5nyg - Revision history

OCA at 12:16, 22 November 2023

OCA — Wed, 22 Nov 2023 12:16:06 GMT

←Older revision		Revision as of 12:16, 22 November 2023
Line 1:		Line 1:

	==Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1)==		==Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1)==
-	<StructureSection load='5nyg' size='340' side='right' caption='[[5nyg]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5nyg' size='340' side='right'caption='[[5nyg]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nyg]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hypsm Hypsm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nyg]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyphomicrobium_sp._MC1 Hyphomicrobium sp. MC1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NYG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=TRS:2-AMINO~~-2~~-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5nyf\|5nyf]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HYPMC_4374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717785 HYPSM])~~</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=5nyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyg OCA], [https://pdbe.org/5nyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nyg RCSB], [https://www.ebi.ac.uk/pdbsum/5nyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyg ProSAT]</span></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=5nyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyg OCA], [~~http~~://pdbe.org/5nyg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nyg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nyg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyg ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F8JB59_HYPSM F8JB59_HYPSM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hypsm~~]]	+	[[Category: Hyphomicrobium sp. MC1]]
-	[[Category: ~~Groll, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Vielberg,~~ M T]]	+	[[Category: Groll M]]
-	[[Category: ~~Evolution]]~~	+	[[Category: Vielberg M-T]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ntn~~-~~hydrolase-fold]]~~	+
-	~~[[Category: Proteasome~~]]	+

OCA at 07:08, 28 February 2018

OCA — Wed, 28 Feb 2018 07:08:19 GMT

←Older revision		Revision as of 07:08, 28 February 2018
Line 3:		Line 3:
	<StructureSection load='5nyg' size='340' side='right' caption='[[5nyg]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5nyg' size='340' side='right' caption='[[5nyg]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nyg]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nyg]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypsm Hypsm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nyf\|5nyf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nyf\|5nyf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HYPMC_4374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717785 HYPSM])</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=5nyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyg OCA], [http://pdbe.org/5nyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyg RCSB], [http://www.ebi.ac.uk/pdbsum/5nyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyg ProSAT]</span></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=5nyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyg OCA], [http://pdbe.org/5nyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyg RCSB], [http://www.ebi.ac.uk/pdbsum/5nyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral beta-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallized Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases. In contrast to their typical architecture, the Anbu protomer is a tightly interacting dimer that can assemble into a helical superstructure. Although Anbu features a catalytic triad of Thr1O(gamma), Asp17O(delta1) and Lys32N(epsilon), it is unable to hydrolyze standard protease substrates. The lack of activity might be caused by the incapacity of Thr1NH2 to function as a Bronsted acid during substrate cleavage due to its missing activation via hydrogen bonding. Altogether, we demonstrate that the topology of the proteasomal fold is conserved in Anbu, but whether it acts as a protease still needs to be clarified.
		+
		+	On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu.,Vielberg MT, Bauer VC, Groll M J Mol Biol. 2018 Feb 2. pii: S0022-2836(18)30007-X. doi:, 10.1016/j.jmb.2018.01.004. PMID:29355501<ref>PMID:29355501</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5nyg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hypsm]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
	[[Category: Vielberg, M T]]		[[Category: Vielberg, M T]]

OCA at 13:47, 24 May 2017

OCA — Wed, 24 May 2017 13:47:45 GMT

←Older revision		Revision as of 13:47, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5nyg is ON HOLD~~	+	==Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1)==
-		+	<StructureSection load='5nyg' size='340' side='right' caption='[[5nyg]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors: Marie-Theres Vielberg, Michael Groll~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nyg]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYG FirstGlance]. <br>
-	~~Description:~~ Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 -SG P2(1)2(1)2(1)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nyf\|5nyf]]</td></tr>
-	[[Category: ~~Marie-Theres~~ Vielberg, ~~Michael Groll~~]]	+	<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=5nyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyg OCA], [http://pdbe.org/5nyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyg RCSB], [http://www.ebi.ac.uk/pdbsum/5nyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyg ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Groll, M]]
		+	[[Category: Vielberg, M T]]
		+	[[Category: Evolution]]
		+	[[Category: Hydrolase]]
		+	[[Category: Ntn-hydrolase-fold]]
		+	[[Category: Proteasome]]

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

OCA — Wed, 17 May 2017 12:25:49 GMT

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

←Older revision

Revision as of 12:25, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5nyg is ON HOLD Authors: Marie-Theres Vielberg, Michael Groll Description: Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 -SG P2(1)2(1)2(1)...

OCA — Wed, 17 May 2017 12:25:48 GMT

New page: '''Unreleased structure''' The entry 5nyg is ON HOLD Authors: Marie-Theres Vielberg, Michael Groll Description: Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 -SG P2(1)2(1)2(1)...

New page

'''Unreleased structure'''

The entry 5nyg is ON HOLD

Authors: Marie-Theres Vielberg, Michael Groll

Description: Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 -SG P2(1)2(1)2(1)
[[Category: Unreleased Structures]]
[[Category: Marie-Theres Vielberg, Michael Groll]]