6huy - Revision history

OCA at 11:40, 24 January 2024

OCA — Wed, 24 Jan 2024 11:40:18 GMT

←Older revision		Revision as of 11:40, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6huy' size='340' side='right'caption='[[6huy]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6huy' size='340' side='right'caption='[[6huy]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6huy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Destd Destd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HUY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6huy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurobacterium_thermolithotrophum_DSM_11699 Desulfurobacterium thermolithotrophum DSM 11699]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HUY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=DMS:DIMETHYL+SULFOXIDE'~~>~~DMS</scene>, <scene name='pdbligand=FE9:IRON~~-~~GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.25Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">Dester_1504 ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=868864 DESTD])</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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [https://pdbe.org/6huy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [https://www.ebi.ac.uk/pdbsum/6huy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </~~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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [~~http~~://pdbe.org/6huy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6huy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F0S2B6_DESTD F0S2B6_DESTD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~5,10-methenyltetrahydromethanopterin hydrogenase]]~~	+	[[Category: Desulfurobacterium thermolithotrophum DSM 11699]]
-	~~[[Category: Destd~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ataka, K]]	+	[[Category: Ataka K]]
-	[[Category: Ermler, U]]	+	[[Category: Ermler U]]
-	[[Category: Huang, G]]	+	[[Category: Huang G]]
-	[[Category: Kahnt, J]]	+	[[Category: Kahnt J]]
-	[[Category: Shima, S]]	+	[[Category: Shima S]]
-	[[Category: Wagner, T]]	+	[[Category: Wagner T]]
-	[[Category: Watanabe, T]]	+	[[Category: Watanabe T]]
-	~~[[Category: Cofactor biosynthesis]]~~	+
-	~~[[Category: H2-activation]]~~	+
-	~~[[Category: Hydrogenase]]~~	+
-	~~[[Category: Lateral gene-transfer]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Paralog]]~~	+
-	~~[[Category: Sulfur-reducing bacteria]]~~	+
-	~~[[Category: Tetrahydrofolate]]~~	+
-	~~[[Category: Tetrahydromethanopterin~~]]	+

OCA at 12:42, 13 March 2019

OCA — Wed, 13 Mar 2019 12:42:46 GMT

←Older revision		Revision as of 12:42, 13 March 2019
Line 1:		Line 1:

	==HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A==		==HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A==
-	<StructureSection load='6huy' size='340' side='right' caption='[[6huy]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='6huy' size='340' side='right'caption='[[6huy]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6huy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HUY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6huy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Destd Destd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HUY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dester_1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=868864 DESTD])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [http://pdbe.org/6huy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [http://www.ebi.ac.uk/pdbsum/6huy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy 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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [http://pdbe.org/6huy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [http://www.ebi.ac.uk/pdbsum/6huy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]		[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
		+	[[Category: Destd]]
		+	[[Category: Large Structures]]
	[[Category: Ataka, K]]		[[Category: Ataka, K]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]

OCA at 06:37, 9 January 2019

OCA — Wed, 09 Jan 2019 06:37:02 GMT

←Older revision		Revision as of 06:37, 9 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6huy is ~~ON HOLD~~	+	==HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A==
		+	<StructureSection load='6huy' size='340' side='right' caption='[[6huy]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6huy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HUY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [http://pdbe.org/6huy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [http://www.ebi.ac.uk/pdbsum/6huy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H4MPT+) with H2. H4MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog (HmdII) and the HcgA-G proteins. The latter are involved in biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H4MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the enzyme reactions using the tetrahydrofolate derivatives, which are the bacterial C1 carrier, albeit with low enzymatic activities. Crystal structure provided the basis for how the enzyme was adapted to the bacterial C1-carrier. This finding has impact on future biotechnology by developing the Hmd variants functioning in Bacteria.

-	~~Authors: Watanabe~~, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S.	+	The bacterial [Fe]-hydrogenase paralog uses tetrahydrofolate derivatives as substrates.,Watanabe T, Wagner T, Huang G, Kahnt J, Ataka K, Ermler U, Shima S Angew Chem Int Ed Engl. 2019 Jan 2. doi: 10.1002/anie.201813465. PMID:30600878<ref>PMID:30600878</ref>

-	~~Description: HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe~~-~~guanylylpyridinol (FeGP) cofactor and co~~-~~crystallized with methenyl-tetrahydrofolate form A~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Shima, S]]~~	+	<div class="pdbe-citations 6huy" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Wagner~~, T]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
	[[Category: Ataka, K]]		[[Category: Ataka, K]]
-	[[Category: Kahnt, J]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Huang, G]]		[[Category: Huang, G]]
		+	[[Category: Kahnt, J]]
		+	[[Category: Shima, S]]
		+	[[Category: Wagner, T]]
	[[Category: Watanabe, T]]		[[Category: Watanabe, T]]
		+	[[Category: Cofactor biosynthesis]]
		+	[[Category: H2-activation]]
		+	[[Category: Hydrogenase]]
		+	[[Category: Lateral gene-transfer]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Paralog]]
		+	[[Category: Sulfur-reducing bacteria]]
		+	[[Category: Tetrahydrofolate]]
		+	[[Category: Tetrahydromethanopterin]]

OCA: Protected "6huy" [edit=sysop:move=sysop]

OCA — Wed, 17 Oct 2018 06:16:23 GMT

Protected "6huy" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:16, 17 October 2018

OCA: New page: '''Unreleased structure''' The entry 6huy is ON HOLD Authors: Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S. Description: HmdII from Desulfurobacteriu...

OCA — Wed, 17 Oct 2018 06:16:21 GMT

New page: '''Unreleased structure''' The entry 6huy is ON HOLD Authors: Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S. Description: HmdII from Desulfurobacteriu...

New page

'''Unreleased structure'''

The entry 6huy is ON HOLD

Authors: Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S.

Description: HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A
[[Category: Unreleased Structures]]
[[Category: Shima, S]]
[[Category: Wagner, T]]
[[Category: Ataka, K]]
[[Category: Kahnt, J]]
[[Category: Ermler, U]]
[[Category: Huang, G]]
[[Category: Watanabe, T]]