RuBisCO - Wikipedia

Download as pdf or txt
Download as pdf or txt
You are on page 1of 86

RuBisCO

Ribulose-1,5-bisphosphate carboxylase-
oxygenase, commonly known by the
abbreviations RuBisCo, rubisco,[1]
RuBPCase, or RuBPco, is an enzyme
involved in the first major step of carbon
fixation, a process by which the
atmospheric carbon dioxide is converted
by plants and other photosynthetic
organisms to energy-rich molecules such
as glucose. In chemical terms, it
catalyzes the carboxylation of ribulose-
1,5-bisphosphate (also known as RuBP).
It is probably the most abundant enzyme
on Earth.[2][3][4]
Ribulose-1,5-bisphosphate
carboxylase oxygenase

A 3d depiction of the activated RuBisCO


from spinach in open form with active site
accessible. The active site Lys175 residues
are marked in pink, and a close-up of the
residue is provided to the right for one of the
monomers composing the enzyme.

Identifiers

EC number 4.1.1.39

CAS number 9027-23-0

Databases

IntEnz IntEnz view


BRENDA BRENDA entry
ExPASy NiceZyme view

KEGG KEGG entry

MetaCyc metabolic pathway

PRIAM profile

PDB structures RCSB PDB PDBe


PDBsum

Gene Ontology AmiGO / QuickGO

Search

PMC articles

PubMed articles

NCBI proteins

Alternative carbon fixation


pathways
RuBisCO is important biologically
because it catalyzes the primary
chemical reaction by which inorganic
carbon enters the biosphere. While many
autotrophic bacteria and archaea fix
carbon via the reductive acetyl CoA
pathway, the 3-hydroxypropionate cycle,
or the reverse Krebs cycle, these
pathways are relatively small
contributors to global carbon fixation
compared to that catalyzed by RuBisCO.
Phosphoenolpyruvate carboxylase, unlike
RuBisCO, only temporarily fixes carbon.
Reflecting its importance, RuBisCO is the
most abundant protein in leaves,
accounting for 50% of soluble leaf
protein in C3 plants (20–30% of total leaf
nitrogen) and 30% of soluble leaf protein
in C4 plants (5–9% of total leaf
nitrogen).[4] Given its important role in
the biosphere, the genetic engineering of
RuBisCO in crops is of continuing
interest (see below).

Structure

Active site of RuBisCO of Galdieria sulphuraria with


CO2. Residues involved in both the active site and
stabilizing CO2 for enzyme catalysis are shown in
color and labeled. Distances of the hydrogen
bonding interactions are shown in Angstroms. Mg2+
ion (green sphere) is shown coordinated to CO2,
and is followed by three water molecules (red
and is followed by three water molecules (red
spheres). All other residues are placed in grayscale.

Location of the rbcL gene in the chloroplast


genome of Arabidopsis thaliana (positions ca. 55-
56.4 kb). rbcL is one of the 21 protein-coding genes
involved in photosynthesis (green boxes).

In plants, algae, cyanobacteria, and


phototrophic and chemoautotrophic
proteobacteria, the enzyme usually
consists of two types of protein subunit,
called the large chain (L, about 55,000
Da) and the small chain (S, about 13,000
Da). The large-chain gene (rbcL) is
encoded by the chloroplast DNA in
plants.[5] There are typically several
related small-chain genes in the nucleus
of plant cells, and the small chains are
imported to the stromal compartment of
chloroplasts from the cytosol by crossing
the outer chloroplast membrane.[6][7] The
enzymatically active substrate (ribulose
1,5-bisphosphate) binding sites are
located in the large chains that form
dimers in which amino acids from each
large chain contribute to the binding
sites. A total of eight large-chains (= 4
dimers) and eight small chains assemble
into a larger complex of about 540,000
Da.[8] In some proteobacteria and
dinoflagellates, enzymes consisting of
only large subunits have been found.[9]

2+
Magnesium ions (Mg ) are needed for
enzymatic activity. Correct positioning of
2+
Mg in the active site of the enzyme
involves addition of an "activating"
carbon dioxide molecule (CO2) to a lysine
in the active site (forming a
carbamate).[10] Mg2+ operates by driving
deprotonation of the Lys210 residue,
causing the Lys residue to rotate by 120
degrees to the trans conformer,
decreasing the distance between the
nitrogen of Lys and the carbon of CO2.
The close proximity allows for the
formation of a covalent bond, resulting in
the carbamate.[11] Mg2+ is first enabled
to bind to the active site by the rotation
of His335 to an alternate conformation.
Mg2+ is then coordinated by the His
residues of the active site (His300,
His302, His335), and is partially
neutralized by the coordination of three
water molecules and their conversion to
−OH.[11] This coordination results in an
unstable complex, but produces a
favorable environment for the binding of
Mg2+. Formation of the carbamate is
favored by an alkaline pH. The pH and
the concentration of magnesium ions in
the fluid compartment (in plants, the
stroma of the chloroplast[12]) increases
in the light. The role of changing pH and
magnesium ion levels in the regulation of
RuBisCO enzyme activity is discussed
below. Once the carbamate is formed,
His335 finalizes the activation by
returning to its initial position through
thermal fluctuation.[11]
RuBisCO large RuBisCO, N-term
chain, domain
catalytic domain Identifiers

Identifiers Symbol RuBisCO_la

Symbol RuBisCO_large Pfam PF027

Pfam PF00016 InterPro IPR01

InterPro IPR000685 SCOP2 3rub

PROSITE PDOC00142 SCOP


SUPFA
SCOP2 3rub /
SCOPe / Available protei
structures:
SUPFAM
Pfam   structu
CDD cd08148
ECOD
Available protein
PDB RCSB
structures:
PDBe
Pfam   structures
/ ECOD   PDBsum structu
PDB RCSB summ
PDB 1aa1, 1
PDB ;
1bwv,
PDBe ;
1ej7, 1
PDBj
1gk8, 1
PDBsum structure 1ir2, 1i
summary 1rba, 1
PDB 1aa1, 1aus, 1rbo, 1
1bwv, 1bxn 1rcx, 1
, 1ej7, 1geh 1rsc, 1
, 1gk8, 1ir1, 1rxo, 1
1ir2, 1iwa, 1tel, 1u
1rba, 1rbl, 1upp, 1
1rbo, 1rco, 1uwa,
1rcx, 1rld, 1uzh, 1
1rsc, 1rus, 1ykw,
1rxo, 1svd, 2cxe, 2
1tel, 1upm, 2qyg, 2
1upp, 1uw9 2v63, 2
, 1uwa, 2v68, 2
1uzd, 1uzh, 2v6a, 3
1wdd, 4rub, 5
1ykw, 2cwx 8ruc, 9
, 2cxe,
2d69, 2qyg,
2rus, 2v63,
2v67, 2v68,
2v69, 2v6a,
3rub, 4rub,
5rub, 8ruc,
9rub

Enzymatic activity
Two main reactions of RuBisCo: CO2 fixation and
oxygenation.

