1djq - Revision history

OCA at 06:54, 7 February 2024

2024-02-07T06:54:51Z

←Older revision		Revision as of 06:54, 7 February 2024
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	<StructureSection load='1djq' size='340' side='right'caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1djq' size='340' side='right'caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Methylophilus_w3a1~~ Methylophilus ~~w3a1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylophilus_methylotrophus_W3A1 Methylophilus methylotrophus W3A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2tmd\|2tmd]], [[1djn\|1djn]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2]~~ </~~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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [https://pdbe.org/1djq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [https://www.ebi.ac.uk/pdbsum/1djq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1djq 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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [https://pdbe.org/1djq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [https://www.ebi.ac.uk/pdbsum/1djq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1djq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DHTM_METME DHTM_METME]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1djq 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=1djq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Trimethylamine dehydrogenase (TMADH) is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN, which is bent by approximately 25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This unusual conformation is thought to modulate the properties of the flavin to facilitate catalysis, and has been postulated to be the result of covalent linkage to Cys-30 at the flavin C6 atom. We report here the crystal structures of recombinant wild-type and the C30A mutant TMADH enzymes, both determined at 2.2 A resolution. Combined crystallographic and NMR studies reveal the presence of inorganic phosphate in the FMN binding site in the deflavo fraction of both recombinant wild-type and C30A proteins. The presence of tightly bound inorganic phosphate in the recombinant enzymes explains the inability to reconstitute the deflavo forms of the recombinant wild-type and C30A enzymes that are generated in vivo. The active site structure and flavin conformation in C30A TMADH are identical to those in recombinant and native TMADH, thus revealing that, contrary to expectation, the 6-S-cysteinyl FMN link is not responsible for the 25 degrees butterfly bending along the N5-N10 axis of the flavin in TMADH. Computational quantum chemistry studies strongly support the proposed role of the butterfly bend in modulating the redox properties of the flavin. Solution studies reveal major differences in the kinetic behavior of the wild-type and C30A proteins. Computational studies reveal a hitherto, unrecognized, contribution made by the S(gamma) atom of Cys-30 to substrate binding, and a role for Cys-30 in the optimal geometrical alignment of substrate with the 6-S-cysteinyl FMN in the enzyme active site.
-
-	Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).,Trickey P, Basran J, Lian LY, Chen Z, Barton JD, Sutcliffe MJ, Scrutton NS, Mathews FS Biochemistry. 2000 Jul 4;39(26):7678-88. PMID:10869173<ref>PMID:10869173</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1djq" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Methylophilus ~~w3a1]]~~	+	[[Category: Methylophilus methylotrophus W3A1]]
-	~~[[Category: Trimethylamine dehydrogenase~~]]	+	[[Category: Barton JD]]
-	[[Category: Barton~~, J D~~]]	+	[[Category: Basran J]]
-	[[Category: Basran, J]]	+	[[Category: Chen Z-W]]
-	[[Category: Chen, Z W]]	+	[[Category: Lian L-Y]]
-	[[Category: Lian, L Y]]	+	[[Category: Mathews FS]]
-	[[Category: Mathews~~, F S~~]]	+	[[Category: Scrutton NS]]
-	[[Category: Scrutton~~, N S~~]]	+	[[Category: Sutcliffe MJ]]
-	[[Category: Sutcliffe~~, M J~~]]	+	[[Category: Trickey P]]
-	[[Category: Trickey, P]]	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Iron-sulfur flavoprotein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:27, 21 July 2021

2021-07-21T09:27:52Z

←Older revision		Revision as of 09:27, 21 July 2021
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	<StructureSection load='1djq' size='340' side='right'caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1djq' size='340' side='right'caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Methylophilus_w3a1 Methylophilus w3a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylophilus_w3a1 Methylophilus w3a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2tmd\|2tmd]], [[1djn\|1djn]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [~~http~~://pdbe.org/1djq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1djq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1djq 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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [https://pdbe.org/1djq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [https://www.ebi.ac.uk/pdbsum/1djq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1djq ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:31, 16 October 2019

2019-10-16T11:31:46Z

←Older revision		Revision as of 11:31, 16 October 2019
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	==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)==		==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)==
-	<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1djq' size='340' side='right'caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_w3a1 Methylophilus w3a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_w3a1 Methylophilus w3a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Methylophilus w3a1]]		[[Category: Methylophilus w3a1]]
	[[Category: Trimethylamine dehydrogenase]]		[[Category: Trimethylamine dehydrogenase]]

OCA at 08:38, 6 December 2017

2017-12-06T08:38:08Z

←Older revision		Revision as of 08:38, 6 December 2017
Line 1:		Line 1:
		+
	==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)==		==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)==
	<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://pdbe.org/1djq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq 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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://pdbe.org/1djq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1djq ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/1djq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/1djq_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 04:23, 8 February 2016

2016-02-08T04:23:50Z

←Older revision		Revision as of 04:23, 8 February 2016
Line 16:		Line 16:
	<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=1djq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:49, 10 September 2015

