5d6s - Revision history

OCA at 11:46, 9 May 2024

OCA — Thu, 09 May 2024 11:46:42 GMT

←Older revision		Revision as of 11:46, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_thermophilus Streptococcus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D6S FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_thermophilus Streptococcus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D6S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [https://pdbe.org/5d6s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [https://www.ebi.ac.uk/pdbsum/5d6s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6s 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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [https://pdbe.org/5d6s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [https://www.ebi.ac.uk/pdbsum/5d6s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6s ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:23, 21 June 2023

OCA — Wed, 21 Jun 2023 10:23:51 GMT

←Older revision		Revision as of 10:23, 21 June 2023
Line 1:		Line 1:

	==Structure of epoxyqueuosine reductase from Streptococcus thermophilus.==		==Structure of epoxyqueuosine reductase from Streptococcus thermophilus.==
-	<StructureSection load='5d6s' size='340' side='right' caption='[[5d6s]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='5d6s' size='340' side='right'caption='[[5d6s]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19258 Atcc 19258~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D6S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_thermophilus Streptococcus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D6S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MNA02_1104 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258])~~</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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [https://pdbe.org/5d6s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [https://www.ebi.ac.uk/pdbsum/5d6s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6s 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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [~~http~~://pdbe.org/5d6s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d6s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6s ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0R4I997_STRTR A0A0R4I997_STRTR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 19258~~]]	+	[[Category: Large Structures]]
-	[[Category: Dunstan~~, M S~~]]	+	[[Category: Streptococcus thermophilus]]
-	[[Category: Fisher, K]]	+	[[Category: Dunstan MS]]
-	[[Category: Leys, D]]	+	[[Category: Fisher K]]
-	[[Category: Payne~~, K A.P~~]]	+	[[Category: Leys D]]
-	[[Category: Sjuts, H]]	+	[[Category: Payne KAP]]
-	~~[[Category: Cobalamin dependent oxidoreductase]]~~	+	[[Category: Sjuts H]]
-	~~[[Category: Iron-sulfur protein]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Trna-binding~~]]	+

OCA at 15:48, 16 November 2017

OCA — Thu, 16 Nov 2017 15:48:23 GMT

←Older revision		Revision as of 15:48, 16 November 2017
Line 1:		Line 1:
		+
	==Structure of epoxyqueuosine reductase from Streptococcus thermophilus.==		==Structure of epoxyqueuosine reductase from Streptococcus thermophilus.==
	<StructureSection load='5d6s' size='340' side='right' caption='[[5d6s]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='5d6s' size='340' side='right' caption='[[5d6s]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D6S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D6S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [http://pdbe.org/5d6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [http://www.ebi.ac.uk/pdbsum/5d6s PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MNA02_1104 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258])</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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [http://pdbe.org/5d6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [http://www.ebi.ac.uk/pdbsum/5d6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6s ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 19258]]
	[[Category: Dunstan, M S]]		[[Category: Dunstan, M S]]
	[[Category: Fisher, K]]		[[Category: Fisher, K]]

OCA at 07:16, 30 September 2015

OCA — Wed, 30 Sep 2015 07:16:36 GMT

←Older revision		Revision as of 07:16, 30 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of epoxyqueuosine reductase from Streptococcus thermophilus.==
		+	<StructureSection load='5d6s' size='340' side='right' caption='[[5d6s]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5d6s]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D6S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5d6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6s OCA], [http://pdbe.org/5d6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d6s RCSB], [http://www.ebi.ac.uk/pdbsum/5d6s PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Queuosine (Q) is a hypermodified RNA base that replaces guanine in the wobble positions of 5prime-GUN-3prime tRNA molecules. Q is exclusively made by bacteria, and the corresponding queuine base is a micronutrient salvaged by eukaryotic species. The final step in Q biosynthesis is the reduction of the epoxide precursor, epoxyqueuosine, to yield the Q cyclopentene ring. The epoxyqueuosine reductase responsible, QueG, shares distant homology with the cobalamin-dependent reductive dehalogenase (RdhA), however the role played by cobalamin in QueG catalysis has remained elusive. We report the solution and structural characterization of Streptococcus thermophilus QueG, revealing the enzyme harbours a redox chain consisting of two [4Fe-4S] clusters and a cob(II)alamin in the base-off form, similar to RdhAs. In contrast to the shared redox chain architecture, the QueG active site shares little homology with RdhA, with the notable exception of a conserved Tyr that is proposed to function as a proton donor during reductive dehalogenation. Docking of an epoxyqueuosine substrate suggests the QueG active site places the substrate cyclopentane moiety in close proximity of the cobalt. Both the Tyr and a conserved Asp are implicated as proton donors to the epoxide leaving group. This suggests that, in contrast to the unusual carbon-halogen bond chemistry catalyzed by RdhAs, QueG acts via Co-C bond formation. Our study establishes the common features of Class III cobalamin-dependent enzymes, and reveal an unexpected diversity in the reductive chemistry catalyzed by these enzymes.

-	~~The entry 5d6s is ON HOLD until Paper Publication~~	+	Epoxyqueuosine Reductase Structure suggests a Mechanism for Cobalamin-dependent tRNA Modification.,Payne KA, Fisher K, Sjuts H, Dunstan MS, Bellina B, Johannissen L, Barran P, Hay S, Rigby SE, Leys D J Biol Chem. 2015 Sep 16. pii: jbc.M115.685693. PMID:26378237<ref>PMID:26378237</ref>

-	~~Authors: Payne~~, ~~K.A.P., Fisher, K., Dunstan, M~~.S.~~, Sjuts, H., Leys, D~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of epoxyqueuosine reductase from Streptococcus thermophilus.~~	+	<div class="pdbe-citations 5d6s" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dunstan, M S]]
		+	[[Category: Fisher, K]]
	[[Category: Leys, D]]		[[Category: Leys, D]]
-	~~[[Category: Dunstan, M.S]]~~	+	[[Category: Payne, K A.P]]
-	[[Category: Payne, K.A.P]]	+
	[[Category: Sjuts, H]]		[[Category: Sjuts, H]]
-	[[Category: ~~Fisher, K~~]]	+	[[Category: Cobalamin dependent oxidoreductase]]
		+	[[Category: Iron-sulfur protein]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Trna-binding]]

OCA: Protected "5d6s" [edit=sysop:move=sysop]

OCA — Thu, 20 Aug 2015 11:27:08 GMT

Protected "5d6s" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:27, 20 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d6s is ON HOLD until Paper Publication Authors: Payne, K.A.P., Fisher, K., Dunstan, M.S., Sjuts, H., Leys, D. Description: Structure of epoxyqueuo...

OCA — Thu, 20 Aug 2015 11:27:06 GMT

New page: '''Unreleased structure''' The entry 5d6s is ON HOLD until Paper Publication Authors: Payne, K.A.P., Fisher, K., Dunstan, M.S., Sjuts, H., Leys, D. Description: Structure of epoxyqueuo...

New page

'''Unreleased structure'''

The entry 5d6s is ON HOLD until Paper Publication

Authors: Payne, K.A.P., Fisher, K., Dunstan, M.S., Sjuts, H., Leys, D.

Description: Structure of epoxyqueuosine reductase from Streptococcus thermophilus.
[[Category: Unreleased Structures]]
[[Category: Leys, D]]
[[Category: Dunstan, M.S]]
[[Category: Payne, K.A.P]]
[[Category: Sjuts, H]]
[[Category: Fisher, K]]