[[Image:2ea3.png|left|200px|thumb|Crystal Structure of ''Cellulomonas Bogoriensis'' Chymotrypsin [[2ea3]]]]
[[Chymotrypsin]] (Chy or α-Chy) is a digestive enzyme containing an active serine residue, which helps to digest proteins in our food. Other related proteases are crucial for blood clotting ([http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer&part=A1378&rendertype=figure&id=A1401 thrombin and other proteases]), for the AIDS virus metabolism ([http://www.proteopedia.org/wiki/index.php/Hiv_protease HIV protease]) and for many other processes relevant to human health and agriculture. Chymotrypsin cleaves peptide bonds of proteins where the amide side of the bond is an aromatic amino acid like tyrosine, phenylalanine or tryptophan. The image at the left is the crystal structure of chymotrypsin from ''Cellulomonas Bogoriensis'' ([[2ea3]]) with sulfate ions. Below is description of the structure of bovine chymotrypsin. Some additional details in 
*[[Molecular Playground/Chymotrypsin]] 
*[[Serine Proteases]].
{{TOC limit|limit=2}}

== Overview ==
<Structure load='7gch' size='300' frame='true' align='right' caption='[[7gch]] Bovine chymotrypsin with bound inhibitor' scene='38/387136/Bovine_chymotrypsin_overview/1' />While chymotrypsin occurs in many organisms, the most-studied chymotrypsin is that from cows (bovine chymotrypsin), shown here with an inhibitor molecule bound to the active site (<scene name='38/387136/Bovine_chymotrypsin_overview/1'>default scene</scene>). It is synthesized as a single polypeptide chain of 245 amino acids, called chymotrypsinogen, that is inactive. The enzyme is activated by one cleavage by trypsin and two cleavages by chymotrypsin (autolytic cleavages) that result in the loss of four amino acids from the remaining three polypeptides, shown here in turquoise, beige, and violet. These three chains are held together by <scene name='38/387136/Bovine_chymotrypsin_overview/5'> two inter-chain disulfide bonds</scene>. The bonded cysteine residues are shown in space fill with yellow sulfur atoms. There also three <scene name='38/387136/Bovine_chymotrypsin_overview/6'>intra-chain disulfide bonds</scene>. Here chymotrypsin is shown in cartoon with pink α-helices and yellow β-strands, and this shows that it is mainly composed of <scene name='38/387136/Bovine_chymotrypsin_overview/7'>two beta barrels</scene>.

== Substrate-binding and Active Sites ==
[[Image:LPFstructure.jpg|left]]Features of the substrate-binding and active sites can be seen in the structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl ketone, which resembles a peptide substrate (see structure in left figure). The colored backgrounds in the figure indicate the four components of structure and shows the bond (yellow on black background) that is position to be cleaved.

Here is chymotrypsin (space fill) with the inhibitor (CPK ball & stick) showing the <scene name='38/387136/Bovine_chymotrypsin_overview/3'>inhibitor sitting in the active site</scene>. Note the active site is in a depression on the surface of the enzyme. Chymotrypsin contains three residues, Ser 195, His 57 and Asp 102, which are known as its <scene name='38/387136/Bovine_chymotrypsin_active_sit/4'>catalytic triad</scene>, shown in CPK ball and stick in this close up of the active site. Similar three-dimensional arrangements of a serine, a histidine and an aspartate are observed in many other proteases, and the role of these three residues in catalysis has been studied extensively. Serine acts as a nucleophile (contributing the electron pair for a new bond) attacking the carbonyl carbon of the peptide bond to be hydrolyzed. Histidine and aspartate turn serine into a better nucleophile by assisting in removing a hydrogen ion from serine.

The <scene name='38/387136/Bovine_chymotrypsin_active_sit/1'>substrate-binding site</scene>, can be seen in this view with the inhibitor in light gray ball & stick with its phenyl group in orchid. By moving the structure back and forth with your mouse, it is easy to see that the phenyl group is located in the hydrophobic binding pocket of the enzyme. This binding pocket determines the enzyme's preference for cleavage of peptides on the C-terminal side of aromatic residues.

