4yt4 - Revision history

OCA at 07:20, 1 May 2024

2024-05-01T07:20:43Z

←Older revision		Revision as of 07:20, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yt4]] is a 1 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=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yt4]] is a 1 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=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [https://pdbe.org/4yt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [https://www.ebi.ac.uk/pdbsum/4yt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt4 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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [https://pdbe.org/4yt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [https://www.ebi.ac.uk/pdbsum/4yt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/HMDY_METJA HMDY_METJA]		[https://www.uniprot.org/uniprot/HMDY_METJA HMDY_METJA]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	[Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4 MPT+ ). Most hydrogenotrophic methanogens contain the hmd related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for an in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4 MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4 MPT+ compared to Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turn-over process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared to in Hmd that impairs the catalytically necessary open-to-close transition and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. This article is protected by copyright. All rights reserved.
-
-	Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs.,Fujishiro T, Ataka K, Ermler U, Shima S FEBS J. 2015 Jun 20. doi: 10.1111/febs.13351. PMID:26094576<ref>PMID:26094576</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4yt4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:24, 10 May 2023

2023-05-10T07:24:22Z

←Older revision		Revision as of 07:24, 10 May 2023
Line 3:		Line 3:
	<StructureSection load='4yt4' size='340' side='right'caption='[[4yt4]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4yt4' size='340' side='right'caption='[[4yt4]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yt4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yt4]] is a 1 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=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yt2\|4yt2]], [[4yte\|4yte]], [[4yt5\|4yt5]], [[4yt8\|4yt8]]</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [https://pdbe.org/4yt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [https://www.ebi.ac.uk/pdbsum/4yt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt4 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1338 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])~~</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [~~http~~://pdbe.org/4yt4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yt4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HMDY_METJA HMDY_METJA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
	[[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: ~~Metal binding protein]]~~	+	[[Category: Shima S]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann-like fold~~]]	+

OCA at 07:08, 12 June 2019

2019-06-12T07:08:36Z

←Older revision		Revision as of 07:08, 12 June 2019
Line 1:		Line 1:
		+
	==Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii==		==Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii==
-	<StructureSection load='4yt4' size='340' side='right' caption='[[4yt4]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4yt4' size='340' side='right'caption='[[4yt4]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yt4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yt4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yt2\|4yt2]], [[4yte\|4yte]], [[4yt5\|4yt5]], [[4yt8\|4yt8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yt2\|4yt2]], [[4yte\|4yte]], [[4yt5\|4yt5]], [[4yt8\|4yt8]]</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [http://www.ebi.ac.uk/pdbsum/4yt4 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1338 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [http://pdbe.org/4yt4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [http://www.ebi.ac.uk/pdbsum/4yt4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 17:
	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 4yt4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Fujishiro, T]]		[[Category: Fujishiro, T]]

OCA at 12:12, 1 July 2015

2015-07-01T12:12:55Z

←Older revision		Revision as of 12:12, 1 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii==
		+	<StructureSection load='4yt4' size='340' side='right' caption='[[4yt4]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yt4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YT4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yt2\|4yt2]], [[4yte\|4yte]], [[4yt5\|4yt5]], [[4yt8\|4yt8]]</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=4yt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yt4 RCSB], [http://www.ebi.ac.uk/pdbsum/4yt4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	[Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4 MPT+ ). Most hydrogenotrophic methanogens contain the hmd related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for an in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4 MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4 MPT+ compared to Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turn-over process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared to in Hmd that impairs the catalytically necessary open-to-close transition and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. This article is protected by copyright. All rights reserved.

-	~~The entry 4yt4 is ON HOLD until Paper Publication~~	+	Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs.,Fujishiro T, Ataka K, Ermler U, Shima S FEBS J. 2015 Jun 20. doi: 10.1111/febs.13351. PMID:26094576<ref>PMID:26094576</ref>

-	~~Authors: Fujishiro, T., Ermler~~, U.~~, Shima,~~ S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Shima, S]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Fujishiro, T]]		[[Category: Fujishiro, T]]
		+	[[Category: Shima, S]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann-like fold]]

OCA at 11:51, 1 April 2015

2015-04-01T11:51:52Z

←Older revision		Revision as of 11:51, 1 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yt4 is ON HOLD	+	The entry 4yt4 is ON HOLD until Paper Publication

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

OCA: Protected "4yt4" [edit=sysop:move=sysop]

2015-03-26T12:48:16Z

Protected "4yt4" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:48, 26 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yt4 is ON HOLD Authors: Fujishiro, T., Ermler, U., Shima, S. Description: Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanoc...

2015-03-26T12:48:15Z

New page: '''Unreleased structure''' The entry 4yt4 is ON HOLD Authors: Fujishiro, T., Ermler, U., Shima, S. Description: Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanoc...

New page

'''Unreleased structure'''

The entry 4yt4 is ON HOLD

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

Description: Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii
[[Category: Unreleased Structures]]
[[Category: Shima, S]]
[[Category: Ermler, U]]
[[Category: Fujishiro, T]]