4nes - Revision history

OCA at 08:25, 11 January 2023

OCA — Wed, 11 Jan 2023 08:25:31 GMT

←Older revision		Revision as of 08:25, 11 January 2023
Line 1:		Line 1:

	==Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP==		==Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP==
-	<StructureSection load='4nes' size='340' side='right' caption='[[4nes]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='4nes' size='340' side='right'caption='[[4nes]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nes]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metja Metja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NES OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NES FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nes]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NES FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UD1~~:~~URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE~~'>~~UD1~~</scene>, <scene name='pdbligand=~~UDP~~:URIDINE-5-DIPHOSPHATE'>~~UDP~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE'>MSE</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=4nes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nes OCA], [https://pdbe.org/4nes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nes RCSB], [https://www.ebi.ac.uk/pdbsum/4nes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nes ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4neq\|4neq]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wecB, MJ1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=243232 METJA])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~UDP~~-N-acetylglucosamine_2-epimerase_(non-hydrolyzing) UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.14 5.1.3.14]~~ </~~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=4nes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nes OCA], [~~http~~://pdbe.org/4nes PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nes RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nes PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nes ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/WECB_METJA WECB_METJA]] Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues (By similarity).	+	[https://www.uniprot.org/uniprot/WECB_METJA WECB_METJA] Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Metja~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Chen, S C~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: Chen~~, Y~~]]	+	[[Category: Chen SC]]
-	[[Category: ~~Huang, C H~~]]	+	[[Category: Chen Y]]
-	[[Category: ~~Yang, C S~~]]	+	[[Category: Huang CH]]
-	[[Category: ~~Isomerase]]~~	+	[[Category: Yang CS]]
-	~~[[Category: Udp-glcnac 2-epimerase]]~~	+
-	~~[[Category: Udp-glycosyltransferase/glycogen phosphorylase fold~~]]	+

OCA at 17:08, 22 March 2017

OCA — Wed, 22 Mar 2017 17:08:51 GMT

←Older revision		Revision as of 17:08, 22 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP==		==Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP==
	<StructureSection load='4nes' size='340' side='right' caption='[[4nes]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='4nes' size='340' side='right' caption='[[4nes]], [[Resolution\|resolution]] 1.42Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wecB, MJ1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wecB, MJ1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_2-epimerase_(non-hydrolyzing) UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.14 5.1.3.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_2-epimerase_(non-hydrolyzing) UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.14 5.1.3.14] </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=4nes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nes RCSB], [http://www.ebi.ac.uk/pdbsum/4nes 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=4nes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nes OCA], [http://pdbe.org/4nes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nes RCSB], [http://www.ebi.ac.uk/pdbsum/4nes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4nes" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:02, 25 December 2014

OCA — Thu, 25 Dec 2014 06:02:03 GMT

←Older revision		Revision as of 06:02, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nes\| PDB=4nes \| SCENE= }}~~	+	==Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP==
-	===Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP===	+	<StructureSection load='4nes' size='340' side='right' caption='[[4nes]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24470206}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4nes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NES FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4neq\|4neq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wecB, MJ1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_2-epimerase_(non-hydrolyzing) UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.14 5.1.3.14] </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=4nes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nes RCSB], [http://www.ebi.ac.uk/pdbsum/4nes PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/WECB_METJA WECB_METJA]] Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues (By similarity).		[[http://www.uniprot.org/uniprot/WECB_METJA WECB_METJA]] Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) 2-epimerase catalyzes the interconversion of UDP-GlcNAc to UDP-N-acetylmannosamine (UDP-ManNAc), which is used in the biosynthesis of cell surface polysaccharides in bacteria. Biochemical experiments have demonstrated that mutation of this enzyme causes changes in cell morphology and the thermoresistance of the cell wall. Here, we present the crystal structures of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in open and closed conformations. A comparison of these crystal structures shows that upon UDP and UDP-GlcNAc binding, the enzyme undergoes conformational changes involving a rigid-body movement of the C-terminal domain. We also present the crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in the closed conformation in the presence of UDP and UDP-GlcNAc. Although a structural overlay of these two closed-form structures reveals that the substrate-binding site is evolutionarily conserved, some areas of the allosteric site are distinct between the archaeal and bacterial UDP-GlcNAc 2-epimerases. This is the first report on the crystal structure of archaeal UDP-GlcNAc 2-epimerase, and our results clearly demonstrate the changes between the open and closed conformations of this enzyme. Proteins 2014. (c) 2014 Wiley Periodicals, Inc.

