6v2t - Revision history

OCA at 08:02, 11 October 2023

OCA — Wed, 11 Oct 2023 08:02:56 GMT

←Older revision		Revision as of 08:02, 11 October 2023
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	<StructureSection load='6v2t' size='340' side='right'caption='[[6v2t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6v2t' size='340' side='right'caption='[[6v2t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v2t]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Shewanella_sp.~~_fdaargos_354~~ Shewanella sp. ~~fdaargos_354~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6V2T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v2t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_sp._FDAARGOS_354 Shewanella sp. FDAARGOS_354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V2T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CEQ32_00475 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1930557 Shewanella sp. FDAARGOS_354])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2t OCA], [~~http~~://pdbe.org/6v2t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6v2t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6v2t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2t ProSAT]</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=6v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2t OCA], [https://pdbe.org/6v2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v2t RCSB], [https://www.ebi.ac.uk/pdbsum/6v2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shewanella sp. ~~fdaargos_354~~]]	+	[[Category: Shewanella sp. FDAARGOS_354]]
-	[[Category: Girardi~~, N M~~]]	+	[[Category: Girardi NM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Lipopolysaccharide]]~~	+
-	~~[[Category: N-formyltransferase]]~~	+
-	~~[[Category: O-antigen]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:28, 8 April 2020

OCA — Wed, 08 Apr 2020 07:28:53 GMT

←Older revision		Revision as of 07:28, 8 April 2020
Line 3:		Line 3:
	<StructureSection load='6v2t' size='340' side='right'caption='[[6v2t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6v2t' size='340' side='right'caption='[[6v2t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v2t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6V2T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v2t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_sp._fdaargos_354 Shewanella sp. fdaargos_354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V2T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2t OCA], [http://pdbe.org/6v2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v2t RCSB], [http://www.ebi.ac.uk/pdbsum/6v2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2t ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CEQ32_00475 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1930557 Shewanella sp. FDAARGOS_354])</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=6v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2t OCA], [http://pdbe.org/6v2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v2t RCSB], [http://www.ebi.ac.uk/pdbsum/6v2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Shewanella sp. fdaargos_354]]
	[[Category: Girardi, N M]]		[[Category: Girardi, N M]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 07:42, 8 January 2020

OCA — Wed, 08 Jan 2020 07:42:42 GMT

←Older revision		Revision as of 07:42, 8 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6v2t is ~~ON HOLD until Paper~~ Publication	+	==X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354==
		+	<StructureSection load='6v2t' size='340' side='right'caption='[[6v2t]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6v2t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6V2T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2t OCA], [http://pdbe.org/6v2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v2t RCSB], [http://www.ebi.ac.uk/pdbsum/6v2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2t ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key to utilizing these vast amounts of data in a biologically meaningful way is to infer the function of the proteins encoded in the genomes via bioinformatics techniques. Whereas these approaches are absolutely critical to the annotation of gene function, there are still issues of misidentifications, which must be experimentally corrected. For example, many of the bacterial DNA sequences encoding sugar N-formyltransferases have been annotated as l-methionyl-tRNA transferases in the databases. These mistakes may be due in part to the fact that until recently the structures and functions of these enzymes were not well known. Herein we describe the misannotation of two genes, WP_088211966.1 and WP_096244125.1, from Shewanella spp. and Pseudomonas congelans, respectively. Although the proteins encoded by these genes were originally suggested to function as l-methionyl-tRNA transferases, we demonstrate that they actually catalyze the conversion of dTDP-4-amino-4,6-dideoxy-d-glucose to dTDP-4-formamido-4,6-dideoxy-d-glucose utilizing N(10) -formyltetrahydrofolate as the carbon source. For this analysis, the genes encoding these enzymes were cloned and the corresponding proteins purified. X-ray structures of the two proteins were determined to high resolution and kinetic analyses were conducted. Both enzymes display classical Michaelis-Menten kinetics and adopt the characteristic three-dimensional structure fold previously observed for other sugar N-formyltransferases. The results presented herein will aid in the future annotation of these fascinating enzymes. This article is protected by copyright. All rights reserved.

-	~~Authors: Girardi,~~ N.M., Thoden, J.B.~~, Holden, H~~.M.	+	Misannotations of the Genes Encoding Sugar N-formyltransferases.,Girardi NM, Thoden JB, Holden HM Protein Sci. 2019 Dec 23. doi: 10.1002/pro.3807. PMID:31867814<ref>PMID:31867814</ref>

-	~~Description: X-ray structure of~~ a ~~sugar N~~-~~formyltransferase from Shewanella sp FDAARGOS_354~~	+	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 6v2t" style="background-color:#fffaf0;"></div>
-	[[Category: Holden, H.M]]	+	== References ==
-	[[Category: ~~Girardi~~, N.M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Girardi, N M]]
		+	[[Category: Holden, H M]]
		+	[[Category: Thoden, J B]]
		+	[[Category: Lipopolysaccharide]]
		+	[[Category: N-formyltransferase]]
		+	[[Category: O-antigen]]
		+	[[Category: Transferase]]

OCA at 06:00, 18 December 2019

OCA — Wed, 18 Dec 2019 06:00:41 GMT

←Older revision		Revision as of 06:00, 18 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6v2t is ON HOLD	+	The entry 6v2t is ON HOLD until Paper Publication

	Authors: Girardi, N.M., Thoden, J.B., Holden, H.M.		Authors: Girardi, N.M., Thoden, J.B., Holden, H.M.
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	Description: X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354		Description: X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Girardi, N.M]]
	[[Category: Thoden, J.B]]		[[Category: Thoden, J.B]]
	[[Category: Holden, H.M]]		[[Category: Holden, H.M]]
		+	[[Category: Girardi, N.M]]

OCA: Protected "6v2t" [edit=sysop:move=sysop]

OCA — Wed, 04 Dec 2019 06:37:51 GMT

Protected "6v2t" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:37, 4 December 2019

OCA: New page: '''Unreleased structure''' The entry 6v2t is ON HOLD Authors: Girardi, N.M., Thoden, J.B., Holden, H.M. Description: X-ray structure of a sugar N-formyltransferase from Shewanella sp F...

OCA — Wed, 04 Dec 2019 06:37:49 GMT

New page: '''Unreleased structure''' The entry 6v2t is ON HOLD Authors: Girardi, N.M., Thoden, J.B., Holden, H.M. Description: X-ray structure of a sugar N-formyltransferase from Shewanella sp F...

New page

'''Unreleased structure'''

The entry 6v2t is ON HOLD

Authors: Girardi, N.M., Thoden, J.B., Holden, H.M.

Description: X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354
[[Category: Unreleased Structures]]
[[Category: Girardi, N.M]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]