7n7b - Revision history

OCA at 16:25, 18 October 2023

OCA — Wed, 18 Oct 2023 16:25:20 GMT

←Older revision		Revision as of 16:25, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='7n7b' size='340' side='right'caption='[[7n7b]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7n7b' size='340' side='right'caption='[[7n7b]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7n7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Helicobacter_canadensis_atcc_700968~~ Helicobacter canadensis ~~atcc 700968~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_canadensis_MIT_98-5491 Helicobacter canadensis MIT 98-5491]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N7B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=T3F:(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>T3F</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7n7a\|7n7a]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=T3F:(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>T3F</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HCAN_0200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=537970 Helicobacter canadensis ATCC 700968])</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=7n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n7b OCA], [https://pdbe.org/7n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n7b RCSB], [https://www.ebi.ac.uk/pdbsum/7n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n7b 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=7n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n7b OCA], [https://pdbe.org/7n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n7b RCSB], [https://www.ebi.ac.uk/pdbsum/7n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n7b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C5ZW02_9HELI C5ZW02_9HELI]
	<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: Helicobacter canadensis ~~atcc 700968~~]]	+	[[Category: Helicobacter canadensis MIT 98-5491]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heisdorf~~, C J~~]]	+	[[Category: Heisdorf CJ]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Aminofucose]]~~	+
-	~~[[Category: Folinic acid]]~~	+
-	~~[[Category: Formyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:36, 25 August 2021

OCA — Wed, 25 Aug 2021 06:36:35 GMT

←Older revision		Revision as of 06:36, 25 August 2021
Line 1:		Line 1:

	==crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose==		==crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose==
-	<StructureSection load='7n7b' size='340' side='right'caption='[[7n7b]]' scene=''>	+	<StructureSection load='7n7b' size='340' side='right'caption='[[7n7b]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_canadensis_atcc_700968 Helicobacter canadensis atcc 700968]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N7B FirstGlance]. <br>
-	</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=7n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n7b OCA], [https://pdbe.org/7n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n7b RCSB], [https://www.ebi.ac.uk/pdbsum/7n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n7b ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=T3F:(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>T3F</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7n7a\|7n7a]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HCAN_0200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=537970 Helicobacter canadensis ATCC 700968])</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=7n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n7b OCA], [https://pdbe.org/7n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n7b RCSB], [https://www.ebi.ac.uk/pdbsum/7n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n7b ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	It is now well-established that the Gram-negative bacterium, Helicobacter pylori, causes gastritis in humans. In recent years it has become apparent that the so-called non-pylori Helicobacters, normally infecting pigs, cats, and dogs, may also be involved in human pathology via zoonotic transmission. Indeed, more than 30 species of non-pylori Helicobacters have been identified thus far. One such organism is Helicobacter canadensis, an emerging pathogen whose genome sequence was published in 2009. Given our long-standing interest in the biosynthesis of N-formylated sugars found in the O-antigens of some Gram-negative bacteria, we were curious as to whether H. canadensis produces such unusual carbohydrates. Here we demonstrate using both biochemical and structural techniques, that the proteins encoded by the HCAN_0198, HCAN_0204, and HCAN_0200 genes in H. canadensis, correspond to a 3,4-ketoisomerase, a pyridoxal 5'-phosphate aminotransferase, and an N-formyltransferase, respectively. For this investigation, five high-resolution X-ray structures were determined and the kinetic parameters for the isomerase and the N-formyltransferase were measured. Based on these data, we suggest that the unusual sugar, 3-formamido-3,6-dideoxy-d-glucose, will most likely be found in the O-antigen of H. canadensis. Whether N-formylated sugars found in the O-antigen contribute to virulence is presently unclear, but it is intriguing that they have been observed in such pathogens as Francisella tularensis, Mycobacterium tuberculosis, and Brucella melitensis. This article is protected by copyright. All rights reserved.
		+
		+	Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis.,Heisdorf CJ, Griffiths WA, Thoden JB, Holden HM Protein Sci. 2021 Aug 11. doi: 10.1002/pro.4169. PMID:34379357<ref>PMID:34379357</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7n7b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Helicobacter canadensis atcc 700968]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heisdorf CJ]]	+	[[Category: Heisdorf, C J]]
-	[[Category: Holden HM]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden JB]]	+	[[Category: Thoden, J B]]
		+	[[Category: Aminofucose]]
		+	[[Category: Folinic acid]]
		+	[[Category: Formyltransferase]]
		+	[[Category: Transferase]]

OCA at 07:33, 25 June 2021

OCA — Fri, 25 Jun 2021 07:33:29 GMT

←Older revision		Revision as of 07:33, 25 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7n7b is ON HOLD~~	+	==crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose==
-		+	<StructureSection load='7n7b' size='340' side='right'caption='[[7n7b]]' scene=''>
-	~~Authors: Heisdorf, C.J., Thoden, J.B., Holden, H.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N7B FirstGlance]. <br>
-	~~Description:~~ crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose	+	</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=7n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n7b OCA], [https://pdbe.org/7n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n7b RCSB], [https://www.ebi.ac.uk/pdbsum/7n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n7b ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Thoden, J.B~~]]	+	__TOC__
-	[[Category: Holden~~, H.M~~]]	+	</StructureSection>
-	[[Category: ~~Heisdorf, C.J~~]]	+	[[Category: Large Structures]]
		+	[[Category: Heisdorf CJ]]
		+	[[Category: Holden HM]]
		+	[[Category: Thoden JB]]

OCA: Protected "7n7b" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:42:36 GMT

Protected "7n7b" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:42, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7n7b is ON HOLD Authors: Heisdorf, C.J., Thoden, J.B., Holden, H.M. Description: crystal structure of the N-formyltrasferase HCAN_0200 from Helicob...

OCA — Thu, 17 Jun 2021 13:42:35 GMT

New page: '''Unreleased structure''' The entry 7n7b is ON HOLD Authors: Heisdorf, C.J., Thoden, J.B., Holden, H.M. Description: crystal structure of the N-formyltrasferase HCAN_0200 from Helicob...

New page

'''Unreleased structure'''

The entry 7n7b is ON HOLD

Authors: Heisdorf, C.J., Thoden, J.B., Holden, H.M.

Description: crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]
[[Category: Heisdorf, C.J]]