5oya - Revision history

OCA at 01:28, 28 December 2023

OCA — Thu, 28 Dec 2023 01:28:18 GMT

←Older revision		Revision as of 01:28, 28 December 2023
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	<StructureSection load='5oya' size='340' side='right'caption='[[5oya]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5oya' size='340' side='right'caption='[[5oya]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oya]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chaetoceros_socialis Chaetoceros socialis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OYA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oya]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetoceros_socialis Chaetoceros socialis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OYA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=CAP:2~~-~~CARBOXYARABINITOL-1~~,~~5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=HL2:(2S,3R)-2-AMINO-3-HYDROXY-4-METHYLPENTANOIC+ACID'>HL2</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LOH:'>LOH</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HL2:(2S,3R)-2-AMINO-3-HYDROXY-4-METHYLPENTANOIC+ACID'>HL2</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LOH:3,4-dihydroxylysine'>LOH</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5oya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oya OCA], [~~http~~://pdbe.org/5oya PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oya RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oya PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oya ProSAT]</span></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=5oya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oya OCA], [https://pdbe.org/5oya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oya RCSB], [https://www.ebi.ac.uk/pdbsum/5oya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oya ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A3B6UEF4_9STRA A0A3B6UEF4_9STRA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5oya" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5oya" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RuBisCO 3D structures\|RuBisCO 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Chaetoceros socialis]]		[[Category: Chaetoceros socialis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Andersson, I]]	+	[[Category: Andersson I]]
-	[[Category: Valegard, K]]	+	[[Category: Valegard K]]
-	~~[[Category: Carbon dioxide fixation]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Photorespiration]]~~	+
-	~~[[Category: Photosynthesis~~]]	+

OCA at 06:25, 17 April 2019

OCA — Wed, 17 Apr 2019 06:25:30 GMT

←Older revision		Revision as of 06:25, 17 April 2019
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	==Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.==		==Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.==
-	<StructureSection load='5oya' size='340' side='right' caption='[[5oya]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5oya' size='340' side='right'caption='[[5oya]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5oya]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Chaetoceros_socialis Chaetoceros socialis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OYA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5oya]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Chaetoceros_socialis Chaetoceros socialis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OYA FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Chaetoceros socialis]]		[[Category: Chaetoceros socialis]]
		+	[[Category: Large Structures]]
	[[Category: Andersson, I]]		[[Category: Andersson, I]]
	[[Category: Valegard, K]]		[[Category: Valegard, K]]

OCA at 07:32, 4 July 2018

OCA — Wed, 04 Jul 2018 07:32:19 GMT

←Older revision		Revision as of 07:32, 4 July 2018
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5oya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oya OCA], [http://pdbe.org/5oya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oya RCSB], [http://www.ebi.ac.uk/pdbsum/5oya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oya ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5oya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oya OCA], [http://pdbe.org/5oya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oya RCSB], [http://www.ebi.ac.uk/pdbsum/5oya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oya ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from Arctic waters were collected, cultivated and analyzed for their CO2 fixing capability. We characterized the kinetic properties of five, and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The Vmax and KM for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (Sc/o) at 15, 25 and 35 degrees C, were determined. The Sc/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO2 relative to O2 Structurally, diatom Rubiscos belong to Form I C/D, containing small subunits characterised by a short betaA-betaB loop and a carboxy-terminal extension that forms a beta-hairpin structure (betaE-betaF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxy-proline, betahydroxyleucine, hydroxylated, and nitrosylated cysteine, mono-, and di-hydroxylated lysine, and tri-methylated lysine. Our studies suggest adaptation toward achieving efficient CO2-fixation in Arctic diatom Rubiscos.
		+
		+	Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.,Valegard K, Andralojc PJ, Haslam RP, Pearce FG, Eriksen GK, Madgwick PJ, Kristoffersen AK, van Lun M, Klein U, Eilertsen HC, Parry MAJ, Andersson I J Biol Chem. 2018 Jun 20. pii: RA118.003518. doi: 10.1074/jbc.RA118.003518. PMID:29925588<ref>PMID:29925588</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5oya" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:26, 27 June 2018

OCA — Wed, 27 Jun 2018 05:26:09 GMT

←Older revision		Revision as of 05:26, 27 June 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5oya is ~~ON HOLD until Paper Publication~~	+	==Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.==
-		+	<StructureSection load='5oya' size='340' side='right' caption='[[5oya]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Valegard~~, K., ~~Andersson~~, I.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5oya]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Chaetoceros_socialis Chaetoceros socialis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OYA FirstGlance]. <br>
-	~~Description~~: ~~Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=HL2:(2S,3R)-2-AMINO-3-HYDROXY-4-METHYLPENTANOIC+ACID'>HL2</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LOH:'>LOH</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5oya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oya OCA], [http://pdbe.org/5oya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oya RCSB], [http://www.ebi.ac.uk/pdbsum/5oya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oya ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chaetoceros socialis]]
		+	[[Category: Andersson, I]]
	[[Category: Valegard, K]]		[[Category: Valegard, K]]
-	[[Category: ~~Andersson, I~~]]	+	[[Category: Carbon dioxide fixation]]
		+	[[Category: Lyase]]
		+	[[Category: Photorespiration]]
		+	[[Category: Photosynthesis]]

OCA at 05:42, 23 May 2018

OCA — Wed, 23 May 2018 05:42:17 GMT

←Older revision		Revision as of 05:42, 23 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5oya is ON HOLD	+	The entry 5oya is ON HOLD until Paper Publication

	Authors: Valegard, K., Andersson, I.		Authors: Valegard, K., Andersson, I.

OCA at 03:46, 16 May 2018

OCA — Wed, 16 May 2018 03:46:38 GMT

←Older revision		Revision as of 03:46, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5oya is ON HOLD ~~until Paper Publication~~	+	The entry 5oya is ON HOLD

	Authors: Valegard, K., Andersson, I.		Authors: Valegard, K., Andersson, I.

OCA at 04:42, 9 May 2018

OCA — Wed, 09 May 2018 04:42:08 GMT

←Older revision		Revision as of 04:42, 9 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5oya is ON HOLD	+	The entry 5oya is ON HOLD until Paper Publication

	Authors: Valegard, K., Andersson, I.		Authors: Valegard, K., Andersson, I.

OCA: Protected "5oya" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:59:55 GMT

Protected "5oya" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:59, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oya is ON HOLD Authors: Valegard, K., Andersson, I. Description: Unusual posttranslational modifications revealed in crystal structures of diatom ...

OCA — Wed, 27 Sep 2017 12:59:54 GMT

New page: '''Unreleased structure''' The entry 5oya is ON HOLD Authors: Valegard, K., Andersson, I. Description: Unusual posttranslational modifications revealed in crystal structures of diatom ...

New page

'''Unreleased structure'''

The entry 5oya is ON HOLD

Authors: Valegard, K., Andersson, I.

Description: Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.
[[Category: Unreleased Structures]]
[[Category: Valegard, K]]
[[Category: Andersson, I]]