This view shows the <scene name='38/387136/Bovine_chymotrypsin_active_sit/3'>carbonyl group of the inhibitor</scene> in CPK colors. The triflouromethyl group is bound to the carbonyl carbon via the yellow bond. In a peptide substrate, the triflouromethyl group would be replaced by the first amino acid residue of the rest of the peptide chain, and the yellow bond would be the bond that is cleaved. The carbonyl carbon of the inhibitor is 1.52 Å away from the side chain oxygen of serine 195, and this indicates they are covalently bound (bond indicated by dotted line). Thus, this structure is similar to the '''tetrahedral intermediate''' that is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stabilized by hydrogen bonds to the backbone nitrogens of Ser 195 and Gly 193, shown in blue spacefill. The hydrogen atoms involved in these hydrogen bonds are not shown.

== 3D Structures of Chymotrypsin ==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

The Chy precursor is the inactive '''chymotrypsinogen''' (Chygen) which gets cleaved 3 times by trypsin and chymotrypsin losing a 4 amino acid long peptide to become the active Chy. '''γ-Chy''' is a covalent acyl adduct of '''α-Chy'''. '''δ-Chy''' results when Chygen is cleaved only twice.

=== Native Chymotrypsin ===

[[1yph]] – bChyA chain A - bovine 
[[4cha]], [[5cha]] – BtChy 
[[1kdq]] – rChyB, chain B (mutant) - rat 
[[2ea3]] – Chy – ''Cellulomonas bogoriensis'' 
[[1ab9]], [[8gch]], [[1gct]], [[2gct]], [[3gct]], [[2gch]] - gamma BtChy 

=== Native Chymotrypsinogen ===

[[2cga]], [[1chg]] – bChygen A 
[[2jet]] – rChygen B chain A,B 

=== Chymotrypsin + polypeptide inhibitors ===

[[1cbw]], [[1mtn]] - bChy+BPTI 
[[1t7c]], [[1t8l]], [[1t8m]], [[1t8n]], [[1t8o]] – bChyA+P1 BPTI variants 
[[1oxg]] – bChyA+autolysis peptide 
[[1p2m]], [[1p2n]], [[1p2o]], [[1p2q]] – bChyA+ 4 amino acids in S1 pocket 
[[1n8o]] – bChyA+ecotin 
[[1ca0]] – bChy+APPI 
[[1acb]], [[4h4f]] – bChy+Elgin C 
[[2cho]] – bChy+turkey ovomucoid third domain

=== Chymotrypsin + inhibitors ===

[[3bg4]] – ChyA chain A+guamerin 
[[2p8o]] - bChyA chain A+benzohydroxamic acid/vanadate 
[[1eq9]] – Chy+PMSF – fire ant 
[[2cha]] – bChy+p-sulfinotoluene

=== γ-Chymotrypsin + inhibitors ===

[[1gg6]] – γ-bChy+N-acetyl-phenylalanine trifluoromethyl ketone 
[[1ggd]] – γ-bChy+N-acetyl-phenylalanine trifluoromethyl aldehyde 
[[1afq]] - γ-bChy+synthetic inhibitor 
[[3gch]], [[4gch]], [[5gch]] - γ-bChy+cinnamate 
[[6gch]], [[7gch]] - γ-bChy+trifluoromethy ketone 
[[6cha]] – γ-bChy+phenylethane boronic acid – transition state inhibitor 
[[1gmc]], [[1gmd]] – γ-bChy+hexane – transition state inhibitor 
[[2gmt]] - γ-bChy+N-acetyl-alanyl-phenylalanyl-chloroethyl ketone 
[[1gmh]], [[1gcd]] - γ-bChy+organophosphoryl 
[[1gha]], [[1ghb]] - γ-bChy+ N-acetyl-tryptophan 

=== γ-Chymotrypsin + reaction transition state inhibitors ===

[[6cha]] – γ-bChy+phenylethane boronic acid 
[[1gmc]], [[1gmd]] – γ-bChy+hexane

=== δ-Chymotrypsin + inhibitors ===

[[1dlk]] – δ-bChy+peptidyl chloromethyl ketone

=== Chymotrypsinogen + inhibitors ===

[[1gl0]], [[1gli]] – ChygenA+PMP_D2v – ''Locusta migratoria'' 
[[1k2i]] - bChygen+7-hydroxycoumarin 
[[2y6t]] – bChygenA + ecotin 
[[3t62]] - bChygenA + Kunitz-type proteinase inhibitor SHPI-1 

==Further reading==
You can learn more about chymotrypsin structure, function and regulation in this publicly available [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer&part=A1170#A1171 chapter] of the Biochemistry textbook by Berg, Tymoczka and Stryer.

