4ltm - Revision history

OCA at 16:25, 20 September 2023

OCA — Wed, 20 Sep 2023 16:25:29 GMT

←Older revision		Revision as of 16:25, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ltm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/EDTA-degrading_bacterium_BNC1 EDTA-degrading bacterium BNC1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ltm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/EDTA-degrading_bacterium_BNC1 EDTA-degrading bacterium BNC1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LTM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.497Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [https://pdbe.org/4ltm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [https://www.ebi.ac.uk/pdbsum/4ltm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ltm 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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [https://pdbe.org/4ltm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [https://www.ebi.ac.uk/pdbsum/4ltm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ltm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:31, 21 December 2022

OCA — Wed, 21 Dec 2022 10:31:32 GMT

←Older revision		Revision as of 10:31, 21 December 2022
Line 1:		Line 1:

	==Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex==		==Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex==
-	<StructureSection load='4ltm' size='340' side='right' caption='[[4ltm]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4ltm' size='340' side='right'caption='[[4ltm]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ltm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Edta~~-~~degrading_bacterium_bnc1 Edta~~-degrading bacterium ~~bnc1~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LTM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ltm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/EDTA-degrading_bacterium_BNC1 EDTA-degrading bacterium BNC1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LTM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [https://pdbe.org/4ltm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [https://www.ebi.ac.uk/pdbsum/4ltm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ltm ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ltd\|4ltd]], [[4ltn\|4ltn]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">emoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85561 EDTA-degrading bacterium BNC1])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/FMN_reductase_(NADH) FMN reductase (NADH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.42 1.5.1.42] </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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [~~http~~://pdbe.org/4ltm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ltm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ltm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9F9T2_9PROT Q9F9T2_9PROT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Edta~~-degrading bacterium ~~bnc1~~]]	+	[[Category: EDTA-degrading bacterium BNC1]]
-	[[Category: Ballinger~~, J W~~]]	+	[[Category: Large Structures]]
-	[[Category: Belchik~~, S M~~]]	+	[[Category: Ballinger JW]]
-	[[Category: Jun, S]]	+	[[Category: Belchik SM]]
-	[[Category: Kang, C]]	+	[[Category: Jun S]]
-	[[Category: Knowles~~, B D~~]]	+	[[Category: Kang C]]
-	[[Category: Nissen~~, M S~~]]	+	[[Category: Knowles BD]]
-	[[Category: Xun, L]]	+	[[Category: Nissen MS]]
-	[[Category: Youn, B]]	+	[[Category: Xun L]]
-	~~[[Category: Oxidoreductase~~]]	+	[[Category: Youn B]]

OCA at 04:49, 5 August 2016

OCA — Fri, 05 Aug 2016 04:49:38 GMT

←Older revision		Revision as of 04:49, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex==		==Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex==
	<StructureSection load='4ltm' size='340' side='right' caption='[[4ltm]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ltm' size='340' side='right' caption='[[4ltm]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">emoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85561 EDTA-degrading bacterium BNC1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">emoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85561 EDTA-degrading bacterium BNC1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/FMN_reductase_(NADH) FMN reductase (NADH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.42 1.5.1.42] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/FMN_reductase_(NADH) FMN reductase (NADH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.42 1.5.1.42] </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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [http://www.ebi.ac.uk/pdbsum/4ltm 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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [http://pdbe.org/4ltm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [http://www.ebi.ac.uk/pdbsum/4ltm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ltm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	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 4ltm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:28, 21 December 2014

OCA — Sun, 21 Dec 2014 15:28:14 GMT

←Older revision		Revision as of 15:28, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ltm\| PDB=4ltm \| SCENE= }}~~	+	==Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex==
-	===Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex===	+	<StructureSection load='4ltm' size='340' side='right' caption='[[4ltm]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18701448}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ltm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Edta-degrading_bacterium_bnc1 Edta-degrading bacterium bnc1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LTM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ltd\|4ltd]], [[4ltn\|4ltn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">emoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85561 EDTA-degrading bacterium BNC1])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/FMN_reductase_(NADH) FMN reductase (NADH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.42 1.5.1.42] </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=4ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ltm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ltm RCSB], [http://www.ebi.ac.uk/pdbsum/4ltm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	EDTA has become a major organic pollutant in the environment because of its extreme usage and resistance to biodegradation. Recently, two critical enzymes, EDTA monooxygenase (EmoA) and NADH:FMN oxidoreductase (EmoB), belonging to the newly established two-component flavin-diffusible monooxygenase family, were identified in the EDTA degradation pathway in Mesorhizobium sp. BNC1. EmoA is an FMNH2-dependent enzyme that requires EmoB to provide FMNH2 for the conversion of EDTA to ethylenediaminediacetate. To understand the molecular basis of this FMN-mediated reaction, the crystal structures of the apo-form, FMN.FMN complex, and FMN.NADH complex of EmoB were determined at 2.5 angstroms resolution. The structure of EmoB is a homotetramer consisting of four alpha/beta-single-domain monomers of five parallel beta-strands flanked by five alpha-helices, which is quite different from those of other known two-component flavin-diffusible monooxygenase family members, such as PheA2 and HpaC, in terms of both tertiary and quaternary structures. For the first time, the crystal structures of both the FMN.FMN and FMN.NADH complexes of an NADH:FMN oxidoreductase were determined. Two stacked isoalloxazine rings and nicotinamide/isoalloxazine rings were at a proper distance for hydride transfer. The structures indicated a ping-pong reaction mechanism, which was confirmed by activity assays. Thus, the structural data offer detailed mechanistic information for hydride transfer between NADH to an enzyme-bound FMN and between the bound FMNH2 and a diffusible FMN.