RuBisCO is one of many enzymes in the


Calvin cycle. When Rubisco facilitates
the attack of CO2 at the C2 carbon of
RuBP and subsequent bond cleavage
between the C3 and C2 carbon, 2
molecules of glycerate-3-phosphate are
formed. The conversion involves these
steps: enolisation, carboxylation,
hydration, C-C bond cleavage, and
protonation.[13][14][15]

Substrates …
Substrates for RuBisCO are ribulose-1,5-
bisphosphate and carbon dioxide
(distinct from the "activating" carbon
dioxide).[16] RuBisCO also catalyses a
reaction of ribulose-1,5-bisphosphate
and molecular oxygen (O2) instead of
carbon dioxide (CO2). Discriminating
between the substrates CO2 and O2 is
attributed to the differing interactions of
the substrate's quadrupole moments and
a high electrostatic field gradient.[11] This
gradient is established by the dimer form
of the minimally active RuBisCO, which
with its two components provides a
combination of oppositely charged
domains required for the enzyme's
interaction with O2 and CO2. These
conditions help explain the low turnover
rate found in RuBisCO: In order to
increase the strength of the electric field
necessary for sufficient interaction with
the substrates’ quadrupole moments, the
C- and N- terminal segments of the
enzyme must be closed off, allowing the
active site to be isolated from the solvent
and lowering the dielectric constant.[17]
This isolation has a significant entropic
cost, and results in the poor turnover
rate.

Binding RuBP …

Carbamylation of the ε-amino group of


Lys201 is stabilized by coordination with
the Mg2+.[18] This reaction involves
binding of the carboxylate termini of
Asp203 and Glu204 to the Mg2+ ion. The
substrate RuBP binds Mg2+ displacing
two of the three aquo ligands.[13][19][20]

Enolisation …

Enolisation of RuBP is the conversion of


the keto tautomer of RuBP to an
enediol(ate). Enolisation is initiated by
deprotonation at C3. The enzyme base in
this step has been debated, [19][21] but the
steric constraints observed in crystal
structures have made Lys201 the most
likely candidate.[13] Specifically, the
carbamate oxygen on Lys201 that is not
coordinated with the Mg ion
deprotonates the C3 carbon of RuBP to
form a 2,3-enediolate.[19][20]

Carboxylation …

A 3D image of the active site of spinach RuBisCO


complexed with the inhibitor 2-Carboxyarabinitol-
1,5-Bisphosphate, CO2, and Mg2+. (PDB: 1IR1;
Ligand View [CAP]501:A)

Carboxylation of the 2,3-enediolate


results in the intermediate 3-keto-2′-
carboxyarabinitol-1,5-bisphosphate and
Lys334 is positioned to facilitate the
addition of the CO2 substrate as it
replaces the third Mg2+-coordinated
water molecule and add directly to the
enediol. No Michaelis complex is formed
in this process.[13][21] Hydration of this
ketone results in an additional hydroxy
group on C3, forming a gem-diol
intermediate.[19][22] Carboxylation and
hydration have been proposed as either a
single concerted step[19] or as two
sequential steps.[22] Concerted
mechanism is supported by the proximity
of the water molecule to C3 of RuBP in
multiple crystal structures. Within the
spinach structure, other residues are well
placed to aid in the hydration step as
they are within hydrogen bonding
distance of the water molecule.[13]
C-C bond cleavage …

The gem-diol intermediate cleaves at the


C2-C3 bond to form one molecule of
glycerate-3-phosphate and a negatively
charge carboxylate.[13] Stereo specific
protonation of C2 of this carbanion
results in another molecule of glycerate-
3-phosphate. This step is thought to be
facilitated by Lys175 or potentially the
carbamylated Lys201.[13]

Products …

When carbon dioxide is the substrate, the


product of the carboxylase reaction is an
unstable six-carbon phosphorylated
intermediate known as 3-keto-2-
carboxyarabinitol-1,5-bisphosphate,
which decays rapidly into two molecules
of glycerate-3-phosphate. The 3-
phosphoglycerate can be used to
produce larger molecules such as
glucose.

Rubisco side activities can lead to


useless or inhibitory by-products; one
such product is xylulose-1,5-
bisphosphate, which inhibits Rubisco
activity.[23]

When molecular oxygen is the substrate,


the products of the oxygenase reaction
are phosphoglycolate and 3-
phosphoglycerate. Phosphoglycolate is
recycled through a sequence of reactions
called photorespiration, which involves
enzymes and cytochromes located in the
mitochondria and peroxisomes (this is a
case of metabolite repair). In this
process, two molecules of
phosphoglycolate are converted to one
molecule of carbon dioxide and one
molecule of 3-phosphoglycerate, which
can reenter the Calvin cycle. Some of the
phosphoglycolate entering this pathway
can be retained by plants to produce
other molecules such as glycine. At
ambient levels of carbon dioxide and
oxygen, the ratio of the reactions is about
4 to 1, which results in a net carbon
dioxide fixation of only 3.5. Thus, the
inability of the enzyme to prevent the
reaction with oxygen greatly reduces the
photosynthetic capacity of many plants.
Some plants, many algae, and
photosynthetic bacteria have overcome
this limitation by devising means to
increase the concentration of carbon
dioxide around the enzyme, including C4
carbon fixation, crassulacean acid
metabolism, and the use of pyrenoid.

