4j7g - Revision history

OCA at 10:57, 24 November 2022

OCA — Thu, 24 Nov 2022 10:57:05 GMT

←Older revision		Revision as of 10:57, 24 November 2022
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	==Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose==		==Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose==
-	<StructureSection load='4j7g' size='340' side='right' caption='[[4j7g]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4j7g' size='340' side='right'caption='[[4j7g]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j7g]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_orientalis"_pittenger_and_brigham_1956 "streptomyces~~ orientalis~~" pittenger and brigham 1956~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4J7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j7g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1JB:[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+[(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]+HYDROGEN+PHOSPHATE'>1JB</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1JB:[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+[(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]+HYDROGEN+PHOSPHATE'>1JB</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j7h\|4j7h]]</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=4j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7g OCA], [https://pdbe.org/4j7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j7g RCSB], [https://www.ebi.ac.uk/pdbsum/4j7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7g ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EvaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 "Streptomyces orientalis" Pittenger and Brigham 1956])</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=4j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7g OCA], [~~http~~://pdbe.org/4j7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4j7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4j7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7g ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/EVAA_AMYOR EVAA_AMYOR] Involved in the biosynthesis of the 2,3,6-trideoxysugar L-epivancosamine, the terminal sugar added to the aglycone scaffold of chloroeremomycin, a member of the glycopeptide antibiotics vancomycin family. Catalyzes the removal of the hydroxyl group at position C-2 of the hexose ring of dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose, and the oxidation of the hydroxyl group at position C-3 to form a carbonyl functionality. The product of the reaction, dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose, is a highly unstable diketosugar, which spontaneously forms dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose.<ref>PMID:11035791</ref> <ref>PMID:23473392</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: ~~Streptomyces~~ orientalis ~~pittenger and brigham 1956~~]]	+	[[Category: Amycolatopsis orientalis]]
-	[[Category: ~~Holden, H M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kubiak, R L~~]]	+	[[Category: Holden HM]]
-	[[Category: ~~Thoden, J B~~]]	+	[[Category: Kubiak RL]]
-	[[Category: ~~Biosynthetic protein]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Dehydration]]~~	+
-	~~[[Category: Nudix hydrolase superfamily~~]]	+

OCA at 19:01, 11 August 2016

OCA — Thu, 11 Aug 2016 19:01:17 GMT

←Older revision		Revision as of 19:01, 11 August 2016
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		+
	==Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose==		==Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose==
	<StructureSection load='4j7g' size='340' side='right' caption='[[4j7g]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4j7g' size='340' side='right' caption='[[4j7g]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j7h\|4j7h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j7h\|4j7h]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EvaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 "Streptomyces orientalis" Pittenger and Brigham 1956])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EvaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 "Streptomyces orientalis" Pittenger and Brigham 1956])</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=4j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j7g RCSB], [http://www.ebi.ac.uk/pdbsum/4j7g PDBsum]</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=4j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7g OCA], [http://pdbe.org/4j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j7g RCSB], [http://www.ebi.ac.uk/pdbsum/4j7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4j7g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:21, 20 January 2015

OCA — Tue, 20 Jan 2015 09:21:23 GMT

←Older revision		Revision as of 09:21, 20 January 2015
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-	~~{{STRUCTURE_4j7g\| PDB=4j7g \| SCENE= }}~~	+	==Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose==
-	===Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose===	+	<StructureSection load='4j7g' size='340' side='right' caption='[[4j7g]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23473392}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4j7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_orientalis"_pittenger_and_brigham_1956 "streptomyces orientalis" pittenger and brigham 1956]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J7G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1JB:[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+[(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]+HYDROGEN+PHOSPHATE'>1JB</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4j7h\|4j7h]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EvaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 "Streptomyces orientalis" Pittenger and Brigham 1956])</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=4j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j7g RCSB], [http://www.ebi.ac.uk/pdbsum/4j7g PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Unusual deoxysugars found appended to natural products often provide or enhance the pharmacokinetic activities of the parent compound. The preferred carbohydrate donors for the biosynthesis of such glycosylated natural products are the dTDP-linked sugars. Many of the biologically relevant dTDP-deoxysugars are constructed around the 2,6-dideoxyhexoses or the 2,3(4),6-trideoxyhexoses. A key step in the biosynthesis of these sugars is the removal of the hexose C-2' hydroxyl group and the oxidation of the C-3' hydroxyl group to a carbonyl moiety. Enzymes that catalyze these reactions are referred to as 2,3-dehydratases and have been, for the most part, largely uncharacterized. Here we report the first structural analysis of a sugar 2,3-dehydratase. For this investigation, the enzyme, EvaA, was cloned from Amycolatopsis orientalis, and the structure was solved and refined to a nominal resolution of 1.7 A. On the basis of the resulting model, it is clear that EvaA belongs to the large Nudix hydrolase superfamily and is most similar to GDP-mannose hydrolase. Each subunit of the EvaA dimer folds into two domains that clearly arose via gene duplication. Two dTDP-sugar binding pockets, A and B, are present in each EvaA subunit. On the basis of site-directed mutagenesis experiments and activity assays, it appears that pocket A functions as the active site and pocket B is simply a remnant left behind from the gene duplication event. As 2,3-dehydration is crucial for the biosynthesis of many unusual deoxysugars, this investigation provides key structural insight into this widely conserved reaction.

