5iq1 - Revision history

OCA at 14:05, 30 August 2023

OCA — Wed, 30 Aug 2023 14:05:53 GMT

←Older revision		Revision as of 14:05, 30 August 2023
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	<StructureSection load='5iq1' size='340' side='right'caption='[[5iq1]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5iq1' size='340' side='right'caption='[[5iq1]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iq1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rosni Rosni~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iq1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseovarius_nubinhibens_ISM Roseovarius nubinhibens ISM]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IQ1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5iq4\|5iq4]], [[5ipy\|5ipy]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ISM_08155 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89187 ROSNI])~~</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=5iq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iq1 OCA], [https://pdbe.org/5iq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iq1 RCSB], [https://www.ebi.ac.uk/pdbsum/5iq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iq1 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5iq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iq1 OCA], [~~http~~://pdbe.org/5iq1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iq1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iq1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iq1 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3SLM3_ROSNI A3SLM3_ROSNI]
	<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: ~~Rosni~~]]	+	[[Category: Roseovarius nubinhibens ISM]]
-	[[Category: Li~~, C Y~~]]	+	[[Category: Li CY]]
-	[[Category: Zhang~~, Y Z]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Flavin-containing monooxygenase]]~~	+
-	~~[[Category: Flavoprotein~~]]	+

OCA at 07:27, 3 June 2020

OCA — Wed, 03 Jun 2020 07:27:28 GMT

←Older revision		Revision as of 07:27, 3 June 2020
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	==Crystal structure of RnTmm mutant Y207S==		==Crystal structure of RnTmm mutant Y207S==
-	<StructureSection load='5iq1' size='340' side='right' caption='[[5iq1]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5iq1' size='340' side='right'caption='[[5iq1]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iq1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iq1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rosni Rosni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IQ1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iq4\|5iq4]], [[5ipy\|5ipy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iq4\|5iq4]], [[5ipy\|5ipy]]</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=5iq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iq1 OCA], [http://pdbe.org/5iq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iq1 RCSB], [http://www.ebi.ac.uk/pdbsum/5iq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iq1 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ISM_08155 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89187 ROSNI])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5iq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iq1 OCA], [http://pdbe.org/5iq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iq1 RCSB], [http://www.ebi.ac.uk/pdbsum/5iq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iq1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5iq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5iq1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rosni]]
	[[Category: Li, C Y]]		[[Category: Li, C Y]]
	[[Category: Zhang, Y Z]]		[[Category: Zhang, Y Z]]
	[[Category: Flavin-containing monooxygenase]]		[[Category: Flavin-containing monooxygenase]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]

OCA at 16:21, 18 January 2017

OCA — Wed, 18 Jan 2017 16:21:30 GMT

←Older revision		Revision as of 16:21, 18 January 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5iq1 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of RnTmm mutant Y207S==
		+	<StructureSection load='5iq1' size='340' side='right' caption='[[5iq1]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5iq1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IQ1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iq4\|5iq4]], [[5ipy\|5ipy]]</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=5iq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iq1 OCA], [http://pdbe.org/5iq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iq1 RCSB], [http://www.ebi.ac.uk/pdbsum/5iq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iq1 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP+ bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP+ undergoes a conformational change in the oxidative half-reaction of FMOs.

-	~~Authors:~~ Li, ~~C.Y.~~, Zhang, Y.Z.	+	Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide.,Li CY, Chen XL, Zhang D, Wang P, Sheng Q, Peng M, Xie BB, Qin QL, Li PY, Zhang XY, Su HN, Song XY, Shi M, Zhou BC, Xun LY, Chen Y, Zhang YZ Mol Microbiol. 2016 Dec 20. doi: 10.1111/mmi.13605. PMID:27997715<ref>PMID:27997715</ref>

-	~~Description: Crystal structure~~ of ~~RnTmm mutant Y207S~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Zhang, Y.Z]]	+	<div class="pdbe-citations 5iq1" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Li, C.Y~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, C Y]]
		+	[[Category: Zhang, Y Z]]
		+	[[Category: Flavin-containing monooxygenase]]
		+	[[Category: Flavoprotein]]

OCA: Protected "5iq1" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 00:46:48 GMT

Protected "5iq1" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:46, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5iq1 is ON HOLD until Paper Publication Authors: Li, C.Y., Zhang, Y.Z. Description: Crystal structure of RnTmm mutant Y207S [[Category: Unreleased ...

OCA — Wed, 11 May 2016 00:46:47 GMT

New page: '''Unreleased structure''' The entry 5iq1 is ON HOLD until Paper Publication Authors: Li, C.Y., Zhang, Y.Z. Description: Crystal structure of RnTmm mutant Y207S [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5iq1 is ON HOLD until Paper Publication

Authors: Li, C.Y., Zhang, Y.Z.

Description: Crystal structure of RnTmm mutant Y207S
[[Category: Unreleased Structures]]
[[Category: Zhang, Y.Z]]
[[Category: Li, C.Y]]