will utilize O2 instead of CO2, forming 3-phospho-D-glycerate and 2-phosphoglycolate.
CAS REGISTRY NUMBER
COMMENTARY
9027-23-0
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-ribulose 1,5-bisphosphate + CO2 + H2O
2 3-phospho-D-glycerate + 2 H+
-
-
-
-
?
D-Ribulose 1,5-bisphosphate + O2
D-3-Phosphoglycerate + 2-phosphoglycolate
-
-
-
-
?
3-phospho-D-glycerate + H+
D-ribulose 1,5-bisphosphate + CO2 + H2O
-
-
-
r
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
-
-
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation, as the entry point of CO2 into the biosphere, enzyme is central to life on earth
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation, CO2 fixing enzyme that enables most forms of photo-and chemoautotrophic life
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
key enzyme responsible for photosynthetic carbon assimilation and photorespiratory carbon oxidation
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate + H+
-
-
-
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate + H+
-
-
-
?
D-ribulose 1,5-bisphosphate + O2
3-phospho-D-glycerate + 2-phosphoglycolate
-
-
-
?
D-ribulose 1,5-bisphosphate + O2
3-phospho-D-glycerate + 2-phosphoglycolate
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-phospho-D-glycerate + H+
D-ribulose 1,5-bisphosphate + CO2 + H2O
-
-
-
r
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation, as the entry point of CO2 into the biosphere, enzyme is central to life on earth
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation, CO2 fixing enzyme that enables most forms of photo-and chemoautotrophic life
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate
-
key enzyme responsible for photosynthetic carbon assimilation and photorespiratory carbon oxidation
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate + H+
-
-
-
-
?
D-ribulose 1,5-bisphosphate + CO2 + H2O
3-phospho-D-glycerate + H+
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
glyphosate
Q5K3B1; Q2QTJ7
N-(phosphonomethyl)glycine, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit is significantly decreased by the treatment with the herbicide
paraquat
Q5K3B1; Q2QTJ7
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit is significantly decreased by the treatment with the herbicide
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.2
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
ribulose-1,5-bisphosphate carboxylase/oxygenase large chain and small subunit; Oryza sativa L. cv. Dongjin
Q5K3B1; Q2QTJ7
UniProt
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
isoform RbcS1 is not expressed in leaf blade but in leaf sheath, culm, anther, and root central cylinder. Isoform RbcS3 is significantly expressed in mesophyll cells of leaf blade but not expressed in the basal, pale-green part of leaf sheath
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
-
comparison of Rubisco kinetics for 20 crop species at three different temperatures. Rubisco kinetics and their temperature dependency are species specific and largely affect the assimilation potential of Rubisco from the different crops
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). RBL_ORYSA
477
0
52881
Swiss-Prot
other Location (Reliability: 2)
A0A877P917_ORYSA
175
0
19403
TrEMBL
other Location (Reliability: 2)
A0A8G0G6R8_ORYSA
198
0
21908
TrEMBL
other Location (Reliability: 2)
A0A8E8PJS0_ORYSA
191
0
21105
TrEMBL
other Location (Reliability: 2)
R4I712_ORYSA
214
0
24017
TrEMBL
other Location (Reliability: 2)
A0A0F7EX29_ORYSA
196
0
21660
TrEMBL
other Location (Reliability: 2)
A0A2I7QEM0_ORYSA
218
0
24498
TrEMBL
other Location (Reliability: 2)
A0A140H518_ORYSA
182
0
20278
TrEMBL
other Location (Reliability: 2)
A0A7G8PYR4_ORYSA
158
0
17419
TrEMBL
other Location (Reliability: 3)
A0A7G8PYR6_ORYSA
159
0
17548
TrEMBL
other Location (Reliability: 2)
A0A0K1CVQ8_ORYSA
200
0
22126
TrEMBL
other Location (Reliability: 2)
A0A8E8PJQ8_ORYSA
189
0
20991
TrEMBL
other Location (Reliability: 2)
Q5K3B1_ORYSA
476
0
52794
TrEMBL
other Location (Reliability: 2)
I7EGE7_ORYSA
155
0
17205
TrEMBL
other Location (Reliability: 2)
Q32753_ORYSA
477
0
52884
TrEMBL
other Location (Reliability: 2)
A0A5P8KMJ9_ORYSA
477
0
52985
TrEMBL
other Location (Reliability: 2)
G9FKZ6_ORYSA
29
0
3446
TrEMBL
