6lve - Revision history

OCA at 10:47, 27 March 2024

OCA — Wed, 27 Mar 2024 10:47:41 GMT

←Older revision		Revision as of 10:47, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6lve' size='340' side='right'caption='[[6lve]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6lve' size='340' side='right'caption='[[6lve]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lve]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp.~~_ssg05~~ Paracoccus sp. ~~ssg05~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lve]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._SSG05 Paracoccus sp. SSG05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dmfase2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=1130061 Paracoccus sp. SSG05]), dmfase1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.1Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~3.5.1~~.56 3.5.1.56] </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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [https://pdbe.org/6lve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [https://www.ebi.ac.uk/pdbsum/6lve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve 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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [https://pdbe.org/6lve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [https://www.ebi.ac.uk/pdbsum/6lve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/I6NT79_9RHOB I6NT79_9RHOB]
-	N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the alpha2 beta2 or (alpha2 beta2 )2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe(3+) ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.	+
-		+
-	A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.,Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R Angew Chem Int Ed Engl. 2020 May 25. doi: ~~10.1002~~/~~anie.202005332. PMID:32452120<ref>PMID:32452120<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6lve" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N,N-dimethylformamidase]]~~	+	[[Category: Paracoccus sp. SSG05]]
-	[[Category: Paracoccus sp. ~~ssg05~~]]	+	[[Category: Arya CA]]
-	[[Category: Arya~~, C A~~]]	+	[[Category: Casanal A]]
-	[[Category: Casanal, A]]	+	[[Category: Chopra G]]
-	[[Category: Chopra, G]]	+	[[Category: Fine J]]
-	[[Category: Fine, J]]	+	[[Category: Ramanathan G]]
-	[[Category: Ramanathan, G]]	+	[[Category: Subramanian R]]
-	[[Category: Subramanian, R]]	+	[[Category: Vinothkumar KR]]
-	[[Category: Vinothkumar~~, K R~~]]	+	[[Category: Yadav S]]
-	[[Category: Yadav, S]]	+
-	~~[[Category: Ab polypeptide]]~~	+
-	~~[[Category: Amidohydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mononuclear iron]]~~	+
-	~~[[Category: Tetramer~~]]	+

OCA at 15:16, 8 June 2021

OCA — Tue, 08 Jun 2021 15:16:24 GMT

←Older revision		Revision as of 15:16, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='6lve' size='340' side='right'caption='[[6lve]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6lve' size='340' side='right'caption='[[6lve]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lve]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Paracoccus_sp._ssg05 Paracoccus sp. ssg05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lve]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._ssg05 Paracoccus sp. ssg05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dmfase2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05]), dmfase1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dmfase2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05]), dmfase1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.56 3.5.1.56] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.56 3.5.1.56] </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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [~~http~~://pdbe.org/6lve PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lve PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve 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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [https://pdbe.org/6lve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [https://www.ebi.ac.uk/pdbsum/6lve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:53, 20 July 2020

OCA — Mon, 20 Jul 2020 08:53:41 GMT

←Older revision		Revision as of 08:53, 20 July 2020
Line 1:		Line 1:

	==Structure of Dimethylformamidase, tetramer, E521A mutant==		==Structure of Dimethylformamidase, tetramer, E521A mutant==
-	<StructureSection load='6lve' size='340' side='right'caption='[[6lve]]' scene=''>	+	<StructureSection load='6lve' size='340' side='right'caption='[[6lve]], [[Resolution\|resolution]] 3.10Å' 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=6LVE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lve]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._ssg05 Paracoccus sp. ssg05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>
-	</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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [http://pdbe.org/6lve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [http://www.ebi.ac.uk/pdbsum/6lve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dmfase2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05]), dmfase1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.56 3.5.1.56] </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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [http://pdbe.org/6lve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [http://www.ebi.ac.uk/pdbsum/6lve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the alpha2 beta2 or (alpha2 beta2 )2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe(3+) ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.
		+
		+	A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.,Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R Angew Chem Int Ed Engl. 2020 May 25. doi: 10.1002/anie.202005332. PMID:32452120<ref>PMID:32452120</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lve" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arya, ~~CA, Yadav, S, Fine, J,~~ Casanal, A, Chopra, G, Ramanathan, G, Subramanian, R, Vinothkumar, KR]]	+	[[Category: N,N-dimethylformamidase]]
		+	[[Category: Paracoccus sp. ssg05]]
		+	[[Category: Arya, C A]]
		+	[[Category: Casanal, A]]
		+	[[Category: Chopra, G]]
		+	[[Category: Fine, J]]
		+	[[Category: Ramanathan, G]]
		+	[[Category: Subramanian, R]]
		+	[[Category: Vinothkumar, K R]]
		+	[[Category: Yadav, S]]
		+	[[Category: Ab polypeptide]]
		+	[[Category: Amidohydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mononuclear iron]]
		+	[[Category: Tetramer]]

OCA at 06:26, 3 June 2020

OCA — Wed, 03 Jun 2020 06:26:54 GMT

←Older revision		Revision as of 06:26, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6lve is ON HOLD until Paper Publication~~	+	==Structure of Dimethylformamidase, tetramer, E521A mutant==
-		+	<StructureSection load='6lve' size='340' side='right'caption='[[6lve]]' scene=''>
-	~~Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LVE FirstGlance]. <br>
-	~~Description:~~ Structure of Dimethylformamidase, tetramer, E521A mutant	+	</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=6lve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lve OCA], [http://pdbe.org/6lve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lve RCSB], [http://www.ebi.ac.uk/pdbsum/6lve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lve ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Yadav, S]~~]	+	__TOC__
-	[[~~Category~~: ~~Ramanathan~~, ~~G]]~~	+	</StructureSection>
-	[~~[Category~~: ~~Vinothkumar, K~~.R]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Subramanian~~, ~~R]]~~	+	[[Category: Arya, CA, Yadav, S, Fine, J, Casanal, A, Chopra, G, Ramanathan, G, Subramanian, R, Vinothkumar, KR]]
-	[~~[Category~~: ~~Casanal~~, ~~A]]~~	+
-	[~~[Category~~: ~~Arya, C~~.A]]	+
-	[[Category: ~~Chopra, G~~]]	+
-	[[Category: Fine, J]]	+

OCA at 05:27, 8 April 2020

OCA — Wed, 08 Apr 2020 05:27:30 GMT

←Older revision		Revision as of 05:27, 8 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lve is ON HOLD	+	The entry 6lve is ON HOLD until Paper Publication

	Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R.		Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R.

OCA: Protected "6lve" [edit=sysop:move=sysop]

OCA — Thu, 13 Feb 2020 02:33:14 GMT

Protected "6lve" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:33, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lve is ON HOLD Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R. Description: ...

OCA — Thu, 13 Feb 2020 02:33:12 GMT

New page: '''Unreleased structure''' The entry 6lve is ON HOLD Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R. Description: ...

New page

'''Unreleased structure'''

The entry 6lve is ON HOLD

Authors: Arya, C.A., Yadav, S., Fine, J., Casanal, A., Chopra, G., Ramanathan, G., Subramanian, R., Vinothkumar, K.R.

Description: Structure of Dimethylformamidase, tetramer, E521A mutant
[[Category: Unreleased Structures]]
[[Category: Yadav, S]]
[[Category: Ramanathan, G]]
[[Category: Vinothkumar, K.R]]
[[Category: Subramanian, R]]
[[Category: Casanal, A]]
[[Category: Arya, C.A]]
[[Category: Chopra, G]]
[[Category: Fine, J]]