5xd8 - Revision history

OCA at 08:00, 22 November 2023

OCA — Wed, 22 Nov 2023 08:00:02 GMT

←Older revision		Revision as of 08:00, 22 November 2023
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	<StructureSection load='5xd8' size='340' side='right'caption='[[5xd8]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5xd8' size='340' side='right'caption='[[5xd8]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xd8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xd8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp._EJY3 Vibrio sp. EJY3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XD8 FirstGlance]. <br>
-	</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>~~</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]] 2.505Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5xd7\|5xd7]], [[5xd9\|5xd9]]</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></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.25 5.5.1.25]~~ </~~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=5xd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd8 OCA], [https://pdbe.org/5xd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xd8 RCSB], [https://www.ebi.ac.uk/pdbsum/5xd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd8 ProSAT]</span></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=5xd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd8 OCA], [~~http~~://pdbe.org/5xd8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xd8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xd8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ACI_VIBSJ ACI_VIBSJ]] Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).<ref>PMID:25156229</ref>	+	[https://www.uniprot.org/uniprot/ACI_VIBSJ ACI_VIBSJ] Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).<ref>PMID:25156229</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Isomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Choi, I G]]	+	[[Category: Vibrio sp. EJY3]]
-	[[Category: Kim, H Y]]	+	[[Category: Choi I-G]]
-	[[Category: Lee, S]]	+	[[Category: Kim H-Y]]
-	~~[[Category: 6-anhydro-l-galactonate cycloisomerase]]~~	+	[[Category: Lee S]]
-	~~[[Category: Barrel domain]]~~	+
-	~~[[Category: Capping domain]]~~	+
-	~~[[Category: Enolase superfamily]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:46, 14 October 2020

OCA — Wed, 14 Oct 2020 06:46:42 GMT

←Older revision		Revision as of 06:46, 14 October 2020
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	==Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase==		==Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase==
-	<StructureSection load='5xd8' size='340' side='right' caption='[[5xd8]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5xd8' size='340' side='right'caption='[[5xd8]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xd8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xd8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XD8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xd7\|5xd7]], [[5xd9\|5xd9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xd7\|5xd7]], [[5xd9\|5xd9]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.25 5.5.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.25 5.5.1.25] </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=5xd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd8 OCA], [http://pdbe.org/5xd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xd8 RCSB], [http://www.ebi.ac.uk/pdbsum/5xd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd8 ProSAT]</span></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=5xd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd8 OCA], [http://pdbe.org/5xd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xd8 RCSB], [http://www.ebi.ac.uk/pdbsum/5xd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Isomerase]]		[[Category: Isomerase]]
		+	[[Category: Large Structures]]
	[[Category: Choi, I G]]		[[Category: Choi, I G]]
	[[Category: Kim, H Y]]		[[Category: Kim, H Y]]

OCA at 10:04, 27 September 2017

OCA — Wed, 27 Sep 2017 10:04:08 GMT

←Older revision		Revision as of 10:04, 27 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xd8 is ~~ON HOLD~~	+	==Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase==
		+	<StructureSection load='5xd8' size='340' side='right' caption='[[5xd8]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xd8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XD8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xd7\|5xd7]], [[5xd9\|5xd9]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.25 5.5.1.25] </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=5xd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd8 OCA], [http://pdbe.org/5xd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xd8 RCSB], [http://www.ebi.ac.uk/pdbsum/5xd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ACI_VIBSJ ACI_VIBSJ]] Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).<ref>PMID:25156229</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3,6-Anydro-l-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-l-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 A and 2.6 A resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common beta-elimination reactions by alpha-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.

-	~~Authors: Lee~~, S., ~~Choi~~, ~~I.-G.~~, Kim, H.-Y.	+	Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily.,Lee S, Kim KH, Kim HY, Choi IG Biochem Biophys Res Commun. 2017 Sep 9;491(1):217-222. doi:, 10.1016/j.bbrc.2017.07.080. Epub 2017 Jul 14. PMID:28716734<ref>PMID:28716734</ref>

-	~~Description: Crystal structure analysis of 3~~,~~6-anhydro~~-L-~~galactonate cycloisomerase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Choi, I.-G]]	+	<div class="pdbe-citations 5xd8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Isomerase]]
		+	[[Category: Choi, I G]]
		+	[[Category: Kim, H Y]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
-	[[Category: ~~Kim, H.~~-Y]]	+	[[Category: 6-anhydro-l-galactonate cycloisomerase]]
		+	[[Category: Barrel domain]]
		+	[[Category: Capping domain]]
		+	[[Category: Enolase superfamily]]
		+	[[Category: Lyase]]

OCA at 10:38, 12 April 2017

OCA — Wed, 12 Apr 2017 10:38:37 GMT

←Older revision		Revision as of 10:38, 12 April 2017
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	The entry 5xd8 is ON HOLD		The entry 5xd8 is ON HOLD

-	Authors: Lee, S, Choi, I.-G., Kim, H.-Y.	+	Authors: Lee, S., Choi, I.-G., Kim, H.-Y.

	Description: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase		Description: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Lee, S,~~ Choi, I.-G]]	+	[[Category: Choi, I.-G]]
		+	[[Category: Lee, S]]
	[[Category: Kim, H.-Y]]		[[Category: Kim, H.-Y]]

OCA: Protected "5xd8" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 12:30:48 GMT

Protected "5xd8" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:30, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xd8 is ON HOLD Authors: Lee, S, Choi, I.-G., Kim, H.-Y. Description: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase [[Cate...

OCA — Wed, 05 Apr 2017 12:30:47 GMT

New page: '''Unreleased structure''' The entry 5xd8 is ON HOLD Authors: Lee, S, Choi, I.-G., Kim, H.-Y. Description: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase [[Cate...

New page

'''Unreleased structure'''

The entry 5xd8 is ON HOLD

Authors: Lee, S, Choi, I.-G., Kim, H.-Y.

Description: Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase
[[Category: Unreleased Structures]]
[[Category: Lee, S, Choi, I.-G]]
[[Category: Kim, H.-Y]]