3fmf - Revision history

OCA at 06:48, 6 September 2023

2023-09-06T06:48:12Z

←Older revision		Revision as of 06:48, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3fmf' size='340' side='right'caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3fmf' size='340' side='right'caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FMF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DSD:7~~-~~(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</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]] 2.05Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3fgn\|3fgn]], [[3fmi\|3fmi]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570~~ (~~[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883~~) ~~Klein 1884])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [https://pdbe.org/3fmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [https://www.ebi.ac.uk/pdbsum/3fmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmf 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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [https://pdbe.org/3fmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [https://www.ebi.ac.uk/pdbsum/3fmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref>	+	[https://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dethiobiotin synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dey, S~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Sacchettini, J C~~]]	+	[[Category: Dey S]]
-	[[Category: ~~Atp-binding]]~~	+	[[Category: Sacchettini JC]]
-	~~[[Category: Biod]]~~	+
-	~~[[Category: Biotin biosynthesis]]~~	+
-	~~[[Category: Dethiobiotin synthetase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Rv1570~~]]	+

OCA at 08:04, 2 March 2022

2022-03-02T08:04:59Z

←Older revision		Revision as of 08:04, 2 March 2022
Line 1:		Line 1:

	==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate==		==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate==
-	<StructureSection load='3fmf' size='340' side='right' caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='3fmf' size='340' side='right'caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FMF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fgn\|3fgn]], [[3fmi\|3fmi]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [~~http~~://pdbe.org/3fmf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fmf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmf 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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [https://pdbe.org/3fmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [https://www.ebi.ac.uk/pdbsum/3fmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref>	+	[[https://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]	+	*[[Dethiobiotin synthetase 3D structures\|Dethiobiotin synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
		+	[[Category: Large Structures]]
	[[Category: Dey, S]]		[[Category: Dey, S]]
	[[Category: Sacchettini, J C]]		[[Category: Sacchettini, J C]]

OCA at 07:33, 5 December 2018

2018-12-05T07:33:47Z

←Older revision		Revision as of 07:33, 5 December 2018
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fm/3fmf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fm/3fmf_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 10:56, 5 August 2016

2016-08-05T10:56:25Z

←Older revision		Revision as of 10:56, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate==		==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate==
	<StructureSection load='3fmf' size='340' side='right' caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3fmf' size='340' side='right' caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [http://www.ebi.ac.uk/pdbsum/3fmf 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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [http://pdbe.org/3fmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [http://www.ebi.ac.uk/pdbsum/3fmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fmf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	<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=3fmf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 3fmf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Dey, S]]		[[Category: Dey, S]]
	[[Category: Sacchettini, J C]]		[[Category: Sacchettini, J C]]

OCA at 18:13, 25 December 2014

2014-12-25T18:13:15Z

←Older revision		Revision as of 18:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FMF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [http://www.ebi.ac.uk/pdbsum/3fmf 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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [http://www.ebi.ac.uk/pdbsum/3fmf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Dey, S.]]	+	[[Category: Dey, S]]
-	[[Category: Sacchettini, J C.]]	+	[[Category: Sacchettini, J C]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Biod]]		[[Category: Biod]]

OCA at 12:19, 29 September 2014

2014-09-29T12:19:48Z

←Older revision		Revision as of 12:19, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3fmf.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate==
		+	<StructureSection load='3fmf' size='340' side='right' caption='[[3fmf]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FMF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSD:7-(CARBOXYAMINO)-8-AMINO-NONANOIC+ACID'>DSD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fmi\|3fmi]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, MT1621, MTCY336.33c, Rv1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=3fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fmf RCSB], [http://www.ebi.ac.uk/pdbsum/3fmf 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/fm/3fmf_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 ==
		+	Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analogue sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.

-	~~{{STRUCTURE_3fmf\| PDB=3fmf \| SCENE= }}~~	+	Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .,Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC Biochemistry. 2010 Aug 10;49(31):6746-60. PMID:20565114<ref>PMID:20565114</ref>

-	~~===Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7~~,~~8 diaminopelargonic acid carbamate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20565114}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3fmf]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].~~	+

	==See Also==		==See Also==
	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]		*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020565114<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]

OCA at 19:50, 20 October 2012

2012-10-20T19:50:37Z

←Older revision		Revision as of 19:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3fmf]] is a 4 chain structure ~~of [[Dethiobiotin synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].	+	[[3fmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].

	==See Also==		==See Also==

OCA: Protected "3fmf" [edit=sysop:move=sysop]

2012-07-27T08:39:38Z

Protected "3fmf" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:39, 27 July 2012

OCA at 08:39, 27 July 2012

2012-07-27T08:39:37Z

←Older revision		Revision as of 08:39, 27 July 2012
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-	{{Seed}}
	[[Image:3fmf.png\|left\|200px]]		[[Image:3fmf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fmf", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3fmf\| PDB=3fmf \| SCENE= }}		{{STRUCTURE_3fmf\| PDB=3fmf \| SCENE= }}

	===Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate===		===Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20565114}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20565114 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20565114}}		{{ABSTRACT_PUBMED_20565114}}

	==About this Structure==		==About this Structure==
-	~~3FMF~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].	+	[[3fmf]] is a 4 chain structure of [[Dethiobiotin synthetase]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].
		+
		+	==See Also==
		+	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20565114~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020565114</ref><references group="xtra"/>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
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	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Rv1570]]		[[Category: Rv1570]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:20:10 2010''

OCA at 04:12, 25 August 2010

2010-08-25T04:12:19Z

←Older revision		Revision as of 04:12, 25 August 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3fmf.~~jpg~~\|left\|200px]]	+	[[Image:3fmf.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate===		===Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20565114}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20565114 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20565114}}

	==About this Structure==		==About this Structure==
-	3FMF is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].	+	3FMF is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FMF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20565114</ref><references group="xtra"/>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
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	[[Category: Rv1570]]		[[Category: Rv1570]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 1 09~~:37:~~42 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:20:10 2010''