2015-09-10T07:49:35Z

←Older revision		Revision as of 07:49, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methylophilus_methylotrophus~~ Methylophilus ~~methylotrophus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_w3a1 Methylophilus w3a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq 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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://pdbe.org/1djq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1djq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methylophilus ~~methylotrophus~~]]	+	[[Category: Methylophilus w3a1]]
	[[Category: Trimethylamine dehydrogenase]]		[[Category: Trimethylamine dehydrogenase]]
	[[Category: Barton, J D]]		[[Category: Barton, J D]]

OCA at 22:55, 22 December 2014

2014-12-22T22:55:55Z

←Older revision		Revision as of 22:55, 22 December 2014
Line 32:		Line 32:
	[[Category: Methylophilus methylotrophus]]		[[Category: Methylophilus methylotrophus]]
	[[Category: Trimethylamine dehydrogenase]]		[[Category: Trimethylamine dehydrogenase]]
-	[[Category: Barton, J D.]]	+	[[Category: Barton, J D]]
-	[[Category: Basran, J.]]	+	[[Category: Basran, J]]
-	[[Category: Chen, Z W.]]	+	[[Category: Chen, Z W]]
-	[[Category: Lian, L Y.]]	+	[[Category: Lian, L Y]]
-	[[Category: Mathews, F S.]]	+	[[Category: Mathews, F S]]
-	[[Category: Scrutton, N S.]]	+	[[Category: Scrutton, N S]]
-	[[Category: Sutcliffe, M J.]]	+	[[Category: Sutcliffe, M J]]
-	[[Category: Trickey, P.]]	+	[[Category: Trickey, P]]
	[[Category: Electron transfer]]		[[Category: Electron transfer]]
	[[Category: Iron-sulfur flavoprotein]]		[[Category: Iron-sulfur flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 06:37, 10 October 2014

2014-10-10T06:37:07Z

←Older revision		Revision as of 06:37, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_methylotrophus Methylophilus methylotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_methylotrophus Methylophilus methylotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq 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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:50, 4 September 2014

2014-09-04T06:50:27Z

←Older revision		Revision as of 06:50, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1djq.~~png~~\|~~left~~\|200px]]	+	==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)==
		+	<StructureSection load='1djq' size='340' side='right' caption='[[1djq]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1djq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylophilus_methylotrophus Methylophilus methylotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DJQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tmd\|2tmd]], [[1djn\|1djn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimethylamine_dehydrogenase Trimethylamine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.2 1.5.8.2] </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=1djq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1djq RCSB], [http://www.ebi.ac.uk/pdbsum/1djq 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/dj/1djq_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 ==
		+	Trimethylamine dehydrogenase (TMADH) is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN, which is bent by approximately 25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This unusual conformation is thought to modulate the properties of the flavin to facilitate catalysis, and has been postulated to be the result of covalent linkage to Cys-30 at the flavin C6 atom. We report here the crystal structures of recombinant wild-type and the C30A mutant TMADH enzymes, both determined at 2.2 A resolution. Combined crystallographic and NMR studies reveal the presence of inorganic phosphate in the FMN binding site in the deflavo fraction of both recombinant wild-type and C30A proteins. The presence of tightly bound inorganic phosphate in the recombinant enzymes explains the inability to reconstitute the deflavo forms of the recombinant wild-type and C30A enzymes that are generated in vivo. The active site structure and flavin conformation in C30A TMADH are identical to those in recombinant and native TMADH, thus revealing that, contrary to expectation, the 6-S-cysteinyl FMN link is not responsible for the 25 degrees butterfly bending along the N5-N10 axis of the flavin in TMADH. Computational quantum chemistry studies strongly support the proposed role of the butterfly bend in modulating the redox properties of the flavin. Solution studies reveal major differences in the kinetic behavior of the wild-type and C30A proteins. Computational studies reveal a hitherto, unrecognized, contribution made by the S(gamma) atom of Cys-30 to substrate binding, and a role for Cys-30 in the optimal geometrical alignment of substrate with the 6-S-cysteinyl FMN in the enzyme active site.

-	~~{{STRUCTURE_1djq\| PDB=1djq \| SCENE= }}~~	+	Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).,Trickey P, Basran J, Lian LY, Chen Z, Barton JD, Sutcliffe MJ, Scrutton NS, Mathews FS Biochemistry. 2000 Jul 4;39(26):7678-88. PMID:10869173<ref>PMID:10869173</ref>

-	~~===STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10869173}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1djq]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methylophilus_methylotrophus Methylophilus methylotrophus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DJQ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010869173<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methylophilus methylotrophus]]		[[Category: Methylophilus methylotrophus]]
	[[Category: Trimethylamine dehydrogenase]]		[[Category: Trimethylamine dehydrogenase]]

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

2012-10-31T10:06:42Z

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

←Older revision

Revision as of 10:06, 31 October 2012