-	~~==About this Structure==~~	+	Crystal structures of the archaeal UDP-GlcNAc 2-epimerase from Methanocaldococcus jannaschii reveal a conformational change induced by UDP-GlcNAc.,Chen SC, Huang CH, Shin Yang C, Liu JS, Kuan SM, Chen Y Proteins. 2014 Jan 27. doi: 10.1002/prot.24516. PMID:24470206<ref>PMID:24470206</ref>
-	~~[[4nes]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4NES OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024470206</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Chen, S C.]]	+	== References ==
-	[[Category: Chen, Y.]]	+	<references/>
-	[[Category: Huang, C H.]]	+	__TOC__
-	[[Category: Yang, C S.]]	+	</StructureSection>
		+	[[Category: Metja]]
		+	[[Category: Chen, S C]]
		+	[[Category: Chen, Y]]
		+	[[Category: Huang, C H]]
		+	[[Category: Yang, C S]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Udp-glcnac 2-epimerase]]		[[Category: Udp-glcnac 2-epimerase]]
	[[Category: Udp-glycosyltransferase/glycogen phosphorylase fold]]		[[Category: Udp-glycosyltransferase/glycogen phosphorylase fold]]

OCA at 07:46, 23 April 2014

OCA — Wed, 23 Apr 2014 07:46:03 GMT

←Older revision		Revision as of 07:46, 23 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nes\| PDB=4nes \| SCENE= }}
		+	===Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP===
		+	{{ABSTRACT_PUBMED_24470206}}

-	~~The entry 4nes is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/WECB_METJA WECB_METJA]] Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues (By similarity).

-	~~Authors~~: ~~Chen, S.C., Yang, C.S~~.~~, Huang, C~~.H.~~, Chen, Y~~.	+	==About this Structure==
		+	[[4nes]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NES OCA].

-	~~Description~~: ~~Crystal structure of Methanocaldococcus jannaschii UDP~~-~~GlcNAc~~ 2-epimerase ~~in complex with UDP~~-~~GlcNAc and UDP~~	+	==Reference==
		+	<ref group="xtra">PMID:024470206</ref><references group="xtra"/><references/>
		+	[[Category: Chen, S C.]]
		+	[[Category: Chen, Y.]]
		+	[[Category: Huang, C H.]]
		+	[[Category: Yang, C S.]]
		+	[[Category: Isomerase]]
		+	[[Category: Udp-glcnac 2-epimerase]]
		+	[[Category: Udp-glycosyltransferase/glycogen phosphorylase fold]]

OCA at 09:48, 27 November 2013

OCA — Wed, 27 Nov 2013 09:48:12 GMT

←Older revision		Revision as of 09:48, 27 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nes is ON HOLD	+	The entry 4nes is ON HOLD until Paper Publication

	Authors: Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.		Authors: Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

	Description: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP		Description: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP

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

OCA — Wed, 13 Nov 2013 07:45:52 GMT

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

←Older revision

Revision as of 07:45, 13 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nes is ON HOLD Authors: Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y. Description: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2...

OCA — Wed, 13 Nov 2013 07:45:51 GMT

New page: '''Unreleased structure''' The entry 4nes is ON HOLD Authors: Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y. Description: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2...

New page

'''Unreleased structure'''

The entry 4nes is ON HOLD

Authors: Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

Description: Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP