1xu3 - Revision history

OCA at 08:53, 14 February 2024

OCA — Wed, 14 Feb 2024 08:53:16 GMT

←Older revision		Revision as of 08:53, 14 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BML:4~~-~~BROMOPHENOL'>BML</scene>~~, ~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25]~~ </~~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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [https://pdbe.org/1xu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1xu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xu3 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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [https://pdbe.org/1xu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1xu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xu3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[https://www.uniprot.org/uniprot/MEMG_METCA MEMG_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[https://www.uniprot.org/uniprot/MEMB_METCA MEMB_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.	+	[https://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xu3 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xu3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.
-
-	Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit.,Sazinsky MH, Lippard SJ J Am Chem Soc. 2005 Apr 27;127(16):5814-25. PMID:15839679<ref>PMID:15839679</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xu3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Methane monooxygenase\|Methane monooxygenase]]	+	*[[Methane monooxygenase 3D structures\|Methane monooxygenase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
-	[[Category: Lippard~~, S J~~]]	+	[[Category: Lippard SJ]]
-	[[Category: Sazinsky~~, M H]]~~	+	[[Category: Sazinsky MH]]
-	~~[[Category: Cavity]]~~	+
-	~~[[Category: Diiron]]~~	+
-	~~[[Category: Four-helix bundle]]~~	+
-	~~[[Category: Methane]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Substrate binding~~]]	+

OCA at 16:19, 3 November 2021

OCA — Wed, 03 Nov 2021 16:19:31 GMT

←Older revision		Revision as of 16:19, 3 November 2021
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	<StructureSection load='1xu3' size='340' side='right'caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1xu3' size='340' side='right'caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [~~http~~://pdbe.org/1xu3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xu3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xu3 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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [https://pdbe.org/1xu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1xu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xu3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[~~http~~://www.uniprot.org/uniprot/MEMG_METCA MEMG_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[~~http~~://www.uniprot.org/uniprot/MEMB_METCA MEMB_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.	+	[[https://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[https://www.uniprot.org/uniprot/MEMG_METCA MEMG_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[https://www.uniprot.org/uniprot/MEMB_METCA MEMB_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:43, 29 January 2020

OCA — Wed, 29 Jan 2020 16:43:40 GMT

←Older revision		Revision as of 16:43, 29 January 2020
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	==Soluble methane monooxygenase hydroxylase-soaked with bromophenol==		==Soluble methane monooxygenase hydroxylase-soaked with bromophenol==
-	<StructureSection load='1xu3' size='340' side='right' caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1xu3' size='340' side='right'caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
	[[Category: Lippard, S J]]		[[Category: Lippard, S J]]

OCA at 07:03, 18 April 2018

OCA — Wed, 18 Apr 2018 07:03:34 GMT

←Older revision		Revision as of 07:03, 18 April 2018
Line 1:		Line 1:
		+
	==Soluble methane monooxygenase hydroxylase-soaked with bromophenol==		==Soluble methane monooxygenase hydroxylase-soaked with bromophenol==
	<StructureSection load='1xu3' size='340' side='right' caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1xu3' size='340' side='right' caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://pdbe.org/1xu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://pdbe.org/1xu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xu3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xu/1xu3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xu/1xu3_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 02:11, 8 February 2016

OCA — Mon, 08 Feb 2016 02:11:56 GMT

←Older revision		Revision as of 02:11, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xu3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:53, 10 September 2015

OCA — Thu, 10 Sep 2015 06:53:42 GMT

←Older revision		Revision as of 06:53, 10 September 2015
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Methane_monooxygenase~~ Methane monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase_(soluble) Methane monooxygenase (soluble)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://pdbe.org/1xu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1xu3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methane monooxygenase]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
	[[Category: Lippard, S J]]		[[Category: Lippard, S J]]

OCA at 19:48, 24 December 2014

OCA — Wed, 24 Dec 2014 19:48:50 GMT

←Older revision		Revision as of 19:48, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase Methane monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase Methane monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</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=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[http://www.uniprot.org/uniprot/MEMG_METCA MEMG_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds. [[http://www.uniprot.org/uniprot/MEMB_METCA MEMB_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Methane monooxygenase]]		[[Category: Methane monooxygenase]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
-	[[Category: Lippard, S J.]]	+	[[Category: Lippard, S J]]
-	[[Category: Sazinsky, M H.]]	+	[[Category: Sazinsky, M H]]
	[[Category: Cavity]]		[[Category: Cavity]]
	[[Category: Diiron]]		[[Category: Diiron]]

OCA at 20:21, 29 September 2014

OCA — Mon, 29 Sep 2014 20:21:39 GMT

←Older revision		Revision as of 20:21, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xu3.~~png~~\|~~left~~\|200px]]	+	==Soluble methane monooxygenase hydroxylase-soaked with bromophenol==
		+	<StructureSection load='1xu3' size='340' side='right' caption='[[1xu3]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XU3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xu5\|1xu5]], [[1xvb\|1xvb]], [[1xvc\|1xvc]], [[1xvd\|1xvd]], [[1xve\|1xve]], [[1xvf\|1xvf]], [[1xvg\|1xvg]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methane_monooxygenase Methane monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.25 1.14.13.25] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xu3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1xu3 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xu/1xu3_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.

-	~~{{STRUCTURE_1xu3\| PDB=1xu3 \| SCENE= }}~~	+	Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit.,Sazinsky MH, Lippard SJ J Am Chem Soc. 2005 Apr 27;127(16):5814-25. PMID:15839679<ref>PMID:15839679</ref>

-	~~===Soluble methane monooxygenase hydroxylase-soaked with bromophenol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15839679}}~~	+	==See Also==
-		+	*[[Methane monooxygenase\|Methane monooxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1xu3~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015839679<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methane monooxygenase]]		[[Category: Methane monooxygenase]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]

OCA: Protected "1xu3" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:01:18 GMT

Protected "1xu3" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:01, 5 January 2013

OCA at 11:01, 5 January 2013

OCA — Sat, 05 Jan 2013 11:01:15 GMT

←Older revision		Revision as of 11:01, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xu3.png\|left\|200px]]		[[Image:1xu3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xu3", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1xu3\| PDB=1xu3 \| SCENE= }}		{{STRUCTURE_1xu3\| PDB=1xu3 \| SCENE= }}

	===Soluble methane monooxygenase hydroxylase-soaked with bromophenol===		===Soluble methane monooxygenase hydroxylase-soaked with bromophenol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15839679}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15839679 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15839679}}		{{ABSTRACT_PUBMED_15839679}}

	==About this Structure==		==About this Structure==
-	~~1XU3~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA].	+	[[1xu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XU3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15839679~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015839679</ref><references group="xtra"/>
	[[Category: Methane monooxygenase]]		[[Category: Methane monooxygenase]]
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
Line 32:		Line 20:
	[[Category: Four-helix bundle]]		[[Category: Four-helix bundle]]
	[[Category: Methane]]		[[Category: Methane]]
		+	[[Category: Oxidoreductase]]
	[[Category: Substrate binding]]		[[Category: Substrate binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:03:29 2009''