5d5q - Revision history

OCA at 11:24, 10 January 2024

2024-01-10T11:24:40Z

←Older revision		Revision as of 11:24, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=57O:(4,6-DIHYDROXY-3,5-DIMETHYLPYRIDIN-2-YL)ACETIC+ACID'>57O</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=57O:(4,6-DIHYDROXY-3,5-DIMETHYLPYRIDIN-2-YL)ACETIC+ACID'>57O</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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [https://pdbe.org/5d5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [https://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q 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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [https://pdbe.org/5d5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [https://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:22, 21 June 2023

2023-06-21T10:22:52Z

←Older revision		Revision as of 10:22, 21 June 2023
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	<StructureSection load='5d5q' size='340' side='right'caption='[[5d5q]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5d5q' size='340' side='right'caption='[[5d5q]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=57O:(4,6-DIHYDROXY-3,5-DIMETHYLPYRIDIN-2-YL)ACETIC+ACID'>57O</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=57O:(4,6-DIHYDROXY-3,5-DIMETHYLPYRIDIN-2-YL)ACETIC+ACID'>57O</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3brc\|3brc]], [[3bw0\|3bw0]], [[3bw1\|3bw1]], [[3bw2\|3bw2]], [[5d5p\|5d5p]]~~</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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [https://pdbe.org/5d5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [https://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q 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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [~~http~~://pdbe.org/5d5q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Y488_METJA Y488_METJA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ermler, U~~]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: ~~Fujishiro, T~~]]	+	[[Category: Ermler U]]
-	[[Category: ~~Shima, S~~]]	+	[[Category: Fujishiro T]]
-	[[Category: ~~Guanylyltransferase]]~~	+	[[Category: Shima S]]
-	~~[[Category: Transferase~~]]	+

OCA at 10:38, 1 April 2020

2020-04-01T10:38:50Z

←Older revision		Revision as of 10:38, 1 April 2020
Line 1:		Line 1:

	==HcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase==		==HcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase==
-	<StructureSection load='5d5q' size='340' side='right' caption='[[5d5q]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5d5q' size='340' side='right'caption='[[5d5q]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Fujishiro, T]]		[[Category: Fujishiro, T]]

OCA at 07:10, 29 March 2017

2017-03-29T07:10:06Z

←Older revision		Revision as of 07:10, 29 March 2017
Line 8:		Line 8:
	<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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [http://pdbe.org/5d5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [http://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q 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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [http://pdbe.org/5d5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [http://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H2 activation at the active site. FeII of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.
		+
		+	Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase.,Bai L, Fujishiro T, Huang G, Koch J, Takabayashi A, Yokono M, Tanaka A, Xu T, Hu X, Ermler U, Shima S Faraday Discuss. 2017 Mar 15. doi: 10.1039/c6fd00209a. PMID:28294213<ref>PMID:28294213</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d5q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:38, 26 October 2016

2016-10-26T18:38:58Z

←Older revision		Revision as of 18:38, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5d5q is ON HOLD until Paper Publication~~	+	==HcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase==
-		+	<StructureSection load='5d5q' size='340' side='right' caption='[[5d5q]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors: Fujishiro, T., Rother, M., Ermler, U., Shima, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d5q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D5Q FirstGlance]. <br>
-	~~Description:~~ HcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=57O:(4,6-DIHYDROXY-3,5-DIMETHYLPYRIDIN-2-YL)ACETIC+ACID'>57O</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3brc\|3brc]], [[3bw0\|3bw0]], [[3bw1\|3bw1]], [[3bw2\|3bw2]], [[5d5p\|5d5p]]</td></tr>
-	[[~~Category~~: ~~Shima~~, S]]	+	<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=5d5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d5q OCA], [http://pdbe.org/5d5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d5q RCSB], [http://www.ebi.ac.uk/pdbsum/5d5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d5q ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Rother~~, M]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Fujishiro, T]]		[[Category: Fujishiro, T]]
		+	[[Category: Shima, S]]
		+	[[Category: Guanylyltransferase]]
		+	[[Category: Transferase]]

OCA: Protected "5d5q" [edit=sysop:move=sysop]

2015-08-20T11:24:22Z

Protected "5d5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:24, 20 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d5q is ON HOLD until Paper Publication Authors: Fujishiro, T., Rother, M., Ermler, U., Shima, S. Description: HcgB from Methanocaldococcus jannasc...

2015-08-20T11:24:21Z

New page: '''Unreleased structure''' The entry 5d5q is ON HOLD until Paper Publication Authors: Fujishiro, T., Rother, M., Ermler, U., Shima, S. Description: HcgB from Methanocaldococcus jannasc...

New page

'''Unreleased structure'''

The entry 5d5q is ON HOLD until Paper Publication

Authors: Fujishiro, T., Rother, M., Ermler, U., Shima, S.

Description: HcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase
[[Category: Unreleased Structures]]
[[Category: Shima, S]]
[[Category: Rother, M]]
[[Category: Ermler, U]]
[[Category: Fujishiro, T]]