other Location (Reliability: 3)
Q37247_ORYSA
401
1
45131
TrEMBL
other Location (Reliability: 2)
L7X352_ORYSA
154
0
17023
TrEMBL
other Location (Reliability: 2)
I7DIZ0_ORYSA
121
0
13389
TrEMBL
other Location (Reliability: 3)
A0A8E8U7A8_ORYSA
190
0
21092
TrEMBL
other Location (Reliability: 2)
A0A8E8PJR0_ORYSA
190
0
21048
TrEMBL
other Location (Reliability: 2)
D3W4H3_ORYSA
234
0
26228
TrEMBL
other Location (Reliability: 2)
A0A7G8PYR8_ORYSA
157
0
17272
TrEMBL
other Location (Reliability: 2)
A0A0K0LL33_ORYSA
477
0
52881
TrEMBL
other Location (Reliability: 2)
A0A7L7YVM2_ORYSA
484
0
53701
TrEMBL
other Location (Reliability: 3)
A0A0N7AZ13_ORYSA
68
0
7233
TrEMBL
other Location (Reliability: 2)
A0A0R6DY16_ORYSA
68
0
7259
TrEMBL
other Location (Reliability: 2)
A0A8G0D3Q4_ORYSA
198
0
21907
TrEMBL
other Location (Reliability: 2)
A0A8E8PJV0_ORYSA
193
0
21319
TrEMBL
other Location (Reliability: 2)
G9FKZ4_ORYSA
29
0
3444
TrEMBL
other Location (Reliability: 2)
A0A8E8U760_ORYSA
188
0
20835
TrEMBL
other Location (Reliability: 2)
G9FKZ9_ORYSA
29
0
3460
TrEMBL
other Location (Reliability: 3)
A0A141KRA2_ORYSA
365
0
40488
TrEMBL
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
52000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterohexadecamer
8 * 55000 + 8 * 15000, calculated from amino acid sequence
hexadecamer
multimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with NADPH, 6-phosphogluconate, or 2-carboxy-D-arabinitol 1,5-bisphosphate, hanging drop vapor diffusion method, using 75 mM HEPES-KOH (pH 7.75 at 20°C), 9% (w/v) polyethylene glycol 4000, and 25% (v/v) glycerol
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
at low H2O2 concentrations (0.2-10 mM), the properties of the enzyme (e.g., structure and susceptibility to heat denaturation) change slightly. At higher H2O2 concentrations (10-200 mM), rubisco undergoes an unfolding process, including the loss of secondary and tertiary structure, forming extended hydrophobic interface, and leading to cross links between large subunits. High concentrations of H2O2 can also result in an increase in susceptibility of rubisco to heat denaturation. Further pretreatments with or without reductive reagents to rubisco show that the disulfide bonds in rubisco help to protect the enzyme from damage by H2O2 as well as other reactive oxygen species
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
rbcS expressed in Escherichia coli, together with rbcL from cyanobacteria generates functional holoenzyme
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
a method is established to remove ribulose bisphosphate carboxylase/oxygenase from plant samples to obtain high quality and high resolution 2D gels in proteome analysis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Makino, A.; Mae, T.; Ohira, K.
Enzymic properties of ribulose-1,5-bisphosphate carboxylase/oxygenase purified from rice leaves
Plant Physiol.
79
57-61
1985
Oryza sativa
Goldthwaite, J.; Bogorad, L.
Ribulose-1,5-diphosphate carboxylase from leaf
Methods Enzymol.
42C
481-484
1975
Citrus sinensis, Glycine max, Gossypium hirsutum, Helianthus annuus, Helianthus maximus, Medicago sativa, Solanum lycopersicum, Nicotiana tabacum, Oryza sativa, Petroselinum crispum, Solanum tuberosum, Sorghum bicolor, Spinacia oleracea, Zea mays
-
Spreitzer, R.J.; Salvucci, M.E.
Rubisco: Structure, regulatory interactions, and possibilities for a better enzyme
Annu. Rev. Plant Biol.
53
449-475
2002
Cupriavidus necator, Anabaena sp., Trichormus variabilis, Synechococcus elongatus PCC 7942 = FACHB-805, Arabidopsis thaliana, Chlamydomonas reinhardtii, Chlorobaculum tepidum, Cylindrotheca sp., Flaveria bidentis, Galdieria partita, Helianthus annuus, Solanum lycopersicum, Nicotiana tabacum, Oryza sativa, Thermococcus kodakarensis, Rhodospirillum rubrum, Spinacia oleracea, Synechococcus sp., Zea mays, Amphidinium carterae, Anabaena sp. CA
John Andrews, T.; Whitney, S.M.
Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants
Arch. Biochem. Biophys.
414
159-169
2003
Synechocystis sp., Arabidopsis thaliana, Flaveria bidentis, Galdieria sulphuraria, Nicotiana tabacum, Oryza sativa, Phaeodactylum tricornutum, Rhodospirillum rubrum, Griffithsia monilis
Parry, M.A.; Andralojc, P.J.; Mitchell, R.A.; Madgwick, P.J.; Keys, A.J.