[[Category:Topic Page]]

2013-12-04T20:07:19Z

Alice Harmon:

{{STRUCTURE_1rcx| PDB=1rcx | SIZE=400| SCENE= |right|CAPTION=Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, [[1rcx]] }}

'''Ribulose-1,5-bisphosphate carboxylase oxygenase – RuBisCO''' (RBCO) catalyzes the first step in photosynthetic carbon fixation, and it is the most abundant protein on earth. RBCO can either carboxylate or oxygenate ribulose-1,5-bisphosphate (RUBP) with CO2 or O2, respectively. RBCO from flowering plants consists of eight large subunits and eight small subunits. Some additional details can be found in [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]].

{{TOC limit|limit=2}}

== Quaternery Structure ==

The structure of the Rubisco <scene name='46/463261/Rubisco_spacefill_holoenzyme/1'>holoenzyme</scene> from spinach is shown in spacefill with its 8 large subunits in shades of blue and and its 8 small subunits in shades of yellow. The large subunits are arranged in head-to-toe pairs like staves in a barrel and the small subunits are arranged at the ends of the barrel. The large subunits contain the active sites and the function of the small subunits is not understood.

== Large Subunit Structure ==

This isolated <scene name='46/463261/Rubisco_lsu_pair/7'>pair of large subunits</scene> shows that each subunit has a large C-terminal lobe and a small N-terminal lobe, and the subunits are arranged head-to-toe (antiparallel). <scene name='46/463261/Rubisco_lsu_pair/5'>Two active sites</scene> are located in the interface of the large subunit pair. The subunits are shown in cartoon with one shown in the secondary structure color scheme. Each active site is occupied by RUBP, which is shown in CPK spacefill. Here is a <scene name='46/463261/Rubisco_lsu_monomer/1'>single large subunit</scene> showing that both lobes contain alpha helices (pink) and beta strands (yellow). The large lobe is dominated by an <scene name='46/463261/Rubisco_lsu_monomer/2'>α-β barrel</scene> (amino acids 166-409), which contributes most of the residues that form the the active site. One residue from the N-terminal lobe of the adjacent large subunit <scene name='46/463261/Asn123/1'>Asn 123</scene> completes the active site. This scene shows RUBP in spacefill and CPK in one of the active sites in the dimer. Both subunits are shown in transparent cartoon with the α-β barrel is pink and yellow. Asn 123 from the adjacent subunit is in blue spacefill, and residues 121-129 are shown in blue cartoon. This residue does not contribute to catalysis, and it will not be considered further.

== Active Site Structure ==
(under construction)

This scene shows an <scene name='46/463261/8ruc_active-site/1'>isolated α-β barrel</scene> (cartoon and colored for secondary structure) of spinach Rubisco [[8ruc]], bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (CAP) and Mg2+, both shown in CPK spacefill. [[Image:CAP.jpg|left|]]The structure of CAP (left figure) is similar to the hydrated reaction intermediate that is formed following the addition of CO2 to RUBP. CAP sits at one end of the α-β barrel, and only residues from the beta strands (gold ball & stick) and loops that link them to helices (silver ball & stick) contribute to the <scene name='46/463261/8ruc_active-site/4'>active site</scene> (the residue contributed by the N-terminal of the adjacent subunit is not shown).

== 3D Structures of RuBisCO ==

''Updated February 2013''

===RuBisCO===

[[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus'' 
[[2ybv]] - RBCO – ''Thermosynechococcus elongatus'' 
[[3qfw]] - RBCO large subunit – ''Rhodopseudomonas palustris'' 
[[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii'' 
[[1uw9]], [[1uwa]] – CrRBCO (mutant) 
[[1svd]] – RBCD – ''Halothiobacillus neapolitanus'' 
[[1bxn]] – RBCO – ''Cupriavidus necator'' 
[[1aus]] - spRBCO – spinach 
[[1rba]] - RrRBCO (mutant) – ''Rhododpirillum rubrum'' 
[[5rub]] - RrRBCO 
[[2wvw]] – RBCO – ''Anabena'' – Cryo EM 
[[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO (mutant) 
[[1mlv]] - pRBCO LSMT – pea 
[[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii'' 
[[1uzd]] – CrRBCO/spRBCO 
[[1geh]] – TkRBCO – ''Thermococcus kodakaraensis'' 
[[1iwa]] - GpRBCO – ''Galdieria partita'' 
[[1tel]] – RBCO large subunit – ''Chlorobium tepidum'' 
[[1rld]], [[3rub]], [[3t15]], [[3zw6]], [[4rub]] – tRBCO – tobacco 
[[3thg]] – RBCO – creosote bush 
[[4hhh]] – RBCO - pea