Rate of enzymatic activity …


Overview of the Calvin cycle and carbon fixation.

Some enzymes can carry out thousands


of chemical reactions each second.
However, RuBisCO is slow, fixing only 3-
10 carbon dioxide molecules each
second per molecule of enzyme.[24] The
reaction catalyzed by RuBisCO is, thus,
the primary rate-limiting factor of the
Calvin cycle during the day. Nevertheless,
under most conditions, and when light is
not otherwise limiting photosynthesis,
the speed of RuBisCO responds
positively to increasing carbon dioxide
concentration.

RuBisCO is usually only active during the


day, as ribulose 1,5-bisphosphate is not
regenerated in the dark. This is due to the
regulation of several other enzymes in
the Calvin cycle. In addition, the activity
of RuBisCO is coordinated with that of
the other enzymes of the Calvin cycle in
several other ways:

By ions …

Upon illumination of the chloroplasts, the


pH of the stroma rises from 7.0 to 8.0
+
because of the proton (hydrogen ion, H )
gradient created across the thylakoid
membrane. The movement of protons
into thylakoids is driven by light and is
fundamental to ATP synthesis in
chloroplasts (Further reading:
Photosynthetic reaction centre; Light-
dependent reactions). To balance ion
potential across the membrane,
2+
magnesium ions (Mg ) move out of the
thylakoids in response, increasing the
concentration of magnesium in the
stroma of the chloroplasts. RuBisCO has
a high optimal pH (can be >9.0,
depending on the magnesium ion
concentration) and, thus, becomes
"activated" by the introduction of carbon
dioxide and magnesium to the active
sites as described above.

By RuBisCO activase …

In plants and some algae, another


enzyme, RuBisCO activase (Rca,
GO:0046863 , P10896), is required to
allow the rapid formation of the critical
carbamate in the active site of
RuBisCO.[25][26] This is required because
ribulose 1,5-bisphosphate (RuBP) binds
more strongly to the active sites of
RuBisCO when excess carbamate is
present, preventing processes form
moving forward. In the light, RuBisCO
activase promotes the release of the
inhibitory (or — in some views — storage)
RuBP from the catalytic sites of RuBisCO.
Activase is also required in some plants
(e.g., tobacco and many beans) because,
in darkness, RuBisCO is inhibited (or
protected from hydrolysis) by a
competitive inhibitor synthesized by
these plants, a substrate analog 2-
Carboxy-D-arabitinol 1-phosphate
(CA1P).[27] CA1P binds tightly to the
active site of carbamylated RuBisCO and
inhibits catalytic activity to an even
greater extent. CA1P has also been
shown to keep RuBisCO in a
conformation that is protected from
proteolysis.[28] In the light, RuBisCO
activase also promotes the release of
CA1P from the catalytic sites. After the
CA1P is released from RuBisCO, it is
rapidly converted to a non-inhibitory form
by a light-activated CA1P-phosphatase.
Even without these strong inhibitors,
once every several hundred reactions, the
normal reactions with carbon dioxide or
oxygen are not completed; other
inhibitory substrate analogs are still
formed in the active site. Once again,
RuBisCO activase can promote the
release of these analogs from the
catalytic sites and maintain the enzyme
in a catalytically active form. However, at
high temperatures, RuBisCO activase
aggregates and can no longer activate
RuBisCO. This contributes to the
decreased carboxylating capacity
observed during heat stress.[29][30]

By ATP/ADP and stromal


reduction/oxidation state through the …

activase

The removal of the inhibitory RuBP, CA1P,


and the other inhibitory substrate
analogs by activase requires the
consumption of ATP. This reaction is
inhibited by the presence of ADP, and,
thus, activase activity depends on the
ratio of these compounds in the
chloroplast stroma. Furthermore, in most
plants, the sensitivity of activase to the
ratio of ATP/ADP is modified by the
stromal reduction/oxidation (redox) state
through another small regulatory protein,
thioredoxin. In this manner, the activity of
activase and the activation state of
RuBisCO can be modulated in response
to light intensity and, thus, the rate of
formation of the ribulose 1,5-
bisphosphate substrate.[31]

By phosphate …

In cyanobacteria, inorganic phosphate


(Pi) also participates in the co-ordinated
regulation of photosynthesis: Pi binds to
the RuBisCO active site and to another
site on the large chain where it can
influence transitions between activated
and less active conformations of the
enzyme. In this way, activation of
bacterial RuBisCO might be particularly
sensitive to Pi levels, which might cause
it to act in a similar way to how RuBisCO
activase functions in higher plants.[32]

By carbon dioxide …

Since carbon dioxide and oxygen


compete at the active site of RuBisCO,
carbon fixation by RuBisCO can be
enhanced by increasing the carbon
dioxide level in the compartment
containing RuBisCO (chloroplast
stroma). Several times during the
evolution of plants, mechanisms have
evolved for increasing the level of carbon
dioxide in the stroma (see C4 carbon
fixation). The use of oxygen as a
substrate appears to be a puzzling
process, since it seems to throw away
captured energy. However, it may be a
mechanism for preventing carbohydrate
overload during periods of high light flux.
This weakness in the enzyme is the
cause of photorespiration, such that
healthy leaves in bright light may have
zero net carbon fixation when the ratio of
O2 to CO2 available to RuBisCO shifts too
far towards oxygen. This phenomenon is
primarily temperature-dependent: High
temperatures can decrease the
concentration of CO2 dissolved in the
moisture of leaf tissues. This
phenomenon is also related to water
stress: Since plant leaves are
evaporatively cooled, limited water
causes high leaf temperatures. C4 plants
use the enzyme PEP carboxylase initially,
which has a higher affinity for CO2. The
process first makes a 4-carbon
intermediate compound, which is
shuttled into a site of C3 photosynthesis
then de-carboxylated, releasing CO2 to
boost the concentration of CO2, hence
the name C4 plants.

Crassulacean acid metabolism (CAM)


plants keep their stomata closed during
the day, which conserves water but
prevents the light-independent reactions
(a.k.a. the Calvin Cycle) from taking
place, since these reactions require CO2
to pass by gas exchange through these
openings. Evaporation through the upper
side of a leaf is prevented by a layer of
wax.

Genetic engineering
Since RuBisCO is often rate-limiting for
photosynthesis in plants, it may be
possible to improve photosynthetic
efficiency by modifying RuBisCO genes in
plants to increase catalytic activity
and/or decrease oxygenation
rates.[33][34][35][36] This could improve
biosequestration of CO2 and be both an
important climate change strategy and a
strategy to increase crop yields.[37]
Approaches under investigation include
transferring RuBisCO genes from one
organism into another organism,
engineering Rubisco activase from
thermophilic cyanobacteria into
temperature sensitive plants, increasing
the level of expression of RuBisCO
subunits, expressing RuBisCO small
chains from the chloroplast DNA, and
altering RuBisCO genes to increase
specificity for carbon dioxide or
otherwise increase the rate of carbon
fixation.[38][39]

Mutagenesis in plants …
In general, site-directed mutagenesis of
RuBisCO has been mostly
unsuccessful,[37] though mutated forms
of the protein have been achieved in
tobacco plants with subunit C4
species,[40] and a RuBisCO with more C4-
like kinetic characteristics have been
attained in rice via nuclear
transformation.[41]

One avenue is to introduce RuBisCO


variants with naturally high specificity
values such as the ones from the red
alga Galdieria partita into plants. This
may improve the photosynthetic
efficiency of crop plants, although
possible negative impacts have yet to be
studied.[42] Advances in this area include
the replacement of the tobacco enzyme
with that of the purple photosynthetic
bacterium Rhodospirillum rubrum.[43] In
2014, two transplastomic tobacco lines
with functional RuBisCO from the
cyanobacterium Synechococcus
elongatus PCC7942 (Se7942) were
created by replacing the RuBisCO with
the large and small subunit genes of the
Se7942 enzyme, in combination with
either the corresponding Se7942
assembly chaperone, RbcX, or an internal
carboxysomal protein, CcmM35. Both
mutants had increased CO2 fixation rates
when measured as carbon molecules per
RuBisCO. However, the mutant plants
grew more slowly than wild-type.[44]

A recent theory explores the trade-off


between the relative specificity (i.e.,
ability to favour CO2 fixation over O2
incorporation, which leads to the energy-
wasteful process of photorespiration)
and the rate at which product is formed.
The authors conclude that RuBisCO may
actually have evolved to reach a point of
'near-perfection' in many plants (with
widely varying substrate availabilities and
environmental conditions), reaching a
compromise between specificity and
reaction rate.[45] It has been also
suggested that the oxygenase reaction of
RuBisCO prevents CO2 depletion near its
active sites and provides the
maintenance of the chloroplast redox
state.[46]

Since photosynthesis is the single most


effective natural regulator of carbon
dioxide in the Earth's atmosphere,[47] a
biochemical model of RuBisCO reaction
is used as the core module of climate
change models. Thus, a correct model of
this reaction is essential to the basic
understanding of the relations and
interactions of environmental models.

Expression in bacterial hosts …


There currently are very few effective
methods for expressing functional plant
Rubisco in bacterial hosts for genetic
manipulation studies. This is largely due
to Rubisco's requirement of complex
cellular machinery for its biogenesis and
metabolic maintenance including the
nuclear-encoded RbcS subunits, which
are typically imported into chloroplasts
as unfolded proteins.[48][49] Furthermore,
sufficient expression and interaction with
Rubisco activase are major challenges as
well.[50] One successful method for
expression of Rubisco in E. coli involves
the co-expression of multiple chloroplast
chaperones, though this has only been
shown for Arabidopsis thaliana
Rubisco.[51]

Depletion in proteomic
studies
Due to its high abundance in plants
(generally 40% of the total protein
content), RuBisCO often impedes
analysis of important signaling proteins
such as transcription factors, kinases,
and regulatory proteins found in lower
abundance (10-100 molecules per cell)
within plants.[52] For example, using
mass spectrometry on plant protein
mixtures would result in multiple intense
RuBisCO subunit peaks that interfere and
hide those of other proteins.

Recently, one efficient method for


precipitating out RuBisCO involves the
usage of protamine sulfate solution.[53]
Other existing methods for depleting
RuBisCO and studying lower abundance
proteins include fractionation techniques
with calcium and phytate,[54] gel
electrophoresis with polyethylene
glycol,[55][56] affinity
chromatography,[57][58] and aggregation
using DTT,[59] though these methods are
more time-consuming and less efficient
when compared to protamine sulfate
precipitation.[52]
Phylogenetic studies
The chloroplast gene rbcL, which codes
for the large subunit of RuBisCO has
been widely used as an appropriate locus
for analysis of phylogenetics in plant
taxonomy.[60]

Evolution of RuBisCO …

With the evolution of the C4-fixation


pathway in certain species of plants, C3
RuBisCO evolved to have faster turnover
of CO2 in exchange for lower specificity
as a result of the greater localization of
CO2 from the mesophyll cells into the
bundle sheath cells.[61] This was
achieved through enhancement of
conformational flexibility of the “open-
closed” transition in the Calvin Cycle.
Laboratory-based phylogenetic studies
have shown that this evolution was
constrained by the trade-off between
stability and activity brought about by the
series of necessary mutations for C4
RuBisCO.[62] Moreover, in order to sustain
the destabilizing mutations, the evolution
to C4 RuBisCO was preceded by a period
in which mutations granted the enzyme
increased stability, establishing a buffer
to sustain and maintain the mutations
required for C4 RuBisCO. To assist with
this buffering process, the newly-evolved
enzyme was found to have further
developed a series of stabilizing
mutations. While RuBisCO has always
been accumulating new mutations, most
of these mutations that have survived
have not had significant effects on
protein stability. The destabilizing C4
mutations on RuBisCO has been
sustained by environmental pressures
such as low CO2 concentrations,
requiring a sacrifice of stability for new
adaptive functions.[62]

History of the term


The term "RuBisCO" was coined
humorously in 1979, by David Eisenberg
at a seminar honouring the retirement of
the early, prominent RuBisCO researcher,
Sam Wildman, and also alluded to the
snack food trade name "Nabisco" in
reference to Wildman's attempts to
create an edible protein supplement from
tobacco leaves.[63][64]

The capitalization of the name has been


long debated. It can be capitalized for
each letter of the full name (Ribulose-1,5
bisphosphate carboxylase/oxgenase),
but it has also been argued that is should
all be in lower case (rubisco), similar to
other terms like scuba or laser.

See also
Carbon cycle
Photorespiration
Pyrenoid

C4 carbon fixation
Crassulacean acid metabolism/CAM
photosynthesis
Carboxysome

References
1. Sharkey, TD (2019). "Discovery of the
canonical Calvin-Benson cycle".
Photosynth Res. 53 (2): 835–18.
doi:10.1007/s11120-018-0600-2 .
OSTI 1607740 . PMID 30374727 .
S2CID 53092349 .
2. Cooper, Geoffrey M. (2000). "10.The
Chloroplast Genome" . The Cell: A
Molecular Approach (2nd ed.).
Washington, D.C: ASM Press.
ISBN 978-0-87893-106-4. ", one of
the subunits of ribulose
bisphosphate carboxylase (rubisco)
is encoded by chloroplast DNA.
Rubisco is the critical enzyme that
catalyzes the addition of CO2 to
ribulose-1,5-bisphosphate during the
Calvin cycle. It is also thought to be
the single most abundant protein on
Earth, so it is noteworthy that one of
its subunits is encoded by the
chloroplast genome."
3. Dhingra A, Portis AR, Daniell H (April
2004). "Enhanced translation of a
chloroplast-expressed RbcS gene
restores small subunit levels and
photosynthesis in nuclear RbcS
antisense plants" . Proceedings of
the National Academy of Sciences of
the United States of America. 101
(16): 6315–20.
Bibcode:2004PNAS..101.6315D .
doi:10.1073/pnas.0400981101 .
PMC 395966 . PMID 15067115 . "
(Rubisco) is the most prevalent
enzyme on this planet, accounting
for 30–50% of total soluble protein
in the chloroplast;"
4. Feller U, Anders I, Mae T (2008).
"Rubiscolytics: fate of Rubisco after
its enzymatic function in a cell is
terminated" (PDF). Journal of
Experimental Botany. 59 (7): 1615–
24. doi:10.1093/jxb/erm242 .
PMID 17975207 .
5. (Entrez GeneID: )
6. Dhingra A, Portis AR, Daniell H (April
2004). "Enhanced translation of a
chloroplast-expressed RbcS gene
restores small subunit levels and
photosynthesis in nuclear RbcS
antisense plants" . Proceedings of
the National Academy of Sciences of
the United States of America. 101
(16): 6315–20.
Bibcode:2004PNAS..101.6315D .
doi:10.1073/pnas.0400981101 .
PMC 395966 . PMID 15067115 .
7. Arabidopsis thaliana has four
RuBisCO small chain genes.
Yoon M, Putterill JJ, Ross GS, Laing
WA (April 2001). "Determination of
the relative expression levels of
rubisco small subunit genes in
Arabidopsis by rapid amplification of
cDNA ends". Analytical
Biochemistry. 291 (2): 237–44.
doi:10.1006/abio.2001.5042 .
PMID 11401297 .
8. Stryer, Lubert; Berg, Jeremy Mark;
Tymoczko, John L. (2002). "20. The
Calvin Cycle and the Pentose
Phosphate Pathway" . Biochemistry
(5th ed.). San Francisco: W.H.
Freeman. ISBN 978-0-7167-3051-4.
"Figure 20.3. Structure of Rubisco.
(Color-coded ribbon diagram)"
9. The structure of RuBisCO from the
photosynthetic bacterium
Rhodospirillum rubrum has been
determined by X-ray crystallography,
see: PDB: 9RUB. A comparison of
the structures of eukaryotic and
bacterial RuBisCO is shown in the
Protein Data Bank feature article on
Rubisco.
10. Molecular Cell Biology , 4th edition,
by Harvey Lodish, Arnold Berk, S.
Lawrence Zipursky, Paul Matsudaira,
David Baltimore and James E.
Darnell. Published by W. H. Freeman
& Co. (2000) New York. Online
textbook. Figure 16-48 shows a
structural model of the active site,
including the involvement of
magnesium. The Protein Data Bank
feature article on RuBisCO also
includes a model of magnesium at
the active site Archived 2006-01-09
at the Wayback Machine.
11. Stec B (November 2012). "Structural
mechanism of RuBisCO activation by
carbamylation of the active site
lysine" . Proceedings of the National
Academy of Sciences of the United
States of America. 109 (46): 18785–
90.
Bibcode:2012PNAS..10918785S .
doi:10.1073/pnas.1210754109 .
PMC 3503183 . PMID 23112176 .
12. The Lodish textbook describes the
localization of RuBisCO to the
stromal space of chloroplasts.
Figure 17-7 illustrates how RuBisCO
small subunits move into the
chloroplast stroma and assemble
with the large subunits.
13. Andersson, Inger (May 2008).
"Catalysis and regulation in
Rubisco" . Journal of Experimental
Botany. 59 (7): 1555–1568.
doi:10.1093/jxb/ern091 .
PMID 18417482 .
14. Erb, Tobias; Zarzycki, Jan (February
2018). "A short history of RubisCO:
the rise and fall (?) of Nature's
predominant CO2 fixing enzyme" .
Current Opinion in Biotechnology.
49: 100–107.
doi:10.1016/j.copbio.2017.07.017 .
PMID 28843191 .
15. Schneider, Gunter; Lundqvis, Tomas
(5 July 1991). "Crystal Structure of
Activated Ribulose- 1,5-bisphosphate
Carboxylase Complexed with Its
Substrate, Ribulose- 1,5-
bisphosphate*" . The Journal of
Biological Chemistry. 266 (19):
12604–12611. doi:10.1016/S0021-
9258(18)98942-8 . PMID 1905726 .
16. The chemical reactions catalyzed
by RuBisCO are described in the
online Biochemistry textbook by
Stryer et al.
17. Satagopan S, Spreitzer RJ (July
2008). "Plant-like substitutions in the
large-subunit carboxy terminus of
Chlamydomonas Rubisco increase
CO2/O2 specificity" . BMC Plant
Biology. 8: 85. doi:10.1186/1471-
2229-8-85 . PMC 2527014 .
PMID 18664299 .
18. Lorimer, G; Miziorko, H (1980).
"Carbamate Formation on the c-
Amino Group of a Lysyl Residue as
the Basis for the Activation of
Ribulosebisphosphate Carboxylase
by C02 and Mg2+". Biochemistry. 19
(23): 5321–5328.
doi:10.1021/bi00564a027 .
PMID 6778504 .
19. Cleland, W; Lorimer, G (1998).
"Mechanism of Rubisco: The
Carbamate as General Base".
Chemical Reviews. 98 (2): 549−561.
doi:10.1021/cr970010r .
PMID 11848907 .
20. Andersson, I; Knight, S; Schneider, G;
Lindqvist, Y; Lindqvist, T; Brändén, CI;
Lorimer, GH (1989). "Crystal
structure of the active site of
ribulose-bisphosphate carboxylase".
Nature. 337 (6204): 229–234.
Bibcode:1989Natur.337..229A .
doi:10.1038/337229a0 .
S2CID 4370073 .
21. Hartman, F. C.; Harpel, M. R. (1994).
"Structure, Function, Regulation, and
Assembly of D-Ribulose-1,5-
Bisphosphate
Carboxylase/Oxygenase". Annual
Review of Biochemistry. 63: 197–
232.
doi:10.1146/annurev.bi.63.070194.0
01213 . PMID 7979237 .
22. Taylor, TC; Andersson, I (1997). "The
structure of the complex between
rubisco and its natural substrate
ribulose-1,5-bisphosphate". Journal
of Molecular Biology. 265 (4): 432–
444. doi:10.1006/jmbi.1996.0738 .
PMID 9034362 .
23. Pearce FG (November 2006).
"Catalytic by-product formation and
ligand binding by ribulose
bisphosphate carboxylases from
different phylogenies" . The
Biochemical Journal. 399 (3): 525–
34. doi:10.1042/BJ20060430 .
PMC 1615894 . PMID 16822231 .
24. Ellis RJ (January 2010).
"Biochemistry: Tackling unintelligent
design". Nature. 463 (7278): 164–5.
Bibcode:2010Natur.463..164E .
doi:10.1038/463164a .
PMID 20075906 .
S2CID 205052478 .
25. Portis AR (2003). "Rubisco activase -
Rubisco's catalytic chaperone".
Photosynthesis Research. 75 (1):
11–27.
doi:10.1023/A:1022458108678 .
PMID 16245090 . S2CID 2632 .
26. Jin SH, Jiang DA, Li XQ, Sun JW
(August 2004). "Characteristics of
photosynthesis in rice plants
transformed with an antisense
Rubisco activase gene" . Journal of
Zhejiang University Science. 5 (8):
897–9.
doi:10.1631/jzus.2004.0897 .
PMID 15236471 . S2CID 1496584 .
27. Andralojc PJ, Dawson GW, Parry MA,
Keys AJ (December 1994).
"Incorporation of carbon from
photosynthetic products into 2-
carboxyarabinitol-1-phosphate and
2-carboxyarabinitol" . The
Biochemical Journal. 304 ( Pt 3) (3):
781–6. doi:10.1042/bj3040781 .
PMC 1137402 . PMID 7818481 .
28. Khan S, Andralojc PJ, Lea PJ, Parry
MA (December 1999). "2'-carboxy-D-
arabitinol 1-phosphate protects
ribulose 1, 5-bisphosphate
carboxylase/oxygenase against
proteolytic breakdown" (PDF).
European Journal of Biochemistry.
266 (3): 840–7. doi:10.1046/j.1432-
1327.1999.00913.x .
PMID 10583377 .
29. Salvucci ME, Osteryoung KW, Crafts-
Brandner SJ, Vierling E (November
2001). "Exceptional sensitivity of
Rubisco activase to thermal
denaturation in vitro and in vivo" .
Plant Physiology. 127 (3): 1053–64.
doi:10.1104/pp.010357 .
PMC 129275 . PMID 11706186 .
30. Crafts-Brandner SJ, Salvucci ME
(November 2000). "Rubisco activase
constrains the photosynthetic
potential of leaves at high
temperature and CO2" . Proceedings
of the National Academy of Sciences
of the United States of America. 97
(24): 13430–5.
Bibcode:2000PNAS...9713430C .
doi:10.1073/pnas.230451497 .
PMC 27241 . PMID 11069297 .
31. Zhang N, Kallis RP, Ewy RG, Portis AR
(March 2002). "Light modulation of
Rubisco in Arabidopsis requires a
capacity for redox regulation of the
larger Rubisco activase isoform" .
Proceedings of the National
Academy of Sciences of the United
States of America. 99 (5): 3330–4.
Bibcode:2002PNAS...99.3330Z .
doi:10.1073/pnas.042529999 .
PMC 122518 . PMID 11854454 .
32. Marcus Y, Gurevitz M (October
2000). "Activation of cyanobacterial
RuBP-carboxylase/oxygenase is
facilitated by inorganic phosphate
via two independent mechanisms".
European Journal of Biochemistry.
267 (19): 5995–6003.
doi:10.1046/j.1432-
1327.2000.01674.x .
PMID 10998060 .
33. Spreitzer RJ, Salvucci ME (2002).
"Rubisco: structure, regulatory
interactions, and possibilities for a
better enzyme" . Annual Review of
Plant Biology. 53: 449–75.
doi:10.1146/annurev.arplant.53.1003
01.135233 . PMID 12221984 .
S2CID 9387705 .
34. Timmer J (7 December 2017). "We
may now be able to engineer the
most important lousy enzyme on the
planet" . Ars Technica. Retrieved
5 January 2019.
35. Timmer J (3 January 2019). "Fixing
photosynthesis by engineering it to
recycle a toxic mistake" . Ars
Technica. Retrieved 5 January 2019.
36. South PF, Cavanagh AP, Liu HW, Ort
DR (January 2019). "Synthetic
glycolate metabolism pathways
stimulate crop growth and
productivity in the field" . Science.
363 (6422): eaat9077.
doi:10.1126/science.aat9077 .
PMC 7745124 . PMID 30606819 .
37. Furbank RT, Quick WP, Sirault XR
(2015). "Improving photosynthesis
and yield potential in cereal crops by
targeted genetic manipulation:
Prospects, progress and
challenges" . Field Crops Research.
182: 19–29.
doi:10.1016/j.fcr.2015.04.009 .
38. Parry MA, Andralojc PJ, Mitchell RA,
Madgwick PJ, Keys AJ (May 2003).
"Manipulation of Rubisco: the
amount, activity, function and
regulation" . Journal of Experimental
Botany. 54 (386): 1321–33.
doi:10.1093/jxb/erg141 .
PMID 12709478 .
39. Ogbaga CC, Stepien P, Athar HU,
Ashraf M (June 2018). "Engineering
Rubisco activase from thermophilic
cyanobacteria into high-temperature
sensitive plants". Critical Reviews in
Biotechnology. 38 (4): 559–572.
doi:10.1080/07388551.2017.13789
98 . PMID 28937283 .
S2CID 4191791 .
40. Whitney SM, Sharwood RE, Orr D,
White SJ, Alonso H, Galmés J
(August 2011). "Isoleucine 309 acts
as a C4 catalytic switch that
increases ribulose-1,5-bisphosphate
carboxylase/oxygenase (rubisco)
carboxylation rate in Flaveria" .
Proceedings of the National
Academy of Sciences of the United
States of America. 108 (35): 14688–
93.
Bibcode:2011PNAS..10814688W .
doi:10.1073/pnas.1109503108 .
PMC 3167554 . PMID 21849620 .
41. Ishikawa C, Hatanaka T, Misoo S,
Miyake C, Fukayama H (July 2011).
"Functional incorporation of
sorghum small subunit increases the
catalytic turnover rate of Rubisco in
transgenic rice" . Plant Physiology.
156 (3): 1603–11.
doi:10.1104/pp.111.177030 .
PMC 3135941 . PMID 21562335 .
42. Whitney SM, Andrews TJ (December
2001). "Plastome-encoded bacterial
ribulose-1,5-bisphosphate
carboxylase/oxygenase (RubisCO)
supports photosynthesis and growth
in tobacco" . Proceedings of the
National Academy of Sciences of the
United States of America. 98 (25):
14738–43.
Bibcode:2001PNAS...9814738W .
doi:10.1073/pnas.261417298 .
PMC 64751 . PMID 11724961 .
43. John Andrews T, Whitney SM (June
2003). "Manipulating ribulose
bisphosphate
carboxylase/oxygenase in the
chloroplasts of higher plants".
Archives of Biochemistry and
Biophysics. 414 (2): 159–69.
doi:10.1016/S0003-9861(03)00100-
0 . PMID 12781767 .
44. Lin MT, Occhialini A, Andralojc PJ,
Parry MA, Hanson MR (September
2014). "A faster Rubisco with
potential to increase photosynthesis
in crops" . Nature. 513 (7519): 547–
50. Bibcode:2014Natur.513..547L .
doi:10.1038/nature13776 .
PMC 4176977 . PMID 25231869 .
45. Tcherkez GG, Farquhar GD, Andrews
TJ (May 2006). "Despite slow
catalysis and confused substrate
specificity, all ribulose bisphosphate
carboxylases may be nearly perfectly
optimized" . Proceedings of the
National Academy of Sciences of the
United States of America. 103 (19):
7246–51.
Bibcode:2006PNAS..103.7246T .
doi:10.1073/pnas.0600605103 .
PMC 1464328 . PMID 16641091 .
46. Igamberdiev AU (2015). "Control of
Rubisco function via homeostatic
equilibration of CO2 supply" .
Frontiers in Plant Science. 6: 106.
doi:10.3389/fpls.2015.00106 .
PMC 4341507 . PMID 25767475 .
47. Igamberdiev AU, Lea PJ (February
2006). "Land plants equilibrate O2
and CO2 concentrations in the
atmosphere". Photosynthesis
Research. 87 (2): 177–94.
doi:10.1007/s11120-005-8388-2 .
PMID 16432665 . S2CID 10709679 .
48. Bracher A, Whitney SM, Hartl FU,
Hayer-Hartl M (April 2017).
"Biogenesis and Metabolic
Maintenance of Rubisco". Annual
Review of Plant Biology. 68: 29–60.
doi:10.1146/annurev-arplant-
043015-111633 . PMID 28125284 .
49. Sjuts I, Soll J, Bölter B (2017).
"Import of Soluble Proteins into
Chloroplasts and Potential
Regulatory Mechanisms" . Frontiers
in Plant Science. 8: 168.
doi:10.3389/fpls.2017.00168 .
PMC 5296341 . PMID 28228773 .
50. Parry, M. A. J. (2003-05-01).
"Manipulation of Rubisco: the
amount, activity, function and
regulation" . Journal of Experimental
Botany. 54 (386): 1321–1333.
doi:10.1093/jxb/erg141 . ISSN 0022-
0957 . PMID 12709478 .
51. Aigner H, Wilson RH, Bracher A,
Calisse L, Bhat JY, Hartl FU, Hayer-
Hartl M (December 2017). "E. coli
with five chloroplast chaperones
including BSD2" . Science. 358
(6368): 1272–1278.
Bibcode:2017Sci...358.1272A .
doi:10.1126/science.aap9221 .
PMID 29217567 .
52. Heazlewood, Joshua (2012).
Proteomic applications in biology.
New York: InTech Manhattan.
ISBN 978-953-307-613-3.
53. Gupta R, Kim ST (2015). Proteomic
Profiling. Methods in Molecular
Biology. 1295. Humana Press, New
York, NY. pp. 225–233.
doi:10.1007/978-1-4939-2550-6_17 .
ISBN 9781493925490.
PMID 25820725 .
54. Krishnan HB, Natarajan SS
(December 2009). "A rapid method
for depletion of Rubisco from
soybean (Glycine max) leaf for
proteomic analysis of lower
abundance proteins".
Phytochemistry. 70 (17–18): 1958–
64.
doi:10.1016/j.phytochem.2009.08.0
20 . PMID 19766275 .
55. Kim ST, Cho KS, Jang YS, Kang KY
(June 2001). "Two-dimensional
electrophoretic analysis of rice
proteins by polyethylene glycol
fractionation for protein arrays".
Electrophoresis. 22 (10): 2103–9.
doi:10.1002/1522-
2683(200106)22:10<2103::aid-
elps2103>3.0.co;2-w .
PMID 11465512 .
56. Xi J, Wang X, Li S, Zhou X, Yue L, Fan
J, Hao D (November 2006).
"Polyethylene glycol fractionation
improved detection of low-abundant
proteins by two-dimensional
electrophoresis analysis of plant
proteome". Phytochemistry. 67 (21):
2341–8.
doi:10.1016/j.phytochem.2006.08.0
05 . PMID 16973185 .
57. Cellar NA, Kuppannan K, Langhorst
ML, Ni W, Xu P, Young SA (January
2008). "Cross species applicability of
abundant protein depletion columns
for ribulose-1,5-bisphosphate
carboxylase/oxygenase". Journal of
Chromatography B. 861 (1): 29–39.
doi:10.1016/j.jchromb.2007.11.024 .
PMID 18063427 .
58. Agrawal GK, Jwa NS, Rakwal R
(February 2009). "Rice proteomics:
ending phase I and the beginning of
phase II". Proteomics. 9 (4): 935–63.
doi:10.1002/pmic.200800594 .
PMID 19212951 . S2CID 2455432 .
59. Cho JH, Hwang H, Cho MH, Kwon
YK, Jeon JS, Bhoo SH, Hahn TR (July
2008). "The effect of DTT in protein
preparations for proteomic analysis:
Removal of a highly abundant plant
enzyme, ribulose bisphosphate
carboxylase/oxygenase". Journal of
Plant Biology. 51 (4): 297–301.
doi:10.1007/BF03036130 .
ISSN 1226-9239 . S2CID 23636617 .
60. Chase et al 1993.
61. Sage RF, Sage TL, Kocacinar F
(2012). "Photorespiration and the
evolution of C4 photosynthesis" .
Annual Review of Plant Biology. 63:
19–47. doi:10.1146/annurev-arplant-
042811-105511 . PMID 22404472 .
S2CID 24199852 .
62. Studer RA, Christin PA, Williams MA,
Orengo CA (February 2014).
"Stability-activity tradeoffs constrain
the adaptive evolution of RubisCO" .
Proceedings of the National
Academy of Sciences of the United
States of America. 111 (6): 2223–8.
Bibcode:2014PNAS..111.2223S .
doi:10.1073/pnas.1310811111 .
PMC 3926066 . PMID 24469821 .
63. Wildman SG (2002). "Along the trail
from Fraction I protein to Rubisco
(ribulose bisphosphate carboxylase-
oxygenase)". Photosynthesis
Research. 73 (1–3): 243–50.
doi:10.1023/A:1020467601966 .
PMID 16245127 . S2CID 7622999 .
64. Portis AR, Parry MA (October 2007).
"Discoveries in Rubisco (Ribulose
1,5-bisphosphate
carboxylase/oxygenase): a historical
perspective". Photosynthesis
Research. 94 (1): 121–43.
doi:10.1007/s11120-007-9225-6 .
PMID 17665149 . S2CID 39767233 .

