5vyq - Revision history

OCA at 14:02, 4 October 2023

OCA — Wed, 04 Oct 2023 14:02:54 GMT

←Older revision		Revision as of 14:02, 4 October 2023
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	<StructureSection load='5vyq' size='340' side='right'caption='[[5vyq]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5vyq' size='340' side='right'caption='[[5vyq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis_cas~~/~~nitr204~~ Mycobacterium tuberculosis ~~cas~~/~~nitr204~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VYQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_CAS/NITR204 Mycobacterium tuberculosis CAS/NITR204]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VYQ 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EP1:3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>EP1</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vyr\|5vyr]], [[5vys\|5vys]], [[5vyt\|5vyt]], [[5vyu\|5vyu]]</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EP1:3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>EP1</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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">J113_23825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1310114 Mycobacterium tuberculosis CAS/NITR204])</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=5vyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyq OCA], [https://pdbe.org/5vyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vyq RCSB], [https://www.ebi.ac.uk/pdbsum/5vyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyq 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=5vyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyq OCA], [~~http~~://pdbe.org/5vyq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vyq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vyq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R4MIX2_MYCTX R4MIX2_MYCTX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mycobacterium tuberculosis ~~cas~~/~~nitr204~~]]	+	[[Category: Mycobacterium tuberculosis CAS/NITR204]]
-	[[Category: Dunsirn~~, M M~~]]	+	[[Category: Dunsirn MM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Deoxysugar]]~~	+
-	~~[[Category: Formyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:43, 1 January 2020

OCA — Wed, 01 Jan 2020 09:43:00 GMT

←Older revision		Revision as of 09:43, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid==		==Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid==
-	<StructureSection load='5vyq' size='340' side='right' caption='[[5vyq]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5vyq' size='340' side='right'caption='[[5vyq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_cas/nitr204 Mycobacterium tuberculosis cas/nitr204]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYQ 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EP1:3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>EP1</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EP1:3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>EP1</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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">[[5vyr\|5vyr]], [[5vys\|5vys]], [[5vyt\|5vyt]], [[5vyu\|5vyu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vyr\|5vyr]], [[5vys\|5vys]], [[5vyt\|5vyt]], [[5vyu\|5vyu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">J113_23825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1310114 Mycobacterium tuberculosis CAS/NITR204])</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=5vyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyq OCA], [http://pdbe.org/5vyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyq RCSB], [http://www.ebi.ac.uk/pdbsum/5vyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyq 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=5vyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyq OCA], [http://pdbe.org/5vyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyq RCSB], [http://www.ebi.ac.uk/pdbsum/5vyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyq ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycobacterium tuberculosis cas/nitr204]]
	[[Category: Dunsirn, M M]]		[[Category: Dunsirn, M M]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

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

OCA — Wed, 09 Aug 2017 09:01:48 GMT

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

←Older revision

Revision as of 09:01, 9 August 2017

OCA: New page: ==Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid==
OCA — Wed, 09 Aug 2017 09:01:46 GMT

New page: ==Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid== <StructureSection load='5vyq' size='340' side='right' c...

New page

==Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid==
<StructureSection load='5vyq' size='340' side='right' caption='[[5vyq]], [[Resolution|resolution]] 1.60Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vyq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYQ 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EP1:3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>EP1</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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">[[5vyr|5vyr]], [[5vys|5vys]], [[5vyt|5vyt]], [[5vyu|5vyu]]</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=5vyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyq OCA], [http://pdbe.org/5vyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyq RCSB], [http://www.ebi.ac.uk/pdbsum/5vyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyq ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The causative agent of tuberculosis, Mycobacterium tuberculosis, is a bacterium with a complex cell wall and a complicated life cycle. The genome of M. tuberculosis contains well over 4000 genes thought to encode proteins. One of these codes for a putative enzyme referred to as Rv3404c, which has attracted research attention as a potential virulence factor for over 12 years. Here we demonstrate that Rv3404c functions as a sugar N-formyltransferase that converts dTDP-4-amino-4,6-dideoxyglucose into dTDP-4-formamido-4,6-dideoxyglucose using N10-formyltetrahydrofolate as the carbon source. Kinetic analyses demonstrate that Rv3404c displays a significant catalytic efficiency of 1.1 x 104 M-1 s-1. In addition, we report the X-ray structure of a ternary complex of Rv3404c solved in the presence of N5-formyltetrahydrofolate and dTDP-4-amino-4,6-dideoxyglucose. The final model of Rv3404c was refined to an overall R-factor of 16.8% at 1.6 A resolution. The results described herein are especially intriguing given that there have been no published reports of N-formylated sugars associated with M. tuberculosis. The data thus provide a new avenue of research into this fascinating, yet deadly, organism that apparently has been associated with human infection since ancient times.

Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis.,Dunsirn MM, Thoden JB, Gilbert M, Holden HM Biochemistry. 2017 Jul 25;56(29):3818-3825. doi: 10.1021/acs.biochem.7b00506., Epub 2017 Jul 14. PMID:28665588<ref>PMID:28665588</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vyq" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Dunsirn, M M]]
[[Category: Holden, H M]]
[[Category: Thoden, J B]]
[[Category: Deoxysugar]]
[[Category: Formyltransferase]]
[[Category: Transferase]]