===RuBisCO complex with inhibitor 2-CABP===

[[3kdn]], [[3a12]] – TkRBCO III + 2-CABP 
[[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP 
[[1ir2]] - CrRBCO + 2-CABP 
[[1upm]], [[1upp]], [[1rbo]], [[3ruc]], [[8ruc]] - spRBCO + 2-CABP + cation 
[[1ir1]] - spRBCO + 2-CABP + CO2 + Mg 
[[1wdd]] – rRBCO + 2-CABP – rice 
[[1bwv]] - GpRBCO + 2-CABP 
[[1rlc]] - tRBCO + 2-CABP

===RuBisCO complex with product===

[[1aa1]] – spRBCO + phosphoglycerate 
[[1rus]] - RrRBCO + phosphoglycerate 

===RuBisCO complex with substrate===

[[1rcx]], [[1rxo]] – spRBCO + ribulose-1,5-bisphosphate 
[[9rub]] - RrRBCO + ribulose-1,5-bisphosphate 
[[1rsc]] - SeRBCO + xylulose-1,5-bisphosphate 
[[1rco]] - spRBCO + xylulose-diol-1,5-bisphosphate 
[[3zxw]] - SeRBCO + carboxyarabinitol-1,5-bisphosphate

===RuBisCO complexes===

[[2h21]] – pRBCO LSMT + AdoMet 
[[2h23]] - pRBCO LSMT + AdoHcy 
[[2h2e]], [[1ozv]], [[1p0y]] - pRBCO LSMT + AdoMet + lysine 
[[2h2j]] - pRBCO LSMT + sinefungin 
[[2d69]] – PhRBCO + sulfate 
[[2rus]] - RrRBCO + CO2 + Mg 
[[4f0h]] – GsRBCO + O2 – ''Galdieria sulphuraria'' 
[[4f0k]] - GsRBCO + CO2 + Mg 
[[4f0m]] - GsRBCO + Mg 
[[1ej7]] – tRBCO + phosphate 
[[3axk]] – rRBCO + NADP 
[[3axm]] – rRBCO + 6PG

[[Category:Topic Page]]

File:CAP.jpg

2013-12-04T18:16:06Z

Alice Harmon: uploaded a new version of "Image:CAP.jpg": Comparison of the structures of 2-carboxyarbintol phosphate (CAP) and the hydrated intemediate of the carboxylation reaction catalyzed by Rubisco.

== Summary ==
Comparison of the structures of 2-carboxyarbintol phosphate (CAP) and the hydrated intemediate of the carboxylation reaction catalyzed by Rubisco.
== Licensing ==
{{self|cc-by-3.0}}

File:CAP.jpg

2013-12-04T18:16:05Z

== Summary ==
Comparison of the structures of 2-carboxyarbintol phosphate (CAP) and the hydrated intemediate of the carboxylation reaction catalyzed by Rubisco.
== Licensing ==
{{self|cc-by-3.0}}

File:CAP.jpg

2013-12-04T18:14:05Z

Alice Harmon: Comparison of the structures of 2-carboxyarbintol phosphate (CAP) and the hydrated intemediate of the carboxylation reaction catalyzed by Rubisco.

== Summary ==
Comparison of the structures of 2-carboxyarbintol phosphate (CAP) and the hydrated intemediate of the carboxylation reaction catalyzed by Rubisco.
== Licensing ==
{{self|cc-by-3.0}}

RuBisCO

2013-12-04T16:15:42Z

Alice Harmon:

{{STRUCTURE_1rcx| PDB=1rcx | SIZE=400| SCENE= |right|CAPTION=Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, [[1rcx]] }}

'''Ribulose-1,5-bisphosphate carboxylase oxygenase – RuBisCO''' (RBCO) catalyzes the first step in photosynthetic carbon fixation, and it is the most abundant protein on earth. RBCO can either carboxylate or oxygenate ribulose-1,5-bisphosphate (RUBP) with CO2 or O2, respectively. RBCO from flowering plants consists of eight large subunits and eight small subunits. Some additional details can be found in [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]].