Manipulation of Rubisco: the amount, activity, function and regulation
J. Exp. Bot.
54
1321-1333
2003
Allochromatium vinosum, Arabidopsis thaliana, Avena sativa, Chlamydomonas reinhardtii, Cylindrotheca sp., Flaveria bidentis, Galdieria partita, Galdieria sulphuraria, Glycine max, Helianthus annuus, Hordeum vulgare, Solanum lycopersicum, Nicotiana tabacum, Olisthodiscus luteus, Oryza sativa, Petunia sp., Phaeodactylum tricornutum, Pisum sativum, Rhodobacter capsulatus, Cereibacter sphaeroides, Rhodospirillum rubrum, Spinacia oleracea, Triticum aestivum, Zea mays, Cylindrotheca sp. N1
Li, S.; Lu, W.; Li, G.F.; Gong, Y.D.; Zhao, N.M.; Zhang, R.X.; Zhou, H.M.
Interaction of hydrogen peroxide with ribulose-1,5-bisphosphate carboxylase/oxygenase from rice
Biochemistry (Moscow)
69
1136-1142
2004
Oryza sativa
Jin, S.; Hong, J.; Li, X.; Jiang, D.
Antisense inhibition of Rubisco activase increases Rubisco content and alters the proportion of Rubisco activase in stroma and thylakoids in chloroplasts of rice leaves
Ann. Bot.
97
739-744
2006
Oryza sativa
Wu, H.R.; Li, L.B.; Jing, Y.X.; Kuang, T.Y.
Over-and anti-sense expressions of the large isoform of ribulose-1,5-bisphosphate carboxylase/oxygenase activase gene in Oryza sativa affect the photosynthetic capacity
Photosynthetica
45
194-201
2007
Oryza sativa
-
Tcherkez, G.G.; Farquhar, G.D.; Andrews, T.J.
Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized
Proc. Natl. Acad. Sci. USA
103
7246-7251
2006
Allochromatium vinosum, Amaranthus hybridus, Trichormus variabilis, Chlamydomonas reinhardtii, Euglena gracilis, Galdieria sulphuraria, Nicotiana tabacum, Oryza sativa, Phaeodactylum tricornutum, Rhodospirillum rubrum, Sorghum bicolor, Spinacia oleracea, Synechococcus sp., Triticum aestivum, Zea mays, Griffithsia monilis, Atriplex glabriuscula, Synechococcus sp. 6301, Synechococcus sp. 7002
Zhang, C.; Chen, L.; Shi, D.; Chen, G.; Lu, C.; Wang, P.; Wang, J.; Chu, H.; Zhou, Q.; Zuo, M.; Sun, L.
Characteristics of ribulose-1,5-bisphosphate carboxylase and C4 pathway key enzymes in flag leaves of a super-high-yield hybrid rice and its parents during the reproductive stage
S. Afr. J. Bot.
73
22-28
2007
Oryza sativa
-
Cho, J.; Hwang, H.; Cho, M.; Kwon, Y.; Jeon, J.; Bhoo, S.H.; Hahn, T.
The effect of DTT in protein preparations for proteomic analysis: Removal of a highly abundant plant enzyme, ribulose bisphosphate carboxylase/oxygenase
J. Plant Biol.
51
297-301
2008
Oryza sativa
-
Ahsan, N.; Lee, D.G.; Lee, K.W.; Alam, I.; Lee, S.H.; Bahk, J.D.; Lee, B.H.
Glyphosate-induced oxidative stress in rice leaves revealed by proteomic approach
Plant Physiol. Biochem.
46
1062-1070
2008
Oryza sativa (Q5K3B1 and Q2QTJ7), Oryza sativa
Andersson, I.; Backlund, A.
Structure and function of Rubisco
Plant Physiol. Biochem.
46
275-291
2008
Cupriavidus necator, Chlorobaculum tepidum, Galdieria partita, Nicotiana tabacum, Thermococcus kodakarensis, Rhodopseudomonas palustris, Synechococcus sp., Halothiobacillus neapolitanus, Geobacillus kaustophilus, Spinacia oleracea (O20253), Pyrococcus horikoshii (O58677), Rhodospirillum rubrum (P04718), Chlamydomonas reinhardtii (P08475), Oryza sativa (Q0INY7)
Matsumura, H.; Mizohata, E.; Ishida, H.; Kogami, A.; Ueno, T.; Makino, A.; Inoue, T.; Yokota, A.; Mae, T.; Kai, Y.
Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
J. Mol. Biol.
422
75-86
2012
Oryza sativa (P0C512 and Q0INY7), Oryza sativa
Morita, K.; Hatanaka, T.; Misoo, S.; Fukayama, H.
Unusual small subunit that is not expressed in photosynthetic cells alters the catalytic properties of Rubisco in rice
Plant Physiol.
164
69-79
2014
Oryza sativa
Studer, R.A.; Christin, P.A.; Williams, M.A.; Orengo, C.A.
Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
Proc. Natl. Acad. Sci. USA
111
2223-2228
2014
Oryza sativa
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