5yxy - Revision history

OCA at 10:25, 27 March 2024

2024-03-27T10:25:46Z

←Older revision		Revision as of 10:25, 27 March 2024
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	==Crystal structure of the HyhL-HypA complex (form I)==		==Crystal structure of the HyhL-HypA complex (form I)==
-	<StructureSection load='5yxy' size='340' side='right' caption='[[5yxy]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='5yxy' size='340' side='right'caption='[[5yxy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yxy]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YXY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yxy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YXY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 3.299Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~hydA, TK2069 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=69014 Pyrococcus kodakaraensis (strain KOD1)]), hypA, TK2008 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5yxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxy OCA], [~~http~~://pdbe.org/5yxy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yxy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yxy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxy 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=5yxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxy OCA], [https://pdbe.org/5yxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yxy RCSB], [https://www.ebi.ac.uk/pdbsum/5yxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~HYPA_THEKO HYPA_THEKO~~]~~] Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity).~~	+	[https://www.uniprot.org/uniprot/Q8NKS2_THEKO Q8NKS2_THEKO]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Thermococcus kodakarensis Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a beta-strand adjacent to its N-terminal beta-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.	+

-	Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.,Kwon S, Watanabe S, Nishitani Y, Kawashima T, Kanai T, Atomi H, Miki K Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):7045-7050. doi:, 10.1073/pnas.1801955115. Epub 2018 Jun 18. PMID:29915046<ref>PMID:29915046</ref>	+	==See Also==
-		+	*[[Beta secretase 3D structures\|Beta secretase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5yxy" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Kwon, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Miki, K~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Nishitani, Y]]~~	+	[[Category: Kwon S]]
-	~~[[Category: Watanabe,~~ S]]	+	[[Category: Miki K]]
-	[[Category: ~~Hydrogenase~~]]	+	[[Category: Nishitani Y]]
-	[[Category: ~~Hyhl~~]]	+	[[Category: Watanabe S]]
-	[[Category: ~~Hypa]]~~	+
-	~~[[Category: Maturation]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 09:37, 18 July 2018

2018-07-18T09:37:08Z

←Older revision		Revision as of 09:37, 18 July 2018
Line 3:		Line 3:
	<StructureSection load='5yxy' size='340' side='right' caption='[[5yxy]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='5yxy' size='340' side='right' caption='[[5yxy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yxy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YXY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yxy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YXY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hydA, TK2069 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)]), hypA, TK2008 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5yxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxy OCA], [http://pdbe.org/5yxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yxy RCSB], [http://www.ebi.ac.uk/pdbsum/5yxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxy 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=5yxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxy OCA], [http://pdbe.org/5yxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yxy RCSB], [http://www.ebi.ac.uk/pdbsum/5yxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/HYPA_THEKO HYPA_THEKO]] Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity).		[[http://www.uniprot.org/uniprot/HYPA_THEKO HYPA_THEKO]] Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Thermococcus kodakarensis Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a beta-strand adjacent to its N-terminal beta-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.
		+
		+	Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.,Kwon S, Watanabe S, Nishitani Y, Kawashima T, Kanai T, Atomi H, Miki K Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):7045-7050. doi:, 10.1073/pnas.1801955115. Epub 2018 Jun 18. PMID:29915046<ref>PMID:29915046</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yxy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:44, 20 June 2018

2018-06-20T05:44:25Z

←Older revision		Revision as of 05:44, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yxy is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the HyhL-HypA complex (form I)==
-		+	<StructureSection load='5yxy' size='340' side='right' caption='[[5yxy]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yxy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YXY FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxy OCA], [http://pdbe.org/5yxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yxy RCSB], [http://www.ebi.ac.uk/pdbsum/5yxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HYPA_THEKO HYPA_THEKO]] Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kwon, S]]
		+	[[Category: Miki, K]]
		+	[[Category: Nishitani, Y]]
		+	[[Category: Watanabe, S]]
		+	[[Category: Hydrogenase]]
		+	[[Category: Hyhl]]
		+	[[Category: Hypa]]
		+	[[Category: Maturation]]
		+	[[Category: Metal binding protein]]

OCA at 05:30, 17 January 2018

2018-01-17T05:30:33Z

←Older revision		Revision as of 05:30, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-12-13T05:49:00Z

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

←Older revision

Revision as of 05:49, 13 December 2017

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

2017-12-13T05:48:59Z

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

New page

'''Unreleased structure'''

The entry 5yxy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]