6czd - Revision history

OCA at 14:31, 13 March 2024

OCA — Wed, 13 Mar 2024 14:31:37 GMT

←Older revision		Revision as of 14:31, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6czd' size='340' side='right'caption='[[6czd]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6czd' size='340' side='right'caption='[[6czd]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CZD 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=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]]~~, [[~~3fpa~~\|~~3fpa]], [[3fmi\|3fmi]], [[3fmf\|3fmf]], [[4wop\|4wop]], [[6cve\|6cve]], [[6cvf\|6cvf]], [[6cvu\|6cvu]], [[6cvv\|6cvv]], [[6czb\|6czb]], [[6czc\|6czc]], [[6cze\|6cze~~]]</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>bioD, Rv1570, MTCY336.33c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83332 MYCTU])</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=6czd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czd OCA], [https://pdbe.org/6czd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6czd RCSB], [https://www.ebi.ac.uk/pdbsum/6czd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6czd ProSAT]</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=6czd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czd OCA], [~~http~~://pdbe.org/6czd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6czd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6czd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6czd 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>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Dethiobiotin synthetase from Mycobacterium tuberculosis (MtDTBS) is a promising antituberculosis drug target. Small-molecule inhibitors that target MtDTBS provide a route towards new therapeutics for the treatment of antibiotic-resistant tuberculosis. Adenosine diphosphate (ADP) is an inhibitor of MtDTBS; however, structural studies into its mechanism of inhibition have been unsuccessful owing to competitive binding to the enzyme by crystallographic precipitants such as citrate and sulfate. Here, a crystallographic technique termed precipitant-ligand exchange has been developed to exchange protein-bound precipitants with ligands of interest. Proof of concept for the exchange method was demonstrated using cytidine triphosphate (CTP), which adopted the same binding mechanism as that obtained with traditional crystal-soaking techniques. Precipitant-ligand exchange also yielded the previously intractable structure of MtDTBS in complex with ADP solved to 2.4 A resolution. This result demonstrates the utility of precipitant-ligand exchange, which may be widely applicable to protein crystallography.	+
-		+
-	Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.,Thompson AP, Wegener KL, Booker GW, Polyak SW, Bruning JB Acta Crystallogr D Struct Biol. 2018 Oct 1;74(Pt 10):965-972. doi:, 10.1107/S2059798318010136. Epub 2018 Oct 2. PMID:30289406<ref>PMID:30289406</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6czd" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dethiobiotin synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Bruning~~, J B~~]]	+	[[Category: Bruning JB]]
-	[[Category: Polyak~~, S W~~]]	+	[[Category: Polyak SW]]
-	[[Category: Thompson~~, A P~~]]	+	[[Category: Thompson AP]]
-	[[Category: Wegener~~, K L]]~~	+	[[Category: Wegener KL]]
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Nucleotide triphosphate binding]]~~	+
-	~~[[Category: Synthetase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:48, 8 January 2020

OCA — Wed, 08 Jan 2020 08:48:10 GMT

←Older revision		Revision as of 08:48, 8 January 2020
Line 1:		Line 1:

	==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine diphosphate==		==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine diphosphate==
-	<StructureSection load='6czd' size='340' side='right' caption='[[6czd]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='6czd' size='340' side='right'caption='[[6czd]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZD 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fpa\|3fpa]], [[3fmi\|3fmi]], [[3fmf\|3fmf]], [[4wop\|4wop]], [[6cve\|6cve]], [[6cvf\|6cvf]], [[6cvu\|6cvu]], [[6cvv\|6cvv]], [[6czb\|6czb]], [[6czc\|6czc]], [[6cze\|6cze]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fpa\|3fpa]], [[3fmi\|3fmi]], [[3fmf\|3fmf]], [[4wop\|4wop]], [[6cve\|6cve]], [[6cvf\|6cvf]], [[6cvu\|6cvu]], [[6cvv\|6cvv]], [[6czb\|6czb]], [[6czc\|6czc]], [[6cze\|6cze]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, Rv1570, MTCY336.33c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=6czd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czd OCA], [http://pdbe.org/6czd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czd RCSB], [http://www.ebi.ac.uk/pdbsum/6czd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czd ProSAT]</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=6czd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czd OCA], [http://pdbe.org/6czd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czd RCSB], [http://www.ebi.ac.uk/pdbsum/6czd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czd ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6czd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6czd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dethiobiotin synthetase 3D structures\|Dethiobiotin synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Bruning, J B]]		[[Category: Bruning, J B]]
	[[Category: Polyak, S W]]		[[Category: Polyak, S W]]

