OCA at 16:13, 18 October 2023

2023-10-18T16:13:48Z

←Older revision		Revision as of 16:13, 18 October 2023
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-	====	+	==MiaB in the complex with s-adenosyl-L-homocysteine and RNA==
-	<StructureSection load='7mjy' size='340' side='right'caption='[[7mjy]]' scene=''>	+	<StructureSection load='7mjy' size='340' side='right'caption='[[7mjy]], [[Resolution\|resolution]] 1.86Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mjy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_uniformis Bacteroides uniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MJY 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=7mjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mjy OCA], [https://pdbe.org/7mjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mjy RCSB], [https://www.ebi.ac.uk/pdbsum/7mjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mjy ProSAT]</span></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]] 1.86Å</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=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=7mjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mjy OCA], [https://pdbe.org/7mjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mjy RCSB], [https://www.ebi.ac.uk/pdbsum/7mjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mjy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A174NUT3_BACUN A0A174NUT3_BACUN] Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine.[ARBA:ARBA00003234][HAMAP-Rule:MF_01864]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Numerous post-transcriptional modifications of transfer RNAs have vital roles in translation. The 2-methylthio-N(6)-isopentenyladenosine (ms(2)i(6)A) modification occurs at position 37 (A37) in transfer RNAs that contain adenine in position 36 of the anticodon, and serves to promote efficient A:U codon-anticodon base-pairing and to prevent unintended base pairing by near cognates, thus enhancing translational fidelity(1-4). The ms(2)i(6)A modification is installed onto isopentenyladenosine (i(6)A) by MiaB, a radical S-adenosylmethionine (SAM) methylthiotransferase. As a radical SAM protein, MiaB contains one [Fe4S4]RS cluster used in the reductive cleavage of SAM to form a 5'-deoxyadenosyl 5'-radical, which is responsible for removing the C(2) hydrogen of the substrate(5). MiaB also contains an auxiliary [Fe4S4]aux cluster, which has been implicated(6-9) in sulfur transfer to C(2) of i(6)A37. How this transfer takes place is largely unknown. Here we present several structures of MiaB from Bacteroides uniformis. These structures are consistent with a two-step mechanism, in which one molecule of SAM is first used to methylate a bridging micro-sulfido ion of the auxiliary cluster. In the second step, a second SAM molecule is cleaved to a 5'-deoxyadenosyl 5'-radical, which abstracts the C(2) hydrogen of the substrate but only after C(2) has undergone rehybridization from sp(2) to sp(3). This work advances our understanding of how enzymes functionalize inert C-H bonds with sulfur.
		+
		+	Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.,Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ Nature. 2021 Sep;597(7877):566-570. doi: 10.1038/s41586-021-03904-6. Epub 2021, Sep 15. PMID:34526715<ref>PMID:34526715</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mjy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides uniformis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Almo SC]]
		+	[[Category: Arcinas AJ]]
		+	[[Category: Booker SJ]]
		+	[[Category: Esakova OA]]
		+	[[Category: Grove TL]]
		+	[[Category: Krebs C]]
		+	[[Category: Wang B]]
		+	[[Category: Yennawar NH]]

OCA at 09:27, 15 September 2021

2021-09-15T09:27:02Z

←Older revision		Revision as of 09:27, 15 September 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7mjy ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7mjy' size='340' side='right'caption='[[7mjy]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7mjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mjy OCA], [https://pdbe.org/7mjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mjy RCSB], [https://www.ebi.ac.uk/pdbsum/7mjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mjy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 11:04, 9 June 2021

2021-06-09T11:04:16Z

←Older revision		Revision as of 11:04, 9 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mjy is ON HOLD	+	The entry 7mjy is ON HOLD until Paper Publication

	Authors:		Authors:

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

2021-04-28T04:21:43Z

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

←Older revision

Revision as of 04:21, 28 April 2021

OCA: New page: '''Unreleased structure''' The entry 7mjy is ON HOLD Authors: Description: Category: Unreleased Structures

2021-04-28T04:21:42Z

New page: '''Unreleased structure''' The entry 7mjy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7mjy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7mjy - Revision history

OCA at 16:13, 18 October 2023

OCA at 09:27, 15 September 2021

OCA at 11:04, 9 June 2021

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

OCA: New page: '''Unreleased structure''' The entry 7mjy is ON HOLD Authors: Description: Category: Unreleased Structures