5hyy - Revision history

OCA at 09:16, 20 March 2024

OCA — Wed, 20 Mar 2024 09:16:25 GMT

←Older revision		Revision as of 09:16, 20 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/N1P8Q8_YEASC N1P8Q8_YEASC]		[https://www.uniprot.org/uniprot/N1P8Q8_YEASC N1P8Q8_YEASC]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.
-
-	Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.,Kim MK, Oh SJ, Lee BG, Song HK Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12438-12443. Epub 2016 Oct 17. PMID:27791147<ref>PMID:27791147</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5hyy" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:00, 16 August 2023

OCA — Wed, 16 Aug 2023 11:00:53 GMT

←Older revision		Revision as of 11:00, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='5hyy' size='340' side='right'caption='[[5hyy]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='5hyy' size='340' side='right'caption='[[5hyy]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hyy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hyy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_CEN.PK113-7D Saccharomyces cerevisiae CEN.PK113-7D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HYY FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CENPK1137D_1355 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=889517 Baker's yeast])~~</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]] 2.323Å</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=5hyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyy OCA], [~~http~~://pdbe.org/5hyy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hyy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hyy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyy 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=5hyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyy OCA], [https://pdbe.org/5hyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hyy RCSB], [https://www.ebi.ac.uk/pdbsum/5hyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/N1P8Q8_YEASC N1P8Q8_YEASC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, M K~~]]	+	[[Category: Saccharomyces cerevisiae CEN PK113-7D]]
-	[[Category: Lee, B G]]	+	[[Category: Kim MK]]
-	[[Category: Oh, S J]]	+	[[Category: Lee B-G]]
-	[[Category: Song~~, H K]]~~	+	[[Category: Oh S-J]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Song HK]]
-	~~[[Category: N-end rule]]~~	+
-	~~[[Category: Nitrilase superfamily]]~~	+
-	~~[[Category: Nta1~~]]	+

OCA at 08:37, 27 May 2020

OCA — Wed, 27 May 2020 08:37:24 GMT

←Older revision		Revision as of 08:37, 27 May 2020
Line 1:		Line 1:

	==Crystal structure of N-terminal amidase==		==Crystal structure of N-terminal amidase==
-	<StructureSection load='5hyy' size='340' side='right' caption='[[5hyy]], [[Resolution\|resolution]] 2.32Å' scene=''>	+	<StructureSection load='5hyy' size='340' side='right'caption='[[5hyy]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hyy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HYY FirstGlance]. <br>
-	</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=5hyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyy OCA], [http://pdbe.org/5hyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hyy RCSB], [http://www.ebi.ac.uk/pdbsum/5hyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyy ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CENPK1137D_1355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=889517 Baker's yeast])</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=5hyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyy OCA], [http://pdbe.org/5hyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hyy RCSB], [http://www.ebi.ac.uk/pdbsum/5hyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Kim, M K]]		[[Category: Kim, M K]]
	[[Category: Lee, B G]]		[[Category: Lee, B G]]

OCA at 16:27, 18 January 2017

OCA — Wed, 18 Jan 2017 16:27:49 GMT

←Older revision		Revision as of 16:27, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hyy is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of N-terminal amidase==
		+	<StructureSection load='5hyy' size='340' side='right' caption='[[5hyy]], [[Resolution\|resolution]] 2.32Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hyy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HYY FirstGlance]. <br>
		+	</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=5hyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyy OCA], [http://pdbe.org/5hyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hyy RCSB], [http://www.ebi.ac.uk/pdbsum/5hyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyy ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.

-	~~Authors:~~ Kim, ~~M.K.~~, Lee, ~~B.-G., Oh,~~ S.-J.~~, Song, H.K~~.	+	Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.,Kim MK, Oh SJ, Lee BG, Song HK Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12438-12443. Epub 2016 Oct 17. PMID:27791147<ref>PMID:27791147</ref>

-	~~Description: Crystal structure~~ of N-~~terminal amidase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Oh, S.-J]]	+	<div class="pdbe-citations 5hyy" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kim~~, M.K]]	+	== References ==
-	[[Category: ~~Lee, B.~~-G]]	+	<references/>
-	[[Category: ~~Song, H.K~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, M K]]
		+	[[Category: Lee, B G]]
		+	[[Category: Oh, S J]]
		+	[[Category: Song, H K]]
		+	[[Category: Hydrolase]]
		+	[[Category: N-end rule]]
		+	[[Category: Nitrilase superfamily]]
		+	[[Category: Nta1]]

OCA at 11:20, 4 January 2017

OCA — Wed, 04 Jan 2017 11:20:38 GMT

←Older revision		Revision as of 11:20, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hyy is ON HOLD	+	The entry 5hyy is ON HOLD until Paper Publication

	Authors: Kim, M.K., Lee, B.-G., Oh, S.-J., Song, H.K.		Authors: Kim, M.K., Lee, B.-G., Oh, S.-J., Song, H.K.

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

OCA — Wed, 10 Feb 2016 15:56:06 GMT

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

←Older revision

Revision as of 15:56, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hyy is ON HOLD Authors: Kim, M.K., Lee, B.-G., Oh, S.-J., Song, H.K. Description: Crystal structure of N-terminal amidase [[Category: Unreleased S...

OCA — Wed, 10 Feb 2016 15:56:05 GMT

New page: '''Unreleased structure''' The entry 5hyy is ON HOLD Authors: Kim, M.K., Lee, B.-G., Oh, S.-J., Song, H.K. Description: Crystal structure of N-terminal amidase [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 5hyy is ON HOLD

Authors: Kim, M.K., Lee, B.-G., Oh, S.-J., Song, H.K.

Description: Crystal structure of N-terminal amidase
[[Category: Unreleased Structures]]
[[Category: Oh, S.-J]]
[[Category: Kim, M.K]]
[[Category: Lee, B.-G]]
[[Category: Song, H.K]]