5uin - Revision history

OCA at 13:28, 4 October 2023

2023-10-04T13:28:08Z

←Older revision		Revision as of 13:28, 4 October 2023
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	<StructureSection load='5uin' size='340' side='right'caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5uin' size='340' side='right'caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UIN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uij\|5uij]], [[5uik\|5uik]], [[5uil\|5uil]], [[5uim\|5uim]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fdtF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28901 "Bacillus cholerae-suis" Smith 1894])</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=5uin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uin OCA], [https://pdbe.org/5uin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uin RCSB], [https://www.ebi.ac.uk/pdbsum/5uin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uin 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=5uin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uin OCA], [~~http~~://pdbe.org/5uin PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uin RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uin PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uin ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/U3GK13_SALER U3GK13_SALER]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus cholerae-suis smith 1894]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Holden, H M~~]]	+	[[Category: Salmonella enterica]]
-	[[Category: ~~Thoden, J B~~]]	+	[[Category: Holden HM]]
-	[[Category: ~~Woodford, C R~~]]	+	[[Category: Thoden JB]]
-	[[Category: ~~Ankyrin repeat]]~~	+	[[Category: Woodford CR]]
-	~~[[Category: Lipopolysaccharide]]~~	+
-	~~[[Category: O-antigen]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:17, 1 January 2020

2020-01-01T09:17:48Z

←Older revision		Revision as of 09:17, 1 January 2020
Line 1:		Line 1:

	==X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60==		==X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60==
-	<StructureSection load='5uin' size='340' side='right' caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5uin' size='340' side='right'caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UIN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UIN FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus cholerae-suis smith 1894]]		[[Category: Bacillus cholerae-suis smith 1894]]
		+	[[Category: Large Structures]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]

OCA at 19:39, 15 November 2017

2017-11-15T19:39:06Z

←Older revision		Revision as of 19:39, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5uin' size='340' side='right' caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5uin' size='340' side='right' caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UIN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uij\|5uij]], [[5uik\|5uik]], [[5uil\|5uil]], [[5uim\|5uim]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uij\|5uij]], [[5uik\|5uik]], [[5uil\|5uil]], [[5uim\|5uim]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fdtF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28901 "Bacillus cholerae-suis" Smith 1894])</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=5uin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uin OCA], [http://pdbe.org/5uin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uin RCSB], [http://www.ebi.ac.uk/pdbsum/5uin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uin 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=5uin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uin OCA], [http://pdbe.org/5uin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uin RCSB], [http://www.ebi.ac.uk/pdbsum/5uin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uin ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cholerae-suis smith 1894]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]

OCA at 16:47, 22 March 2017

2017-03-22T16:47:10Z

←Older revision		Revision as of 16:47, 22 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uin is ~~ON HOLD until Paper~~ Publication	+	==X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60==
		+	<StructureSection load='5uin' size='340' side='right' caption='[[5uin]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uin]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UIN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uij\|5uij]], [[5uik\|5uik]], [[5uil\|5uil]], [[5uim\|5uim]]</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=5uin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uin OCA], [http://pdbe.org/5uin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uin RCSB], [http://www.ebi.ac.uk/pdbsum/5uin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uin ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-formylated sugars are found on the lipopolysaccharides of various pathogenic Gram negative bacteria including Campylobacter jejuni 81116, Francisella tularensis, Providencia alcalifaciens O30, and Providencia alcalifaciens O40. The last step in the biosynthetic pathways for these unusual sugars is catalyzed by N-formyltransferases that utilize N10-formyltetrahydrofolate as the carbon source. The substrates are dTDP-linked amino sugars with the functional groups installed at either the C-3' or C-4' positions of the pyranosyl rings. Here we describe a structural and enzymological investigation of the putative N-formyltransferase, FdtF, from Salmonella enterica O60. In keeping with its proposed role in the organism, the kinetic data reveal that the enzyme is more active with dTDP-3-amino-3,6-dideoxy-d-galactose than with dTDP-3-amino-3,6-dideoxy-d-glucose. The structural data demonstrate that the enzyme contains, in addition to the canonical N-formyltransferase fold, an ankyrin repeat moiety that houses a second dTDP-sugar binding pocket. This is only the second time an ankyrin repeat has been shown to be involved in small molecule binding. The research described herein represents the first structural analysis of a sugar N-formyltransferase that specifically functions on dTDP-3-amino-3,6-dideoxy-d-galactose in vivo and thus adds to our understanding of these intriguing enzymes.

-	~~Authors: Woodford, C.R~~., Thoden, J.B., ~~Holden, H~~.M.	+	Molecular Architecture of an N-formyltransferase from Salmonella enterica O60.,Woodford CR, Thoden JB, Holden HM J Struct Biol. 2017 Mar 2. pii: S1047-8477(17)30036-9. doi:, 10.1016/j.jsb.2017.03.002. PMID:28263875<ref>PMID:28263875</ref>

-	~~Description: X-ray structure~~ of the ~~W305A variant~~ of ~~the FdtF N~~-~~formyltransferase from salmonella enteric O60~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Thoden, J.B]]	+	<div class="pdbe-citations 5uin" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Holden~~, ~~H.M~~]]	+	== References ==
-	[[Category: ~~Woodford, C.R~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Holden, H M]]
		+	[[Category: Thoden, J B]]
		+	[[Category: Woodford, C R]]
		+	[[Category: Ankyrin repeat]]
		+	[[Category: Lipopolysaccharide]]
		+	[[Category: O-antigen]]
		+	[[Category: Transferase]]

OCA at 16:40, 1 February 2017

2017-02-01T16:40:02Z

←Older revision		Revision as of 16:40, 1 February 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Woodford, C.R., Thoden, J.B., Holden, H.M.		Authors: Woodford, C.R., Thoden, J.B., Holden, H.M.

-	Description: x-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60,	+	Description: X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Thoden, J.B]]		[[Category: Thoden, J.B]]
	[[Category: Holden, H.M]]		[[Category: Holden, H.M]]
	[[Category: Woodford, C.R]]		[[Category: Woodford, C.R]]

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

2017-01-25T22:10:51Z

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

←Older revision

Revision as of 22:10, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5uin is ON HOLD Authors: Woodford, C.R., Thoden, J.B., Holden, H.M. Description: x-ray structure of the W305A variant of the FdtF N-formyltransfera...

2017-01-25T22:10:50Z

New page: '''Unreleased structure''' The entry 5uin is ON HOLD Authors: Woodford, C.R., Thoden, J.B., Holden, H.M. Description: x-ray structure of the W305A variant of the FdtF N-formyltransfera...

New page

'''Unreleased structure'''

The entry 5uin is ON HOLD

Authors: Woodford, C.R., Thoden, J.B., Holden, H.M.

Description: x-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60,
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]
[[Category: Woodford, C.R]]