{{TOC limit|limit=2}}

== Quaternery Structure ==

The Rubisco <scene name='46/463261/Rubisco_spacefill_holoenzyme/1'>holoenzyme</scene> is shown in spacefill with its 8 large subunits in shades of blue and and its 8 small subunits in shades of yellow. The large subunits are arranged in head-to-toe pairs like staves in a barrel and the small subunits are arranged at the ends of the barrel. The large subunits contain the active sites and the function of the small subunits is not understood.

== Large Subunit Structure ==

Here is an isolated <scene name='46/463261/Rubisco_lsu_pair/7'>pair of large subunits</scene>. Each subunit has a large C-terminal lobe and a small N-terminal lobe, and the subunits are arranged head-to-toe (antiparallel) in the pair. <scene name='46/463261/Rubisco_lsu_pair/5'>Two active sites</scene> are located in the interface of the large subunit pair. The subunits are shown in cartoon with one shown in the secondary structure color scheme. Each active site is occupied by RUBP, which is shown in CPK spacefill. Here is a <scene name='46/463261/Rubisco_lsu_monomer/1'>single large subunit</scene> showing that both lobes contain alpha helices (pink) and beta strands (yellow). The large lobe is dominated by an <scene name='46/463261/Rubisco_lsu_monomer/2'>α-β barrel</scene> (amino acids 166-409), which contributes most of the residues that form the the active site. One residue from the N-terminal lobe of the adjacent large subunit <scene name='46/463261/Asn123/1'>Asn 123</scene> completes the active site. This scene shows RUBP in spacefill and CPK in one of the active sites in the dimer. Both subunits are shown in transparent cartoon with the α-β barrel is pink and yellow. Asn 123 from the adjacent subunit is in blue spacefill, and residues 121-129 are shown in blue cartoon. This residue does not contribute to catalysis, and it will not be considered further.

== Active Site Structure ==
(under construction)

This scene shows an <scene name='46/463261/8ruc_active-site/1'>isolated α-β barrel</scene> (cartoon and colored for secondary structure) of spinach Rubisco [[8ruc]], bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (2-CABP) and Mg2+, both shown in CPK spacefill. 2-CABP sits at one end of the α-β barrel, only residues from the beta strands and loops that link them to helices contribute to the active site.

== 3D Structures of RuBisCO ==

''Updated February 2013''

===RuBisCO===

[[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus'' 
[[2ybv]] - RBCO – ''Thermosynechococcus elongatus'' 
[[3qfw]] - RBCO large subunit – ''Rhodopseudomonas palustris'' 
[[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii'' 
[[1uw9]], [[1uwa]] – CrRBCO (mutant) 
[[1svd]] – RBCD – ''Halothiobacillus neapolitanus'' 
[[1bxn]] – RBCO – ''Cupriavidus necator'' 
[[1aus]] - spRBCO – spinach 
[[1rba]] - RrRBCO (mutant) – ''Rhododpirillum rubrum'' 
[[5rub]] - RrRBCO 
[[2wvw]] – RBCO – ''Anabena'' – Cryo EM 
[[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO (mutant) 
[[1mlv]] - pRBCO LSMT – pea 
[[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii'' 
[[1uzd]] – CrRBCO/spRBCO 
[[1geh]] – TkRBCO – ''Thermococcus kodakaraensis'' 
[[1iwa]] - GpRBCO – ''Galdieria partita'' 
[[1tel]] – RBCO large subunit – ''Chlorobium tepidum'' 
[[1rld]], [[3rub]], [[3t15]], [[3zw6]], [[4rub]] – tRBCO – tobacco 
[[3thg]] – RBCO – creosote bush 
[[4hhh]] – RBCO - pea

