3a12: Difference between revisions
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< | ==Crystal structure of Type III Rubisco complexed with 2-CABP== | ||
<StructureSection load='3a12' size='340' side='right'caption='[[3a12]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3a12]] is a 10 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=3A12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A12 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a12 OCA], [https://pdbe.org/3a12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a12 RCSB], [https://www.ebi.ac.uk/pdbsum/3a12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a12 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> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a1/3a12_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3a12 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire alpha-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the alpha-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of alpha-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the alpha-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures. | |||
Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile.,Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376<ref>PMID:20926376</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3a12" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[RuBisCO 3D structures|RuBisCO 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | [[Category: Thermococcus kodakarensis KOD1]] | ||
[[Category: Atomi H]] | |||
== | [[Category: Doi T]] | ||
< | [[Category: Fujihashi M]] | ||
[[Category: | [[Category: Imanaka T]] | ||
[[Category: Thermococcus kodakarensis]] | [[Category: Miki K]] | ||
[[Category: Atomi | [[Category: Nishitani Y]] | ||
[[Category: Doi | [[Category: Yoshida S]] | ||
[[Category: Fujihashi | |||
[[Category: Imanaka | |||
[[Category: Miki | |||
[[Category: Nishitani | |||
[[Category: Yoshida | |||
Latest revision as of 17:06, 1 November 2023
Crystal structure of Type III Rubisco complexed with 2-CABPCrystal structure of Type III Rubisco complexed with 2-CABP
Structural highlights
FunctionRBL_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] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire alpha-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the alpha-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of alpha-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the alpha-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures. Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile.,Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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