7wg2 - Revision history

OCA at 19:44, 29 May 2024

OCA — Wed, 29 May 2024 19:44:16 GMT

←Older revision		Revision as of 19:44, 29 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7wg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WG2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7wg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WG2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.76Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7wg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wg2 OCA], [https://pdbe.org/7wg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wg2 RCSB], [https://www.ebi.ac.uk/pdbsum/7wg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wg2 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=7wg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wg2 OCA], [https://pdbe.org/7wg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wg2 RCSB], [https://www.ebi.ac.uk/pdbsum/7wg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wg2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q6CXX6_KLULA Q6CXX6_KLULA]]	+	[https://www.uniprot.org/uniprot/Q6CXX6_KLULA Q6CXX6_KLULA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNA(Arg) as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNA(Arg), and a 3'-proximal segment of the tRNA(Arg) moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe(3+)-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.		N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNA(Arg) as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNA(Arg), and a 3'-proximal segment of the tRNA(Arg) moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe(3+)-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.

-	Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.,Kim BH, Kim MK, Oh SJ, Nguyen KT, Kim JH, Varshavsky A, Hwang CS, Song HK Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2209597119. doi:, 10.1073/pnas.2209597119. Epub 2022 Jul 25. PMID:35878037<ref>PMID:35878037</ref>	+	Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.,Kim BH, Kim MK, Oh SJ, Nguyen KT, Kim JH, Varshavsky A, Hwang CS, Song HK Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2209597119. doi: , 10.1073/pnas.2209597119. Epub 2022 Jul 25. PMID:35878037<ref>PMID:35878037</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 06:57, 14 September 2022

OCA — Wed, 14 Sep 2022 06:57:24 GMT

←Older revision		Revision as of 06:57, 14 September 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7wg2 is ~~ON HOLD until Paper~~ Publication	+	==EVAA-KlAte1==
		+	<StructureSection load='7wg2' size='340' side='right'caption='[[7wg2]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7wg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WG2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7wg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wg2 OCA], [https://pdbe.org/7wg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wg2 RCSB], [https://www.ebi.ac.uk/pdbsum/7wg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wg2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q6CXX6_KLULA Q6CXX6_KLULA]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNA(Arg) as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNA(Arg), and a 3'-proximal segment of the tRNA(Arg) moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe(3+)-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.

-	~~Authors~~:	+	Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.,Kim BH, Kim MK, Oh SJ, Nguyen KT, Kim JH, Varshavsky A, Hwang CS, Song HK Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2209597119. doi:, 10.1073/pnas.2209597119. Epub 2022 Jul 25. PMID:35878037<ref>PMID:35878037</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7wg2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kluyveromyces lactis NRRL Y-1140]]
		+	[[Category: Large Structures]]
		+	[[Category: Kim BH]]
		+	[[Category: Kim MK]]
		+	[[Category: Oh S-J]]
		+	[[Category: Song HK]]

OCA at 06:25, 9 February 2022

OCA — Wed, 09 Feb 2022 06:25:20 GMT

←Older revision		Revision as of 06:25, 9 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wg2 is ON HOLD	+	The entry 7wg2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7wg2" [edit=sysop:move=sysop]

OCA — Wed, 05 Jan 2022 09:27:33 GMT

Protected "7wg2" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:27, 5 January 2022

OCA: New page: '''Unreleased structure''' The entry 7wg2 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Jan 2022 09:27:32 GMT

New page: '''Unreleased structure''' The entry 7wg2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7wg2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]