5auq - Revision history

OCA at 15:48, 8 November 2023

OCA — Wed, 08 Nov 2023 15:48:41 GMT

←Older revision		Revision as of 15:48, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5auq]] is a 8 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=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5auq]] is a 8 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=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.525Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [https://pdbe.org/5auq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [https://www.ebi.ac.uk/pdbsum/5auq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq 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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [https://pdbe.org/5auq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [https://www.ebi.ac.uk/pdbsum/5auq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:26, 31 May 2023

OCA — Wed, 31 May 2023 06:26:31 GMT

←Older revision		Revision as of 06:26, 31 May 2023
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	<StructureSection load='5auq' size='340' side='right'caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='5auq' size='340' side='right'caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5auq]] is a 8 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=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5auq]] is a 8 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=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [https://pdbe.org/5auq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [https://www.ebi.ac.uk/pdbsum/5auq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK2007 ([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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [~~http~~://pdbe.org/5auq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5auq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5JIH4_THEKO Q5JIH4_THEKO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kawashima, T]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: Miki, K]]	+	[[Category: Kawashima T]]
-	[[Category: Nishitani, Y]]	+	[[Category: Miki K]]
-	[[Category: Watanabe, S]]	+	[[Category: Nishitani Y]]
-	~~[[Category: Atpase]]~~	+	[[Category: Watanabe S]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:17, 3 July 2019

OCA — Wed, 03 Jul 2019 07:17:45 GMT

←Older revision		Revision as of 07:17, 3 July 2019
Line 1:		Line 1:

	==Crystal structure of ATPase-type HypB in the nucleotide free state==		==Crystal structure of ATPase-type HypB in the nucleotide free state==
-	<StructureSection load='5auq' size='340' side='right' caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>	+	<StructureSection load='5auq' size='340' side='right'caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5auq]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5auq]] is a 8 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=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK2007 ([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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [http://pdbe.org/5auq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [http://www.ebi.ac.uk/pdbsum/5auq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq 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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [http://pdbe.org/5auq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [http://www.ebi.ac.uk/pdbsum/5auq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kawashima, T]]		[[Category: Kawashima, T]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
Line 26:		Line 28:
	[[Category: Watanabe, S]]		[[Category: Watanabe, S]]
	[[Category: Atpase]]		[[Category: Atpase]]
		+	[[Category: Hydrolase]]

OCA at 12:07, 12 April 2017

OCA — Wed, 12 Apr 2017 12:07:16 GMT

←Older revision		Revision as of 12:07, 12 April 2017
Line 1:		Line 1:
		+
	==Crystal structure of ATPase-type HypB in the nucleotide free state==		==Crystal structure of ATPase-type HypB in the nucleotide free state==
	<StructureSection load='5auq' size='340' side='right' caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='5auq' size='340' side='right' caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [http://www.ebi.ac.uk/pdbsum/5auq PDBsum]</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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [http://pdbe.org/5auq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [http://www.ebi.ac.uk/pdbsum/5auq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5auq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 5auq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:55, 24 June 2015

OCA — Wed, 24 Jun 2015 12:55:42 GMT

←Older revision		Revision as of 12:55, 24 June 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of ATPase-type HypB in the nucleotide free state==
		+	<StructureSection load='5auq' size='340' side='right' caption='[[5auq]], [[Resolution\|resolution]] 2.52Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5auq]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vx3\|3vx3]], [[5aun\|5aun]], [[5auo\|5auo]], [[5aup\|5aup]]</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=5auq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5auq RCSB], [http://www.ebi.ac.uk/pdbsum/5auq PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Ni atom at the catalytic center of [NiFe] hydrogenases is incorporated by a Ni-metallochaperone, HypA, and a GTPase/ATPase, HypB. We report the crystal structures of the transient complex formed between HypA and ATPase-type HypB (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT can interact with HypA and induces drastic conformational changes of HypA. Consequently, upon complex formation, a conserved His residue of HypA comes close to the N-terminal conserved motif of HypA and forms a Ni-binding site, to which a Ni ion is bound with a nearly square-planar geometry. The Ni binding site in the HypABAT complex has a nanomolar affinity (Kd = 7 nM), which is in contrast to the micromolar affinity (Kd = 4 microM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypBAT, affecting its association with HypA. These findings indicate that HypA and HypBAT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypBAT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA.

-	~~The entry 5auq is ON HOLD~~	+	Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.,Watanabe S, Kawashima T, Nishitani Y, Kanai T, Wada T, Inaba K, Atomi H, Imanaka T, Miki K Proc Natl Acad Sci U S A. 2015 Jun 8. pii: 201503102. PMID:26056269<ref>PMID:26056269</ref>

-	~~Authors: Watanabe~~, S.~~, Kawashima, T., Nishitani, Y., Miki, K~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of ATPase-type HypB in the nucleotide free state~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kawashima, T]]		[[Category: Kawashima, T]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
		+	[[Category: Nishitani, Y]]
	[[Category: Watanabe, S]]		[[Category: Watanabe, S]]
-	[[Category: ~~Nishitani, Y~~]]	+	[[Category: Atpase]]

OCA at 12:46, 10 June 2015

OCA — Wed, 10 Jun 2015 12:46:00 GMT

←Older revision		Revision as of 12:46, 10 June 2015
Line 5:		Line 5:
	Authors: Watanabe, S., Kawashima, T., Nishitani, Y., Miki, K.		Authors: Watanabe, S., Kawashima, T., Nishitani, Y., Miki, K.

-	Description: Crystal structure of ATPase-type HypB in the nucleotide free state.	+	Description: Crystal structure of ATPase-type HypB in the nucleotide free state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kawashima, T]]		[[Category: Kawashima, T]]

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

OCA — Wed, 03 Jun 2015 11:37:01 GMT

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

←Older revision

Revision as of 11:37, 3 June 2015

OCA: New page: '''Unreleased structure''' The entry 5auq is ON HOLD Authors: Watanabe, S., Kawashima, T., Nishitani, Y., Miki, K. Description: Crystal structure of ATPase-type HypB in the nucleotide ...

OCA — Wed, 03 Jun 2015 11:36:59 GMT

New page: '''Unreleased structure''' The entry 5auq is ON HOLD Authors: Watanabe, S., Kawashima, T., Nishitani, Y., Miki, K. Description: Crystal structure of ATPase-type HypB in the nucleotide ...

New page

'''Unreleased structure'''

The entry 5auq is ON HOLD

Authors: Watanabe, S., Kawashima, T., Nishitani, Y., Miki, K.

Description: Crystal structure of ATPase-type HypB in the nucleotide free state.
[[Category: Unreleased Structures]]
[[Category: Kawashima, T]]
[[Category: Miki, K]]
[[Category: Watanabe, S]]
[[Category: Nishitani, Y]]