7o6z - Revision history

OCA at 12:45, 1 February 2024

OCA — Thu, 01 Feb 2024 12:45:52 GMT

←Older revision		Revision as of 12:45, 1 February 2024
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	<StructureSection load='7o6z' size='340' side='right'caption='[[7o6z]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='7o6z' size='340' side='right'caption='[[7o6z]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7o6z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylacidimicrobium_sp.~~_ap8~~ Methylacidimicrobium sp. ~~ap8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O6Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o6z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylacidimicrobium_sp._AP8 Methylacidimicrobium sp. AP8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O6Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=ND:2,2-DIMETHYL-3-DEHYDROQUINIC+ACID'>ND</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</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]] 2.3Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methanol_dehydrogenase_(cytochrome_c) Methanol dehydrogenase (cytochrome c)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.7 1.1.2.7] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=ND:2,2-DIMETHYL-3-DEHYDROQUINIC+ACID'>ND</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</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=7o6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o6z OCA], [https://pdbe.org/7o6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o6z RCSB], [https://www.ebi.ac.uk/pdbsum/7o6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o6z 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=7o6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o6z OCA], [https://pdbe.org/7o6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o6z RCSB], [https://www.ebi.ac.uk/pdbsum/7o6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o6z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A7R8L7W4_9BACT A0A7R8L7W4_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Methylacidimicrobium sp. ~~ap8~~]]	+	[[Category: Methylacidimicrobium sp. AP8]]
-	[[Category: Barends, T]]	+	[[Category: Barends T]]
-	[[Category: ~~Camp, H Op den~~]]	+	[[Category: Dietl A]]
-	[[Category: ~~Dietl, A~~]]	+	[[Category: Op den Camp H]]
-	[[Category: Schmitz, R]]	+	[[Category: Schmitz R]]
-	~~[[Category: Lanthanide]]~~	+
-	~~[[Category: Methanol dehydrogenase]]~~	+
-	~~[[Category: Neodymium]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Xoxf1~~]]	+

OCA at 08:00, 10 November 2021

OCA — Wed, 10 Nov 2021 08:00:24 GMT

←Older revision		Revision as of 08:00, 10 November 2021
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	==Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase==		==Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase==
-	<StructureSection load='7o6z' size='340' side='right'caption='[[7o6z]]' scene=''>	+	<StructureSection load='7o6z' size='340' side='right'caption='[[7o6z]], [[Resolution\|resolution]] 2.30Å' 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=7O6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O6Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o6z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylacidimicrobium_sp._ap8 Methylacidimicrobium sp. ap8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O6Z 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=7o6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o6z OCA], [https://pdbe.org/7o6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o6z RCSB], [https://www.ebi.ac.uk/pdbsum/7o6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o6z 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=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=ND:2,2-DIMETHYL-3-DEHYDROQUINIC+ACID'>ND</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methanol_dehydrogenase_(cytochrome_c) Methanol dehydrogenase (cytochrome c)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.7 1.1.2.7] </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=7o6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o6z OCA], [https://pdbe.org/7o6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o6z RCSB], [https://www.ebi.ac.uk/pdbsum/7o6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o6z ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% +/- 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 +/- 0.01 mumol . min(-1) . mg protein(-1) and an affinity constant (Km) of 1.4 +/- 0.6 muM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
		+
		+	Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase.,Schmitz RA, Picone N, Singer H, Dietl A, Seifert KA, Pol A, Jetten MSM, Barends TRM, Daumann LJ, Op den Camp HJM mBio. 2021 Sep 21:e0170821. doi: 10.1128/mBio.01708-21. PMID:34544276<ref>PMID:34544276</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7o6z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Methanol dehydrogenase\|Methanol dehydrogenase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Barends T~~]]	+	[[Category: Methylacidimicrobium sp. ap8]]
-	[[Category: ~~Dietl A~~]]	+	[[Category: Barends, T]]
-	[[Category: ~~Op den~~ Camp H]]	+	[[Category: Camp, H Op den]]
-	[[Category: Schmitz R]]	+	[[Category: Dietl, A]]
		+	[[Category: Schmitz, R]]
		+	[[Category: Lanthanide]]
		+	[[Category: Methanol dehydrogenase]]
		+	[[Category: Neodymium]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Xoxf1]]

OCA at 12:56, 13 October 2021

OCA — Wed, 13 Oct 2021 12:56:33 GMT

←Older revision		Revision as of 12:56, 13 October 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7o6z ~~is ON HOLD until Paper Publication~~	+	==Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase==
-		+	<StructureSection load='7o6z' size='340' side='right'caption='[[7o6z]]' scene=''>
-	~~Authors~~: ~~Schmitz~~, R., ~~Dietl~~, A., ~~Op den Camp, H~~., ~~Barends, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O6Z FirstGlance]. <br>
-	~~Description: Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase~~	+	</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=7o6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o6z OCA], [https://pdbe.org/7o6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o6z RCSB], [https://www.ebi.ac.uk/pdbsum/7o6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o6z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Schmitz, R~~]]	+	__TOC__
-	[[Category: Dietl, A]]	+	</StructureSection>
-	[[Category: ~~Barends, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Op Den Camp, H~~]]	+	[[Category: Barends T]]
		+	[[Category: Dietl A]]
		+	[[Category: Op den Camp H]]
		+	[[Category: Schmitz R]]

OCA at 09:01, 19 May 2021

OCA — Wed, 19 May 2021 09:01:46 GMT

←Older revision		Revision as of 09:01, 19 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o6z is ON HOLD	+	The entry 7o6z is ON HOLD until Paper Publication

	Authors: Schmitz, R., Dietl, A., Op den Camp, H., Barends, T.		Authors: Schmitz, R., Dietl, A., Op den Camp, H., Barends, T.
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	[[Category: Schmitz, R]]		[[Category: Schmitz, R]]
	[[Category: Dietl, A]]		[[Category: Dietl, A]]
-	[[Category: Op Den Camp, H]]
	[[Category: Barends, T]]		[[Category: Barends, T]]
		+	[[Category: Op Den Camp, H]]

OCA: Protected "7o6z" [edit=sysop:move=sysop]

OCA — Wed, 21 Apr 2021 06:39:29 GMT

Protected "7o6z" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:39, 21 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o6z is ON HOLD Authors: Schmitz, R., Dietl, A., Op den Camp, H., Barends, T. Description: Structure of a neodymium-containing, XoxF1-type methanol...

OCA — Wed, 21 Apr 2021 06:39:28 GMT

New page: '''Unreleased structure''' The entry 7o6z is ON HOLD Authors: Schmitz, R., Dietl, A., Op den Camp, H., Barends, T. Description: Structure of a neodymium-containing, XoxF1-type methanol...

New page

'''Unreleased structure'''

The entry 7o6z is ON HOLD

Authors: Schmitz, R., Dietl, A., Op den Camp, H., Barends, T.

Description: Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase
[[Category: Unreleased Structures]]
[[Category: Schmitz, R]]
[[Category: Dietl, A]]
[[Category: Op Den Camp, H]]
[[Category: Barends, T]]