7tom - Revision history

OCA at 10:43, 22 May 2024

2024-05-22T10:43:55Z

←Older revision		Revision as of 10:43, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7tom]] 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=7TOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TOM FirstGlance]. <br>		<table><tr><td colspan='2'>[[7tom]] 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=7TOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TOM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=7tom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tom OCA], [https://pdbe.org/7tom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tom RCSB], [https://www.ebi.ac.uk/pdbsum/7tom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tom 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=7tom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tom OCA], [https://pdbe.org/7tom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tom RCSB], [https://www.ebi.ac.uk/pdbsum/7tom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tom ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HMPTM_METJA HMPTM_METJA]] Is responsible for the addition of methyl groups at C-7 and C-9 of the pterin ring during methanopterin (MPT) biosynthesis. Catalyzes methylation of 7,8-dihydro-6-hydroxymethylpterin, likely using methylenetetrahydromethanopterin as a methyl group donor, via a radical-based mechanism.<ref>PMID:25002541</ref>	+	[https://www.uniprot.org/uniprot/HMPTM_METJA HMPTM_METJA] Is responsible for the addition of methyl groups at C-7 and C-9 of the pterin ring during methanopterin (MPT) biosynthesis. Catalyzes methylation of 7,8-dihydro-6-hydroxymethylpterin, likely using methylenetetrahydromethanopterin as a methyl group donor, via a radical-based mechanism.<ref>PMID:25002541</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values(1-5). In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon-carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon-carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)(1,2). GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp(3)-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids(6). Structures of the enzyme show the presence of four metallocofactors: three [~~Fe4S4~~] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp(3)-Csp(3) bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [~~Fe4S4~~] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices(7-10).	+	Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values(1-5). In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon-carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon-carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)(1,2). GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp(3)-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids(6). Structures of the enzyme show the presence of four metallocofactors: three [Fe(4)S(4)] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp(3)-Csp(3) bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe(4)S(4)] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices(7-10).

-	Discovery, structure and mechanism of a tetraether lipid synthase.,Lloyd CT, Iwig DF, Wang B, Cossu M, Metcalf WW, Boal AK, Booker SJ Nature. 2022 ~~Jul 26. pii~~: ~~10.1038/s41586~~-~~022-05120-2~~. doi:, 10.1038/s41586-022-05120-2. PMID:35882349<ref>PMID:35882349</ref>	+	Discovery, structure and mechanism of a tetraether lipid synthase.,Lloyd CT, Iwig DF, Wang B, Cossu M, Metcalf WW, Boal AK, Booker SJ Nature. 2022 Sep;609(7925):197-203. doi: 10.1038/s41586-022-05120-2. Epub 2022 , Jul 26. PMID:35882349<ref>PMID:35882349</ref>

	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>

OCA at 19:26, 7 September 2022

2022-09-07T19:26:12Z

←Older revision		Revision as of 19:26, 7 September 2022
Line 1:		Line 1:

	==X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with bacterial lipid substrate analog, 5'deoxyadenosine, and methionine bound==		==X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with bacterial lipid substrate analog, 5'deoxyadenosine, and methionine bound==
-	<StructureSection load='7tom' size='340' side='right'caption='[[7tom]]' scene=''>	+	<StructureSection load='7tom' size='340' side='right'caption='[[7tom]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tom]] 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=7TOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TOM FirstGlance]. <br>
-	</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=7tom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tom OCA], [https://pdbe.org/7tom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tom RCSB], [https://www.ebi.ac.uk/pdbsum/7tom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tom ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=7tom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tom OCA], [https://pdbe.org/7tom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tom RCSB], [https://www.ebi.ac.uk/pdbsum/7tom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tom ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/HMPTM_METJA HMPTM_METJA]] Is responsible for the addition of methyl groups at C-7 and C-9 of the pterin ring during methanopterin (MPT) biosynthesis. Catalyzes methylation of 7,8-dihydro-6-hydroxymethylpterin, likely using methylenetetrahydromethanopterin as a methyl group donor, via a radical-based mechanism.<ref>PMID:25002541</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values(1-5). In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon-carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon-carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)(1,2). GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp(3)-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids(6). Structures of the enzyme show the presence of four metallocofactors: three [Fe4S4] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp(3)-Csp(3) bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe4S4] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices(7-10).
		+
		+	Discovery, structure and mechanism of a tetraether lipid synthase.,Lloyd CT, Iwig DF, Wang B, Cossu M, Metcalf WW, Boal AK, Booker SJ Nature. 2022 Jul 26. pii: 10.1038/s41586-022-05120-2. doi:, 10.1038/s41586-022-05120-2. PMID:35882349<ref>PMID:35882349</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tom" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Methanocaldococcus jannaschii]]
	[[Category: Boal AK]]		[[Category: Boal AK]]
	[[Category: Booker SJ]]		[[Category: Booker SJ]]
	[[Category: Lloyd CT]]		[[Category: Lloyd CT]]

OCA at 06:36, 31 August 2022

2022-08-31T06:36:50Z

←Older revision		Revision as of 06:36, 31 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7tom is ~~ON HOLD until Paper Publication~~	+	==X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with bacterial lipid substrate analog, 5'deoxyadenosine, and methionine bound==
-		+	<StructureSection load='7tom' size='340' side='right'caption='[[7tom]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TOM FirstGlance]. <br>
-	~~Description~~:	+	</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=7tom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tom OCA], [https://pdbe.org/7tom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tom RCSB], [https://www.ebi.ac.uk/pdbsum/7tom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tom ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Boal AK]]
		+	[[Category: Booker SJ]]
		+	[[Category: Lloyd CT]]

OCA at 10:21, 27 April 2022

2022-04-27T10:21:46Z

←Older revision		Revision as of 10:21, 27 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7tom is ON HOLD	+	The entry 7tom is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7tom" [edit=sysop:move=sysop]

2022-02-02T05:39:18Z

Protected "7tom" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:39, 2 February 2022

OCA: New page: '''Unreleased structure''' The entry 7tom is ON HOLD Authors: Description: Category: Unreleased Structures

2022-02-02T05:39:17Z

New page: '''Unreleased structure''' The entry 7tom is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7tom is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]