7ebc - Revision history

OCA at 16:49, 29 November 2023

2023-11-29T16:49:53Z

←Older revision		Revision as of 16:49, 29 November 2023
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	==Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae==		==Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae==
-	<StructureSection load='7ebc' size='340' side='right'caption='[[7ebc]]' scene=''>	+	<StructureSection load='7ebc' size='340' side='right'caption='[[7ebc]], [[Resolution\|resolution]] 2.30Å' 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=7EBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ebc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBC FirstGlance]. <br>
-	</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=7ebc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebc OCA], [https://pdbe.org/7ebc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebc RCSB], [https://www.ebi.ac.uk/pdbsum/7ebc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebc 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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=7ebc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebc OCA], [https://pdbe.org/7ebc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebc RCSB], [https://www.ebi.ac.uk/pdbsum/7ebc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ACEA_YEAST ACEA_YEAST] Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2-methylisocitrate.<ref>PMID:11452311</ref> <ref>PMID:1551398</ref> <ref>PMID:22876324</ref> <ref>PMID:23159490</ref> <ref>PMID:3059712</ref> <ref>PMID:4259654</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 A, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix alpha1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination.
		+
		+	Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.,Hiragi K, Nishio K, Moriyama S, Hamaguchi T, Mizoguchi A, Yonekura K, Tani K, Mizushima T J Struct Biol. 2021 May 24;213(3):107748. doi: 10.1016/j.jsb.2021.107748. PMID:34033899<ref>PMID:34033899</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ebc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae]]
	[[Category: Hamaguchi T]]		[[Category: Hamaguchi T]]
	[[Category: Hiragi K]]		[[Category: Hiragi K]]

OCA at 07:31, 25 June 2021

2021-06-25T07:31:08Z

←Older revision		Revision as of 07:31, 25 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7ebc ~~is ON HOLD~~	+	==Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae==
-		+	<StructureSection load='7ebc' size='340' side='right'caption='[[7ebc]]' scene=''>
-	~~Authors~~: ~~Hiragi, K~~.~~, Nishio, K~~.~~, Moriyama, S~~., ~~Hamaguchi, T~~., ~~Mizoguchi, A~~., ~~Yonekura, K~~., ~~Tani, K~~., ~~Mizushima, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBC FirstGlance]. <br>
-	~~Description: Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae~~	+	</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=7ebc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebc OCA], [https://pdbe.org/7ebc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebc RCSB], [https://www.ebi.ac.uk/pdbsum/7ebc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebc ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Yonekura, K~~]]	+	__TOC__
-	[[Category: ~~Hamaguchi, T~~]]	+	</StructureSection>
-	[[Category: ~~Moriyama, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mizoguchi, A~~]]	+	[[Category: Hamaguchi T]]
-	[[Category: ~~Hiragi, K~~]]	+	[[Category: Hiragi K]]
-	[[Category: ~~Mizushima, T~~]]	+	[[Category: Mizoguchi A]]
-	[[Category: ~~Nishio,~~ K]]	+	[[Category: Mizushima T]]
-	[[Category: ~~Tani,~~ K]]	+	[[Category: Moriyama S]]
		+	[[Category: Nishio K]]
		+	[[Category: Tani K]]
		+	[[Category: Yonekura K]]

OCA at 10:54, 9 June 2021

2021-06-09T10:54:52Z

←Older revision		Revision as of 10:54, 9 June 2021
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	Authors: Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.		Authors: Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.

-	Description: Crystal structure of Isocitrate lyase ~~Icl1~~ from Saccaromyces cervisiae	+	Description: Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yonekura, K]]		[[Category: Yonekura, K]]

OCA: Protected "7ebc" [edit=sysop:move=sysop]

2021-03-17T05:19:00Z

Protected "7ebc" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:19, 17 March 2021

OCA: New page: '''Unreleased structure''' The entry 7ebc is ON HOLD Authors: Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T. Description: Cry...

2021-03-17T05:18:59Z

New page: '''Unreleased structure''' The entry 7ebc is ON HOLD Authors: Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T. Description: Cry...

New page

'''Unreleased structure'''

The entry 7ebc is ON HOLD

Authors: Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.

Description: Crystal structure of Isocitrate lyase Icl1 from Saccaromyces cervisiae
[[Category: Unreleased Structures]]
[[Category: Yonekura, K]]
[[Category: Hamaguchi, T]]
[[Category: Moriyama, S]]
[[Category: Mizoguchi, A]]
[[Category: Hiragi, K]]
[[Category: Mizushima, T]]
[[Category: Nishio, K]]
[[Category: Tani, K]]