===RuBisCO complex with inhibitor 2-CABP===

[[3kdn]], [[3a12]] – TkRBCO III + 2-CABP 
[[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP 
[[1ir2]] - CrRBCO + 2-CABP 
[[1upm]], [[1upp]], [[1rbo]], [[3ruc]], [[8ruc]] - spRBCO + 2-CABP + cation 
[[1ir1]] - spRBCO + 2-CABP + CO2 + Mg 
[[1wdd]] – rRBCO + 2-CABP – rice 
[[1bwv]] - GpRBCO + 2-CABP 
[[1rlc]] - tRBCO + 2-CABP

===RuBisCO complex with product===

[[1aa1]] – spRBCO + phosphoglycerate 
[[1rus]] - RrRBCO + phosphoglycerate 

===RuBisCO complex with substrate===

[[1rcx]], [[1rxo]] – spRBCO + ribulose-1,5-bisphosphate 
[[9rub]] - RrRBCO + ribulose-1,5-bisphosphate 
[[1rsc]] - SeRBCO + xylulose-1,5-bisphosphate 
[[1rco]] - spRBCO + xylulose-diol-1,5-bisphosphate 
[[3zxw]] - SeRBCO + carboxyarabinitol-1,5-bisphosphate

===RuBisCO complexes===

[[2h21]] – pRBCO LSMT + AdoMet 
[[2h23]] - pRBCO LSMT + AdoHcy 
[[2h2e]], [[1ozv]], [[1p0y]] - pRBCO LSMT + AdoMet + lysine 
[[2h2j]] - pRBCO LSMT + sinefungin 
[[2d69]] – PhRBCO + sulfate 
[[2rus]] - RrRBCO + CO2 + Mg 
[[4f0h]] – GsRBCO + O2 – ''Galdieria sulphuraria'' 
[[4f0k]] - GsRBCO + CO2 + Mg 
[[4f0m]] - GsRBCO + Mg 
[[1ej7]] – tRBCO + phosphate 
[[3axk]] – rRBCO + NADP 
[[3axm]] – rRBCO + 6PG

[[Category:Topic Page]]

RuBisCO

2013-12-04T15:29:01Z

Alice Harmon:

{{STRUCTURE_1rcx| PDB=1rcx | SIZE=400| SCENE= |right|CAPTION=Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, [[1rcx]] }}

'''Ribulose-1,5-bisphosphate carboxylase oxygenase – RuBisCO''' (RBCO) catalyzes the first step in photosynthetic carbon fixation, and it is the most abundant protein on earth. RBCO can either carboxylate or oxygenate ribulose-1,5-bisphosphate (RUBP) with CO2 or O2, respectively. RBCO from flowering plants consists of eight large subunits and eight small subunits. 2-carboxylarabinitol-1,5-bisphosphate (2-CABP) is an inhibitor of RCBO. Some additional details can be found in [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]].

{{TOC limit|limit=2}}

== Quaternery Structure ==

The Rubisco <scene name='46/463261/Rubisco_spacefill_holoenzyme/1'>holoenzyme</scene> is shown in spacefill with its 8 large subunits in shades of blue and and its 8 small subunits in shades of yellow. The large subunits are arranged in head-to-toe pairs like staves in a barrel and the small subunits are arranged at the ends of the barrel. The large subunits contain the active sites and the function of the small subunits is not understood.

== Large Subunit Structure ==
(under construction)

Here is an isolated <scene name='46/463261/Rubisco_lsu_pair/7'>pair of large subunits</scene>. Each subunit has a large C-terminal lobe and a small N-terminal lobe, and the subunits are arranged head-to-toe (antiparallel) in the pair. <scene name='46/463261/Rubisco_lsu_pair/5'>Two active sites</scene> are located in the interface of the large subunit pair. The subunits are shown in cartoon with one shown in the secondary structure color scheme. Each active site is occupied by RUBP, which is shown in CPK spacefill. Here is a <scene name='46/463261/Rubisco_lsu_monomer/1'>single large subunit</scene> showing that both lobes contain alpha helices (pink) and beta strands (yellow). The large lobe is dominated by an <scene name='46/463261/Rubisco_lsu_monomer/2'>α-β barrel</scene> (amino acids 166-409), which contributes most of the residues that form the the active site. One residue from the N-terminal lobe of the adjacent large subunit <scene name='46/463261/Asn123/1'>Asn 123</scene> completes the active site. This scene shows RUBP in spacefill and CPK in one of the active sites in the dimer. Both subunits are shown in transparent cartoon with the α-β barrel is pink and yellow. Asn 123 from the adjacent subunit is in blue spacefill, and residues 121-129 are shown in blue cartoon. This residue does not contribute to catalysis, and it will not be considered further.

