2z1u - Revision history

OCA at 13:55, 13 March 2024

OCA — Wed, 13 Mar 2024 13:55:51 GMT

←Older revision		Revision as of 13:55, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2z1u' size='340' side='right'caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z1u' size='340' side='right'caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Desvh Desvh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2z1t\|2z1t]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">hypE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])~~</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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [https://pdbe.org/2z1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [https://www.ebi.ac.uk/pdbsum/2z1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1u 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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [https://pdbe.org/2z1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [https://www.ebi.ac.uk/pdbsum/2z1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72F88_DESVH Q72F88_DESVH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z1u ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z1u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively. Comparison of the apo structure with the ATP-bound structure reveals that binding ATP causes an induced-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions.
-
-	Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.,Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y J Mol Biol. 2007 Sep 28;372(4):1045-54. Epub 2007 Jul 26. PMID:17706667<ref>PMID:17706667</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2z1u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures\|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]		*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures\|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desvh~~]]	+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Shomura, Y]]	+	[[Category: Shomura Y]]
-	~~[[Category: Alpha-beta fold]]~~	+
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:43, 8 December 2021

OCA — Wed, 08 Dec 2021 10:43:55 GMT

←Older revision		Revision as of 10:43, 8 December 2021
Line 1:		Line 1:

	==Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP==		==Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP==
-	<StructureSection load='2z1u' size='340' side='right' caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2z1u' size='340' side='right'caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z1t\|2z1t]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [~~http~~://pdbe.org/2z1u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z1u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1u 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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [https://pdbe.org/2z1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [https://www.ebi.ac.uk/pdbsum/2z1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1u ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]	+	*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures\|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Desvh]]		[[Category: Desvh]]
		+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Shomura, Y]]		[[Category: Shomura, Y]]

OCA at 09:17, 17 October 2018

OCA — Wed, 17 Oct 2018 09:17:49 GMT

←Older revision		Revision as of 09:17, 17 October 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z1/2z1u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z1/2z1u_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:29, 11 August 2016

OCA — Thu, 11 Aug 2016 09:29:59 GMT

←Older revision		Revision as of 09:29, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP==		==Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP==
	<StructureSection load='2z1u' size='340' side='right' caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z1u' size='340' side='right' caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 ~~Desulfovibrio vulgaris str. Hildenborough~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [http://www.ebi.ac.uk/pdbsum/2z1u 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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [http://pdbe.org/2z1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [http://www.ebi.ac.uk/pdbsum/2z1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1u ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z1u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 2z1u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris str. hildenborough~~]]	+	[[Category: Desvh]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Shomura, Y]]		[[Category: Shomura, Y]]

OCA at 10:34, 20 January 2015

OCA — Tue, 20 Jan 2015 10:34:42 GMT

←Older revision		Revision as of 10:34, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [http://www.ebi.ac.uk/pdbsum/2z1u 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=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [http://www.ebi.ac.uk/pdbsum/2z1u PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
-	[[Category: Higuchi, Y.]]	+	[[Category: Higuchi, Y]]
-	[[Category: Shomura, Y.]]	+	[[Category: Shomura, Y]]
	[[Category: Alpha-beta fold]]		[[Category: Alpha-beta fold]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 05:01, 2 October 2014

OCA — Thu, 02 Oct 2014 05:01:22 GMT

←Older revision		Revision as of 05:01, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2z1u.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP==
		+	<StructureSection load='2z1u' size='340' side='right' caption='[[2z1u]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z1U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z1t\|2z1t]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z1u RCSB], [http://www.ebi.ac.uk/pdbsum/2z1u PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z1/2z1u_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively. Comparison of the apo structure with the ATP-bound structure reveals that binding ATP causes an induced-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions.

-	~~{{STRUCTURE_2z1u\| PDB=2z1u \| SCENE= }}~~	+	Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.,Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y J Mol Biol. 2007 Sep 28;372(4):1045-54. Epub 2007 Jul 26. PMID:17706667<ref>PMID:17706667</ref>

-	~~===Crystal Structure~~ of ~~Hydrogenase Maturation Protein HypE in complex with ATP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17706667}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2z1u]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_vulgaris_str~~.~~_hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017706667<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
	[[Category: Higuchi, Y.]]		[[Category: Higuchi, Y.]]

OCA: Protected "2z1u" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:35:33 GMT

Protected "2z1u" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:35, 7 January 2013

OCA at 19:35, 7 January 2013

OCA — Mon, 07 Jan 2013 19:35:30 GMT

←Older revision		Revision as of 19:35, 7 January 2013
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-	{{Seed}}
	[[Image:2z1u.png\|left\|200px]]		[[Image:2z1u.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z1u", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_2z1u\| PDB=2z1u \| SCENE= }}		{{STRUCTURE_2z1u\| PDB=2z1u \| SCENE= }}

	===Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP===		===Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17706667}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17706667 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_17706667}}		{{ABSTRACT_PUBMED_17706667}}

	==About this Structure==		==About this Structure==
-	~~2Z1U~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris~~ Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA].	+	[[2z1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17706667~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017706667</ref><references group="xtra"/>
-	[[Category: Desulfovibrio vulgaris]]	+	[[Category: Desulfovibrio vulgaris str. hildenborough]]
	[[Category: Higuchi, Y.]]		[[Category: Higuchi, Y.]]
	[[Category: Shomura, Y.]]		[[Category: Shomura, Y.]]
Line 30:		Line 18:
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:36:35 2009''

OCA at 19:36, 17 February 2009

OCA — Tue, 17 Feb 2009 19:36:36 GMT

←Older revision		Revision as of 19:36, 17 February 2009
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	==About this Structure==		==About this Structure==
-	2Z1U is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA].	+	2Z1U is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1U OCA].

	==Reference==		==Reference==
-	Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms., Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y, J Mol Biol. 2007 Sep 28;372(4):1045-54. Epub 2007 Jul 26. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17706667 17706667]~~	+	<ref group="xtra">PMID:17706667</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Single protein]]
	[[Category: Higuchi, Y.]]		[[Category: Higuchi, Y.]]
	[[Category: Shomura, Y.]]		[[Category: Shomura, Y.]]
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	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 05~~:45:~~19 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:36:35 2009''

OCA at 02:45, 29 July 2008

OCA — Tue, 29 Jul 2008 02:45:23 GMT

←Older revision		Revision as of 02:45, 29 July 2008
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-	[[Image:2z1u.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2z1u.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2z1u\| PDB=2z1u \| SCENE= }}		{{STRUCTURE_2z1u\| PDB=2z1u \| SCENE= }}

-	~~'''~~Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP~~'''~~	+	===Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP===


-	~~==Overview==~~	+	<!--
-	The ~~hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group~~, ~~which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here~~, ~~we present~~ the ~~crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in~~ the ~~presence and in the absence of ATP~~ at ~~a resolution of 2~~.~~0 A and 2~~.~~6 A~~, ~~respectively~~. ~~Comparison of the apo structure with the ATP~~-~~bound structure reveals that binding ATP causes an induced~~-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17706667}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17706667 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17706667}}

	==About this Structure==		==About this Structure==
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	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 19~~:50:22 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:45:19 2008''