5ipy - Revision history

OCA at 14:05, 30 August 2023

2023-08-30T14:05:50Z

←Older revision		Revision as of 14:05, 30 August 2023
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	<StructureSection load='5ipy' size='340' side='right'caption='[[5ipy]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5ipy' size='340' side='right'caption='[[5ipy]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ipy]] 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=5IPY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IPY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ipy]] 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=5IPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPY 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]] 1.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5iq4\|5iq4]], [[5iq1\|5iq1]]~~<~~/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=5ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipy OCA], [https://pdbe.org/5ipy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ipy RCSB], [https://www.ebi.ac.uk/pdbsum/5ipy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipy 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=5ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipy OCA], [~~http~~://pdbe.org/5ipy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ipy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ipy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipy 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

2020-06-03T07:27:13Z

←Older revision		Revision as of 07:27, 3 June 2020
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	==Crystal structure of WT RnTmm==		==Crystal structure of WT RnTmm==
-	<StructureSection load='5ipy' size='340' side='right' caption='[[5ipy]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5ipy' size='340' side='right'caption='[[5ipy]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ipy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IPY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ipy]] 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=5IPY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IPY 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]], [[5iq1\|5iq1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iq4\|5iq4]], [[5iq1\|5iq1]]</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=5ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipy OCA], [http://pdbe.org/5ipy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipy RCSB], [http://www.ebi.ac.uk/pdbsum/5ipy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipy 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=5ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipy OCA], [http://pdbe.org/5ipy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipy RCSB], [http://www.ebi.ac.uk/pdbsum/5ipy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipy 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 5ipy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ipy" 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 16:15, 18 January 2017

2017-01-18T16:15:51Z

←Older revision		Revision as of 16:15, 18 January 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ipy is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of WT RnTmm==
		+	<StructureSection load='5ipy' size='340' side='right' caption='[[5ipy]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ipy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPY 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]], [[5iq1\|5iq1]]</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=5ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipy OCA], [http://pdbe.org/5ipy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipy RCSB], [http://www.ebi.ac.uk/pdbsum/5ipy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipy 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 ~~WT RnTmm~~	+	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 5ipy" 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 "5ipy" [edit=sysop:move=sysop]

2016-05-11T00:46:36Z

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

←Older revision

Revision as of 00:46, 11 May 2016

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

2016-05-11T00:46:35Z

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

New page

'''Unreleased structure'''

The entry 5ipy is ON HOLD until Paper Publication

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

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