Figure 3. In this figure, each protein chain in the


(LS)2 complex is given its own color for easy
identification.

Bibliography
Chase MW, Soltis DE, Olmstead RG, Morgan
D, Les DH, Mishler BD, et al. (1993).
"Phylogenetics of Seed Plants: An Analysis
of Nucleotide Sequences from the Plastid
Gene rbcL" (PDF). Annals of the Missouri
Botanical Garden. 80 (3): 528–580.
doi:10.2307/2399846 . JSTOR 2399846 .
Sugawara H, Yamamoto H, Shibata N, Inoue
T, Okada S, Miyake C, Yokota A, Kai Y (May
1999). "Crystal structure of carboxylase
reaction-oriented ribulose 1, 5-
bisphosphate carboxylase/oxygenase from
a thermophilic red alga, Galdieria partita" .
The Journal of Biological Chemistry. 274
(22): 15655–61.
doi:10.1074/jbc.274.22.15655 .
PMID 10336462 .
Portis AR, Parry MA (October 2007).
"Discoveries in Rubisco (Ribulose 1,5-
bisphosphate carboxylase/oxygenase): a
historical perspective". Photosynthesis
Research. 94 (1): 121–43.
doi:10.1007/s11120-007-9225-6 .
PMID 17665149 . S2CID 39767233 .
Ashida H, Danchin A, Yokota A (2005). "Was
photosynthetic RuBisCO recruited by
acquisitive evolution from RuBisCO-like
proteins involved in sulfur metabolism?".
Research in Microbiology. 156 (5–6): 611–
8. doi:10.1016/j.resmic.2005.01.014 .
PMID 15950120 .
Marcus Y, Altman-Gueta H, Finkler A,
Gurevitz M (June 2005). "Mutagenesis at
two distinct phosphate-binding sites
unravels their differential roles in regulation
of Rubisco activation and catalysis" .
Journal of Bacteriology. 187 (12): 4222–8.
doi:10.1128/JB.187.12.4222-4228.2005 .
PMC 1151729 . PMID 15937184 .
External links
See here for the mechanism of the
RuBisCO-catalysed reaction
Rubisco: RCSB PDB Molecule of the
Month
The Plant Kingdom's sloth: Protein
Spotlight article on the "slothful"
enzyme Rubisco

Retrieved from
"https://en.wikipedia.org/w/index.php?
title=RuBisCO&oldid=1010636660"

Last edited 2 hours ago by 2804:431:C7F2:96D6:70DB:4293:C0FB:85EE

Content is available under CC BY-SA 3.0 unless


otherwise noted.

You might also like