-	~~==About this~~ Structure==	+	Structure of EvaA: A Paradigm for Sugar 2,3-Dehydratases.,Kubiak RL, Thoden JB, Holden HM Biochemistry. 2013 Mar 12. PMID:23473392<ref>PMID:23473392</ref>
-	~~[[4j7g]] is a~~ 2 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"streptomyces_orientalis"_pittenger_and_brigham_1956 "streptomyces orientalis" pittenger and brigham 1956]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023473392</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Streptomyces orientalis pittenger and brigham 1956]]		[[Category: Streptomyces orientalis pittenger and brigham 1956]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
-	[[Category: Kubiak, R L.]]	+	[[Category: Kubiak, R L]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
	[[Category: Biosynthetic protein]]		[[Category: Biosynthetic protein]]
	[[Category: Dehydration]]		[[Category: Dehydration]]
	[[Category: Nudix hydrolase superfamily]]		[[Category: Nudix hydrolase superfamily]]

OCA at 12:23, 20 November 2013

OCA — Wed, 20 Nov 2013 12:23:47 GMT

←Older revision		Revision as of 12:23, 20 November 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4j7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Amycolatopsis_orientalis Amycolatopsis~~ orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA].	+	[[4j7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_orientalis"_pittenger_and_brigham_1956 "streptomyces orientalis" pittenger and brigham 1956]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023473392</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023473392</ref><references group="xtra"/><references/>
-	[[Category: ~~Amycolatopsis~~ orientalis]]	+	[[Category: Streptomyces orientalis pittenger and brigham 1956]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]
	[[Category: Kubiak, R L.]]		[[Category: Kubiak, R L.]]

OCA at 15:44, 19 June 2013

OCA — Wed, 19 Jun 2013 15:44:57 GMT

←Older revision		Revision as of 15:44, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4j7g\| PDB=4j7g \| SCENE= }}
		+	===Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose===
		+	{{ABSTRACT_PUBMED_23473392}}

-	~~The entry~~ 4j7g is ~~ON HOLD~~	+	==About this Structure==
		+	[[4j7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7G OCA].

-	~~Authors~~: Holden, H.M., Kubiak, R.L., Thoden, J.B.	+	==Reference==
-		+	<ref group="xtra">PMID:023473392</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose~~	+	[[Category: Amycolatopsis orientalis]]
		+	[[Category: Holden, H M.]]
		+	[[Category: Kubiak, R L.]]
		+	[[Category: Thoden, J B.]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Dehydration]]
		+	[[Category: Nudix hydrolase superfamily]]

OCA: Protected "4j7g" [edit=sysop:move=sysop]

OCA — Wed, 20 Feb 2013 13:33:08 GMT

Protected "4j7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:33, 20 February 2013

OCA: New page: '''Unreleased structure''' The entry 4j7g is ON HOLD Authors: Holden, H.M., Kubiak, R.L., Thoden, J.B. Description: Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fu...

OCA — Wed, 20 Feb 2013 13:33:07 GMT

New page: '''Unreleased structure''' The entry 4j7g is ON HOLD Authors: Holden, H.M., Kubiak, R.L., Thoden, J.B. Description: Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fu...

New page

'''Unreleased structure'''

The entry 4j7g is ON HOLD

Authors: Holden, H.M., Kubiak, R.L., Thoden, J.B.

Description: Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose