OCA at 10:47, 22 November 2023

2023-11-22T10:47:13Z

←Older revision		Revision as of 10:47, 22 November 2023
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-	====	+	==Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions==
-	<StructureSection load='6kyj' size='340' side='right'caption='[[6kyj]]' scene=''>	+	<StructureSection load='6kyj' size='340' side='right'caption='[[6kyj]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kyj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa] and [https://en.wikipedia.org/wiki/Sorghum_bicolor Sorghum bicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KYJ FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kyj OCA], [~~http~~://pdbe.org/6kyj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kyj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kyj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kyj ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6kyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kyj OCA], [https://pdbe.org/6kyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kyj RCSB], [https://www.ebi.ac.uk/pdbsum/6kyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kyj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RBL_ORYSA RBL_ORYSA] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Photosynthetic rate at the present atmospheric condition is limited by the CO2-fixing-enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) because of its extremely low catalytic rate (kcat) and poor affinity for CO2 (Kc) and specificity for CO2 (Sc/o). Rubisco in C4 plants generally shows higher kcat than that in C3 plants. Rubisco consists of eight large subunits and eight small subunits (RbcS). Previously, the chimeric incorporation of sorghum C4-type RbcS significantly increased the kcat of Rubisco in a C3 plant, rice. In this study, we knocked out rice RbcS multigene family by CRISPR/Cas9 and completely replaced the rice RbcS with sorghum RbcS in rice Rubisco. Obtained hybrid-Rubisco showed almost C4-plant-like catalytic properties, i.e., higher kcat, higher Kc and lower Sc/o. Transgenic lines expressing the hybrid-Rubisco accumulated reduced levels of Rubisco, whereas these showed slight but significantly higher photosynthetic capacity and similar biomass production under high CO2 condition compared to wild-type rice. High-resolution crystal structural analysis of the wild-type Rubisco and hybrid-Rubisco revealed the structural differences around the central pore of Rubisco and the betaC-betaD hairpin in RbcS. We speculate that such differences, particularly in the betaC-betaD hairpin, may impact the flexibility of Rubisco catalytic site and change the catalytic properties.
		+
		+	Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C4-Plant-like High Catalytic Activity.,Matsumura H, Shiomi K, Yamamoto A, Taketani Y, Kobayashi N, Yoshizawa T, Tanaka SI, Yoshikawa H, Endo M, Fukayama H Mol Plant. 2020 Aug 24. pii: S1674-2052(20)30268-9. doi:, 10.1016/j.molp.2020.08.012. PMID:32882392<ref>PMID:32882392</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kyj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Oryza sativa]]
		+	[[Category: Sorghum bicolor]]
		+	[[Category: Matsumura H]]
		+	[[Category: Tanaka S]]
		+	[[Category: Yoshikawa H]]
		+	[[Category: Yoshizawa T]]

OCA at 09:45, 16 September 2020

2020-09-16T09:45:17Z

←Older revision		Revision as of 09:45, 16 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6kyj ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6kyj' size='340' side='right'caption='[[6kyj]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kyj OCA], [http://pdbe.org/6kyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kyj RCSB], [http://www.ebi.ac.uk/pdbsum/6kyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kyj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:34, 18 December 2019

2019-12-18T05:34:53Z

←Older revision		Revision as of 05:34, 18 December 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kyj is ON HOLD	+	The entry 6kyj is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6kyj" [edit=sysop:move=sysop]

2019-10-02T06:59:58Z

Protected "6kyj" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:59, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6kyj is ON HOLD Authors: Description: Category: Unreleased Structures

2019-10-02T06:59:56Z

New page: '''Unreleased structure''' The entry 6kyj is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kyj is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6kyj - Revision history

OCA at 10:47, 22 November 2023

OCA at 09:45, 16 September 2020

OCA at 05:34, 18 December 2019

OCA: Protected "6kyj" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6kyj is ON HOLD Authors: Description: Category: Unreleased Structures