6y3g - Revision history

OCA at 13:18, 24 January 2024

2024-01-24T13:18:42Z

←Older revision		Revision as of 13:18, 24 January 2024
Line 1:		Line 1:

	==Crystal structure of phenylalanine tRNA from Escherichia coli==		==Crystal structure of phenylalanine tRNA from Escherichia coli==
-	<StructureSection load='6y3g' size='340' side='right'caption='[[6y3g]]' scene=''>	+	<StructureSection load='6y3g' size='340' side='right'caption='[[6y3g]], [[Resolution\|resolution]] 3.10Å' 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=6Y3G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y3G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y3G FirstGlance]. <br>
-	</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=6y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3g OCA], [~~http~~://pdbe.org/6y3g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y3g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y3g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3g 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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AU:3-[(3S)-3-AMINO-3-CARBOXYPROPYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>3AU</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=6y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3g OCA], [https://pdbe.org/6y3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y3g RCSB], [https://www.ebi.ac.uk/pdbsum/6y3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNA(Phe) to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNA(Phe) complex to 5 A resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic beta2 and beta7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
		+
		+	Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.,Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E RNA. 2020 Nov;26(11):1589-1602. doi: 10.1261/rna.075184.120. Epub 2020 Jul 17. PMID:32680846<ref>PMID:32680846</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y3g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bourgeois G]]		[[Category: Bourgeois G]]
	[[Category: Mechulam Y]]		[[Category: Mechulam Y]]
	[[Category: Schmitt E]]		[[Category: Schmitt E]]

OCA at 06:45, 30 December 2020

2020-12-30T06:45:00Z

←Older revision		Revision as of 06:45, 30 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6y3g ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of phenylalanine tRNA from Escherichia coli==
-		+	<StructureSection load='6y3g' size='340' side='right'caption='[[6y3g]]' scene=''>
-	~~Authors~~: ~~Bourgeois~~, G., ~~Mechulam~~, Y., ~~Schmitt~~, E.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y3G FirstGlance]. <br>
-	~~Description: Crystal structure of phenylalanine tRNA from Escherichia coli~~	+	</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=6y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3g OCA], [http://pdbe.org/6y3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y3g RCSB], [http://www.ebi.ac.uk/pdbsum/6y3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3g ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Schmitt, E~~]]	+	__TOC__
-	[[Category: Mechulam, Y]]	+	</StructureSection>
-	[[Category: ~~Bourgeois, G~~]]	+	[[Category: Large Structures]]
		+	[[Category: Bourgeois G]]
		+	[[Category: Mechulam Y]]
		+	[[Category: Schmitt E]]

OCA at 07:09, 22 July 2020

2020-07-22T07:09:58Z

←Older revision		Revision as of 07:09, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y3g is ON HOLD	+	The entry 6y3g is ON HOLD until Paper Publication

	Authors: Bourgeois, G., Mechulam, Y., Schmitt, E.		Authors: Bourgeois, G., Mechulam, Y., Schmitt, E.
Line 7:		Line 7:
	Description: Crystal structure of phenylalanine tRNA from Escherichia coli		Description: Crystal structure of phenylalanine tRNA from Escherichia coli
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bourgeois, G]]
	[[Category: Schmitt, E]]		[[Category: Schmitt, E]]
	[[Category: Mechulam, Y]]		[[Category: Mechulam, Y]]
		+	[[Category: Bourgeois, G]]

OCA: Protected "6y3g" [edit=sysop:move=sysop]

2020-02-26T08:19:22Z

Protected "6y3g" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:19, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y3g is ON HOLD Authors: Bourgeois, G., Mechulam, Y., Schmitt, E. Description: Crystal structure of phenylalanine tRNA from Escherichia coli [[Cate...

2020-02-26T08:19:20Z

New page: '''Unreleased structure''' The entry 6y3g is ON HOLD Authors: Bourgeois, G., Mechulam, Y., Schmitt, E. Description: Crystal structure of phenylalanine tRNA from Escherichia coli [[Cate...

New page

'''Unreleased structure'''

The entry 6y3g is ON HOLD

Authors: Bourgeois, G., Mechulam, Y., Schmitt, E.

Description: Crystal structure of phenylalanine tRNA from Escherichia coli
[[Category: Unreleased Structures]]
[[Category: Bourgeois, G]]
[[Category: Schmitt, E]]
[[Category: Mechulam, Y]]