-	~~==About this Structure==~~	+	Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis.,Nissen MS, Youn B, Knowles BD, Ballinger JW, Jun SY, Belchik SM, Xun L, Kang C J Biol Chem. 2008 Oct 17;283(42):28710-20. Epub 2008 Aug 12. PMID:18701448<ref>PMID:18701448</ref>
-	~~[[4ltm]] is a 1 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Edta~~-~~degrading_bacterium_bnc1 Edta-degrading bacterium bnc1]~~. ~~This structure supersedes the now removed PDB entry [http://oca~~.~~weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:018701448</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Edta-degrading bacterium bnc1]]		[[Category: Edta-degrading bacterium bnc1]]
-	[[Category: Ballinger, J W.]]	+	[[Category: Ballinger, J W]]
-	[[Category: Belchik, S M.]]	+	[[Category: Belchik, S M]]
-	[[Category: Jun, S.]]	+	[[Category: Jun, S]]
-	[[Category: Kang, C.]]	+	[[Category: Kang, C]]
-	[[Category: Knowles, B D.]]	+	[[Category: Knowles, B D]]
-	[[Category: Nissen, M S.]]	+	[[Category: Nissen, M S]]
-	[[Category: Xun, L.]]	+	[[Category: Xun, L]]
-	[[Category: Youn, B.]]	+	[[Category: Youn, B]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 20:48, 7 August 2013

OCA — Wed, 07 Aug 2013 20:48:41 GMT

←Older revision		Revision as of 20:48, 7 August 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ltm\| PDB=4ltm \| SCENE= }}
		+	===Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN complex===
		+	{{ABSTRACT_PUBMED_18701448}}

-	~~The entry~~ 4ltm is ~~ON HOLD~~	+	==About this Structure==
		+	[[4ltm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Edta-degrading_bacterium_bnc1 Edta-degrading bacterium bnc1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vzh 2vzh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LTM OCA].

-	~~Authors~~: ~~Nissen~~, M.S., ~~Youn, B~~., Knowles, B.D., ~~Ballinger, J.W., Jun,~~ S.~~, Belchik, S.M.,~~ Xun, L., ~~Kang, C~~.	+	==Reference==
-		+	<ref group="xtra">PMID:018701448</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structures of NADH:FMN oxidoreductase (EMOB) -FMN complex~~	+	[[Category: Edta-degrading bacterium bnc1]]
		+	[[Category: Ballinger, J W.]]
		+	[[Category: Belchik, S M.]]
		+	[[Category: Jun, S.]]
		+	[[Category: Kang, C.]]
		+	[[Category: Knowles, B D.]]
		+	[[Category: Nissen, M S.]]
		+	[[Category: Xun, L.]]
		+	[[Category: Youn, B.]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4ltm" [edit=sysop:move=sysop]

OCA — Thu, 01 Aug 2013 04:23:40 GMT

Protected "4ltm" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:23, 1 August 2013

OCA: New page: '''Unreleased structure''' The entry 4ltm is ON HOLD Authors: Nissen, M.S., Youn, B., Knowles, B.D., Ballinger, J.W., Jun, S., Belchik, S.M., Xun, L., Kang, C. Description: Crystal str...

OCA — Thu, 01 Aug 2013 04:23:39 GMT

New page: '''Unreleased structure''' The entry 4ltm is ON HOLD Authors: Nissen, M.S., Youn, B., Knowles, B.D., Ballinger, J.W., Jun, S., Belchik, S.M., Xun, L., Kang, C. Description: Crystal str...

New page

'''Unreleased structure'''

The entry 4ltm is ON HOLD

Authors: Nissen, M.S., Youn, B., Knowles, B.D., Ballinger, J.W., Jun, S., Belchik, S.M., Xun, L., Kang, C.

Description: Crystal structures of NADH:FMN oxidoreductase (EMOB) -FMN complex