== Active Site Structure ==
(under construction)

The active site is formed by an α-β barrel, which comprises the C-terminal lobe of the large subunit. Some additional residues are contributed by the N-terminal lobe of the adjacent subunit. Here is an <scene name='46/463261/Rubisco_lsu_pair/5'>isolated pair of subunits</scene>, , and here is the α-β barrel of that subunit.

== 3D Structures of RuBisCO ==

''Updated February 2013''

===RuBisCO===

[[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus'' 
[[2ybv]] - RBCO – ''Thermosynechococcus elongatus'' 
[[3qfw]] - RBCO large subunit – ''Rhodopseudomonas palustris'' 
[[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii'' 
[[1uw9]], [[1uwa]] – CrRBCO (mutant) 
[[1svd]] – RBCD – ''Halothiobacillus neapolitanus'' 
[[1bxn]] – RBCO – ''Cupriavidus necator'' 
[[1aus]] - spRBCO – spinach 
[[1rba]] - RrRBCO (mutant) – ''Rhododpirillum rubrum'' 
[[5rub]] - RrRBCO 
[[2wvw]] – RBCO – ''Anabena'' – Cryo EM 
[[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO (mutant) 
[[1mlv]] - pRBCO LSMT – pea 
[[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii'' 
[[1uzd]] – CrRBCO/spRBCO 
[[1geh]] – TkRBCO – ''Thermococcus kodakaraensis'' 
[[1iwa]] - GpRBCO – ''Galdieria partita'' 
[[1tel]] – RBCO large subunit – ''Chlorobium tepidum'' 
[[1rld]], [[3rub]], [[3t15]], [[3zw6]], [[4rub]] – tRBCO – tobacco 
[[3thg]] – RBCO – creosote bush 
[[4hhh]] – RBCO - pea

===RuBisCO complex with inhibitor 2-CABP===

[[3kdn]], [[3a12]] – TkRBCO III + 2-CABP 
[[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP 
[[1ir2]] - CrRBCO + 2-CABP 
[[1upm]], [[1upp]], [[1rbo]], [[3ruc]], [[8ruc]] - spRBCO + 2-CABP + cation 
[[1ir1]] - spRBCO + 2-CABP + CO2 + Mg 
[[1wdd]] – rRBCO + 2-CABP – rice 
[[1bwv]] - GpRBCO + 2-CABP 
[[1rlc]] - tRBCO + 2-CABP

===RuBisCO complex with product===

[[1aa1]] – spRBCO + phosphoglycerate 
[[1rus]] - RrRBCO + phosphoglycerate 

===RuBisCO complex with substrate===

[[1rcx]], [[1rxo]] – spRBCO + ribulose-1,5-bisphosphate 
[[9rub]] - RrRBCO + ribulose-1,5-bisphosphate 
[[1rsc]] - SeRBCO + xylulose-1,5-bisphosphate 
[[1rco]] - spRBCO + xylulose-diol-1,5-bisphosphate 
[[3zxw]] - SeRBCO + carboxyarabinitol-1,5-bisphosphate

===RuBisCO complexes===

[[2h21]] – pRBCO LSMT + AdoMet 
[[2h23]] - pRBCO LSMT + AdoHcy 
[[2h2e]], [[1ozv]], [[1p0y]] - pRBCO LSMT + AdoMet + lysine 
[[2h2j]] - pRBCO LSMT + sinefungin 
[[2d69]] – PhRBCO + sulfate 
[[2rus]] - RrRBCO + CO2 + Mg 
[[4f0h]] – GsRBCO + O2 – ''Galdieria sulphuraria'' 
[[4f0k]] - GsRBCO + CO2 + Mg 
[[4f0m]] - GsRBCO + Mg 
[[1ej7]] – tRBCO + phosphate 
[[3axk]] – rRBCO + NADP 
[[3axm]] – rRBCO + 6PG

[[Category:Topic Page]]

RuBisCO

2013-12-03T20:05:36Z

Alice Harmon:

RuBisCO

2013-12-03T19:33:59Z

Alice Harmon: