5nyf - Revision history

OCA at 12:16, 22 November 2023

2023-11-22T12:16:05Z

←Older revision		Revision as of 12:16, 22 November 2023
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	==Selenomethionine labelled Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1==		==Selenomethionine labelled Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1==
-	<StructureSection load='5nyf' size='340' side='right' caption='[[5nyf]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5nyf' size='340' side='right'caption='[[5nyf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nyf]] is a 1 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=5NYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nyf]] is a 1 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=5NYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NYF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NA:SODIUM+ION'>NA</scene~~>, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyf OCA], [https://pdbe.org/5nyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nyf RCSB], [https://www.ebi.ac.uk/pdbsum/5nyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyf 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=5nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyf OCA], [~~http~~://pdbe.org/5nyf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nyf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nyf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyf 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

2018-02-28T07:08:11Z

←Older revision		Revision as of 07:08, 28 February 2018
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	<StructureSection load='5nyf' size='340' side='right' caption='[[5nyf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5nyf' size='340' side='right' caption='[[5nyf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nyf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nyf]] is a 1 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=5NYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyf OCA], [http://pdbe.org/5nyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyf RCSB], [http://www.ebi.ac.uk/pdbsum/5nyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyf 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=5nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyf OCA], [http://pdbe.org/5nyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyf RCSB], [http://www.ebi.ac.uk/pdbsum/5nyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyf 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 5nyf" 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

2017-05-24T13:47:42Z

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

-	~~The entry~~ 5nyf is ~~ON HOLD~~	+	==Selenomethionine labelled Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1==
-		+	<StructureSection load='5nyf' size='340' side='right' caption='[[5nyf]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nyf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyf OCA], [http://pdbe.org/5nyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyf RCSB], [http://www.ebi.ac.uk/pdbsum/5nyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyf 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 "5nyf" [edit=sysop:move=sysop]

2017-05-17T12:25:46Z

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

←Older revision

Revision as of 12:25, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5nyf is ON HOLD Authors: Description: Category: Unreleased Structures

2017-05-17T12:25:45Z

New page: '''Unreleased structure''' The entry 5nyf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5nyf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]