OCA at 05:52, 24 October 2018

OCA — Wed, 24 Oct 2018 05:52:45 GMT

←Older revision		Revision as of 05:52, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6czd is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine diphosphate==
		+	<StructureSection load='6czd' size='340' side='right' caption='[[6czd]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6czd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZD 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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fgn\|3fgn]], [[3fpa\|3fpa]], [[3fmi\|3fmi]], [[3fmf\|3fmf]], [[4wop\|4wop]], [[6cve\|6cve]], [[6cvf\|6cvf]], [[6cvu\|6cvu]], [[6cvv\|6cvv]], [[6czb\|6czb]], [[6czc\|6czc]], [[6cze\|6cze]]</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=6czd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czd OCA], [http://pdbe.org/6czd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czd RCSB], [http://www.ebi.ac.uk/pdbsum/6czd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czd ProSAT]</span></td></tr>
		+	</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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dethiobiotin synthetase from Mycobacterium tuberculosis (MtDTBS) is a promising antituberculosis drug target. Small-molecule inhibitors that target MtDTBS provide a route towards new therapeutics for the treatment of antibiotic-resistant tuberculosis. Adenosine diphosphate (ADP) is an inhibitor of MtDTBS; however, structural studies into its mechanism of inhibition have been unsuccessful owing to competitive binding to the enzyme by crystallographic precipitants such as citrate and sulfate. Here, a crystallographic technique termed precipitant-ligand exchange has been developed to exchange protein-bound precipitants with ligands of interest. Proof of concept for the exchange method was demonstrated using cytidine triphosphate (CTP), which adopted the same binding mechanism as that obtained with traditional crystal-soaking techniques. Precipitant-ligand exchange also yielded the previously intractable structure of MtDTBS in complex with ADP solved to 2.4 A resolution. This result demonstrates the utility of precipitant-ligand exchange, which may be widely applicable to protein crystallography.

-	~~Authors: Thompson, A.P~~., Wegener, ~~K.L.~~, ~~Bruning~~, J.B., ~~Polyak, S~~.W.	+	Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.,Thompson AP, Wegener KL, Booker GW, Polyak SW, Bruning JB Acta Crystallogr D Struct Biol. 2018 Oct 1;74(Pt 10):965-972. doi:, 10.1107/S2059798318010136. Epub 2018 Oct 2. PMID:30289406<ref>PMID:30289406</ref>

-	~~Description: Crystal structure~~ of ~~Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine diphosphate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Polyak~~, ~~S.W~~]]	+	<div class="pdbe-citations 6czd" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Bruning~~, ~~J.B~~]]	+	== References ==
-	[[Category: Thompson, A.P]]	+	<references/>
-	[[Category: Wegener, K.L]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Dethiobiotin synthase]]
		+	[[Category: Bruning, J B]]
		+	[[Category: Polyak, S W]]
		+	[[Category: Thompson, A P]]
		+	[[Category: Wegener, K L]]
		+	[[Category: Enzyme]]
		+	[[Category: Nucleotide triphosphate binding]]
		+	[[Category: Synthetase]]
		+	[[Category: Transferase]]

OCA at 04:04, 25 April 2018

OCA — Wed, 25 Apr 2018 04:04:22 GMT

←Older revision		Revision as of 04:04, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Thompson, A.P., Wegener, K.L., Bruning, J.B., Polyak, S.W.		Authors: Thompson, A.P., Wegener, K.L., Bruning, J.B., Polyak, S.W.

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

OCA — Wed, 18 Apr 2018 04:15:11 GMT

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

←Older revision

Revision as of 04:15, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6czd is ON HOLD Authors: Thompson, A.P., Wegener, K.L., Bruning, J.B., Polyak, S.W. Description: Crystal structure of Mycobacterium tuberculosis de...

OCA — Wed, 18 Apr 2018 04:15:10 GMT

New page: '''Unreleased structure''' The entry 6czd is ON HOLD Authors: Thompson, A.P., Wegener, K.L., Bruning, J.B., Polyak, S.W. Description: Crystal structure of Mycobacterium tuberculosis de...

New page

'''Unreleased structure'''

The entry 6czd is ON HOLD

Authors: Thompson, A.P., Wegener, K.L., Bruning, J.B., Polyak, S.W.

Description: Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine diphosphate
[[Category: Unreleased Structures]]
[[Category: Polyak, S.W]]
[[Category: Bruning, J.B]]
[[Category: Thompson, A.P]]
[[Category: Wegener, K.L]]