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| + | ==CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)== |
| - | The line below this paragraph, containing "STRUCTURE_1geh", creates the "Structure Box" on the page.
| + | <StructureSection load='1geh' size='340' side='right'caption='[[1geh]], [[Resolution|resolution]] 2.80Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1geh]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GEH FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | {{STRUCTURE_1geh| PDB=1geh | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1geh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1geh OCA], [https://pdbe.org/1geh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1geh RCSB], [https://www.ebi.ac.uk/pdbsum/1geh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1geh ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RBL_THEKO RBL_THEKO] Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.[HAMAP-Rule:MF_01133]<ref>PMID:17303759</ref> <ref>PMID:20926376</ref> <ref>PMID:9988755</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco. |
| | | | |
| - | '''CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)'''
| + | Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.,Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K Structure. 2001 Jun;9(6):473-81. PMID:11435112<ref>PMID:11435112</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 1GEH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEH OCA].
| + | </div> |
| | + | <div class="pdbe-citations 1geh" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry., Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K, Structure. 2001 Jun;9(6):473-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11435112 11435112]
| + | *[[RuBisCO 3D structures|RuBisCO 3D structures]] |
| - | [[Category: Ribulose-bisphosphate carboxylase]] | + | == References == |
| - | [[Category: Single protein]] | + | <references/> |
| - | [[Category: Thermococcus kodakarensis]] | + | __TOC__ |
| - | [[Category: Atomi, H.]] | + | </StructureSection> |
| - | [[Category: Fukui, T.]] | + | [[Category: Large Structures]] |
| - | [[Category: Imanaka, T.]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Kitano, K.]] | + | [[Category: Atomi H]] |
| - | [[Category: Maeda, N.]] | + | [[Category: Fukui T]] |
| - | [[Category: Miki, K.]] | + | [[Category: Imanaka T]] |
| - | [[Category: Pentagonal toroid decamer]]
| + | [[Category: Kitano K]] |
| - | [[Category: Rubisco]]
| + | [[Category: Maeda N]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:28:23 2008''
| + | [[Category: Miki K]] |
| Structural highlights
Function
RBL_THEKO Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.[HAMAP-Rule:MF_01133][1] [2] [3]
Publication Abstract from PubMed
BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.
Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.,Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K Structure. 2001 Jun;9(6):473-81. PMID:11435112[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science. 2007 Feb 16;315(5814):1003-6. PMID:17303759 doi:http://dx.doi.org/10.1126/science.1135999
- ↑ Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K. Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile. J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376 doi:10.1074/jbc.M110.147587
- ↑ Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J Biol Chem. 1999 Feb 19;274(8):5078-82. PMID:9988755
- ↑ Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Structure. 2001 Jun;9(6):473-81. PMID:11435112
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