5k5v - Revision history

OCA at 09:17, 20 March 2024

OCA — Wed, 20 Mar 2024 09:17:55 GMT

←Older revision		Revision as of 09:17, 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 5k5v" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:40, 27 September 2023

OCA — Wed, 27 Sep 2023 10:40:47 GMT

←Older revision		Revision as of 10:40, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5k5v' size='340' side='right'caption='[[5k5v]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5k5v' size='340' side='right'caption='[[5k5v]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k5v]] 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=5K5V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k5v]] 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=5K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K5V FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5k5u\|5k5u]], [[5k60\|5k60]], [[5k61\|5k61]], [[5k62\|5k62]], [[5k63\|5k63]], [[5k66\|5k66]], [[5b62\|5b62]]</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]] 1.947Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=5k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5v OCA], [https://pdbe.org/5k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k5v RCSB], [https://www.ebi.ac.uk/pdbsum/5k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5v ProSAT]</span></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=5k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5v OCA], [~~http~~://pdbe.org/5k5v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k5v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k5v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5v 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 21:		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 09:21, 25 June 2020

OCA — Thu, 25 Jun 2020 09:21:17 GMT

←Older revision		Revision as of 09:21, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of N-terminal amidase C187S==		==Crystal structure of N-terminal amidase C187S==
-	<StructureSection load='5k5v' size='340' side='right' caption='[[5k5v]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5k5v' size='340' side='right'caption='[[5k5v]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k5v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k5v]] 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=5K5V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K5V FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k5u\|5k5u]], [[5k60\|5k60]], [[5k61\|5k61]], [[5k62\|5k62]], [[5k63\|5k63]], [[5k66\|5k66]], [[5b62\|5b62]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k5u\|5k5u]], [[5k60\|5k60]], [[5k61\|5k61]], [[5k62\|5k62]], [[5k63\|5k63]], [[5k66\|5k66]], [[5b62\|5b62]]</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=5k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5v OCA], [http://pdbe.org/5k5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5v RCSB], [http://www.ebi.ac.uk/pdbsum/5k5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5v ProSAT]</span></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=5k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5v OCA], [http://pdbe.org/5k5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5v RCSB], [http://www.ebi.ac.uk/pdbsum/5k5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__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 13:16, 5 April 2017

OCA — Wed, 05 Apr 2017 13:16:55 GMT

←Older revision		Revision as of 13:16, 5 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k5v is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of N-terminal amidase C187S==
		+	<StructureSection load='5k5v' size='340' side='right' caption='[[5k5v]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k5v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K5V FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k5u\|5k5u]], [[5k60\|5k60]], [[5k61\|5k61]], [[5k62\|5k62]], [[5k63\|5k63]], [[5k66\|5k66]], [[5b62\|5b62]]</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=5k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5v OCA], [http://pdbe.org/5k5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5v RCSB], [http://www.ebi.ac.uk/pdbsum/5k5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5v 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.~~, Oh~~, S.-J.~~, Lee, B.-G.~~, 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 C187S~~	+	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 5k5v" 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 12:20, 4 January 2017

OCA — Wed, 04 Jan 2017 12:20:26 GMT

←Older revision		Revision as of 12:20, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k5v is ON HOLD	+	The entry 5k5v is ON HOLD until Paper Publication

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

OCA: Protected "5k5v" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:22:01 GMT

Protected "5k5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:22, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k5v is ON HOLD Authors: Kim, M.K., Oh, S.-J., Lee, B.-G., Song, H.K. Description: Crystal structure of N-terminal amidase C187S [[Category: Unrele...

OCA — Wed, 01 Jun 2016 14:22:00 GMT

New page: '''Unreleased structure''' The entry 5k5v is ON HOLD Authors: Kim, M.K., Oh, S.-J., Lee, B.-G., Song, H.K. Description: Crystal structure of N-terminal amidase C187S [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5k5v is ON HOLD

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

Description: Crystal structure of N-terminal amidase C187S
[[Category: Unreleased Structures]]
[[Category: Oh, S.-J]]
[[Category: Kim, M.K]]
[[Category: Lee, B.-G]]
[[Category: Song, H.K]]