3s55 - Revision history

OCA at 12:47, 14 March 2024

OCA — Thu, 14 Mar 2024 12:47:04 GMT

←Older revision		Revision as of 12:47, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3s55' size='340' side='right'caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3s55' size='340' side='right'caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Myca9 Myca9~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus_ATCC_19977 Mycobacteroides abscessus ATCC 19977]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3oec\|3oec]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MAB_1408c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])~~</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [https://pdbe.org/3s55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [https://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [https://pdbe.org/3s55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [https://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/B1MLR7_MYCA9 B1MLR7_MYCA9]
-	During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.	+
-		+
-	Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.,Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE Sci Rep. 2017 Jan 25;7:~~41074. doi: 10.1038~~/~~srep41074. PMID:28120876<ref>PMID:28120876<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3s55" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myca9]]~~	+	[[Category: Mycobacteroides abscessus ATCC 19977]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Ortholog]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sdr]]~~	+
-	~~[[Category: Ssgcid~~]]	+

OCA at 10:38, 22 June 2022

OCA — Wed, 22 Jun 2022 10:38:41 GMT

←Older revision		Revision as of 10:38, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD==		==Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD==
-	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3s55' size='340' side='right'caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Myca9 Myca9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Myca9 Myca9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3oec\|3oec]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [~~http~~://pdbe.org/3s55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [https://pdbe.org/3s55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [https://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Myca9]]		[[Category: Myca9]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 10:15, 13 February 2019

OCA — Wed, 13 Feb 2019 10:15:24 GMT

←Older revision		Revision as of 10:15, 13 February 2019
Line 3:		Line 3:
	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Myca9 Myca9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://pdbe.org/3s55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://pdbe.org/3s55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Myca9]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ortholog]]		[[Category: Ortholog]]

OCA at 07:00, 9 March 2017

OCA — Thu, 09 Mar 2017 07:00:52 GMT

←Older revision		Revision as of 07:00, 9 March 2017
Line 3:		Line 3:
	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Myca9 Myca9]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://pdbe.org/3s55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://pdbe.org/3s55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~High-resolution three-dimensional structures of essential~~ Mycobacterium tuberculosis (Mtb) ~~proteins provide templates for TB drug design, but are available for only a small fraction~~ of ~~the~~ Mtb ~~proteome. Here we evaluate an intra-genus "homolog-rescue" strategy~~ to ~~increase~~ the ~~structural information available for TB drug discovery by using~~ mycobacterial ~~homologs with conserved active sites~~. ~~Of 179 potential TB drug targets selected for x-ray structure determination~~, ~~only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species~~ to ~~the pipeline~~, ~~structures representing an additional 52 otherwise intractable targets were solved~~. ~~To determine whether these homolog structures would be useful surrogates in TB drug design~~, ~~we compared the active sites of 106 pairs of Mtb and non-TB~~ mycobacterial (~~NTM~~) ~~enzyme homologs with experimentally determined~~ structures~~, using three metrics~~ of ~~active site similarity, including superposition~~ of ~~continuous pharmacophoric property distributions~~. ~~Pair~~-~~wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based~~ on ~~pharmacophoric properties) indicating highly conserved active site shape and chemistry~~. ~~Applying these results to~~ the ~~52 NTM structures described above~~, ~~41 shared >55% sequence identity with~~ the ~~Mtb target~~, ~~thus increasing~~ the ~~effective structural coverage of the 179 Mtb targets over three~~-~~fold~~ (~~from 9% to 32%~~). ~~The utility of~~ these ~~structures~~ in ~~TB drug design can be tested by designing inhibitors using~~ the ~~homolog structure and assaying~~ the ~~cognate Mtb enzyme; a promising test case~~, ~~Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable~~ to ~~drug targets for other diseases~~.	+	During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.

-	~~Increasing the structural coverage of tuberculosis drug targets~~.,~~Baugh L~~, ~~Phan I~~, ~~Begley DW~~, ~~Clifton MC~~, ~~Armour B, Dranow DM, Taylor BM, Muruthi MM~~, Abendroth J, ~~Fairman JW~~, ~~Fox D 3rd, Dieterich SH~~, Staker BL, ~~Gardberg AS~~, ~~Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D~~, Lorimer ~~D, Buchko GW, Stacy R, Stewart LJ~~, Edwards TE~~, Van Voorhis WC, Myler PJ Tuberculosis (Edinb)~~. ~~2014 Dec 19. pii~~: ~~S1472-9792(14)20565-8~~. doi:, 10.~~1016~~/~~j.tube.2014.12.003~~. PMID:~~25613812~~<ref>PMID:~~25613812~~</ref>	+	Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.,Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE Sci Rep. 2017 Jan 25;7:41074. doi: 10.1038/srep41074. PMID:28120876<ref>PMID:28120876</ref>

	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>
Line 22:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Myca9]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ortholog]]		[[Category: Ortholog]]

OCA at 18:43, 1 February 2017

OCA — Wed, 01 Feb 2017 18:43:50 GMT

←Older revision		Revision as of 18:43, 1 February 2017
Line 1:		Line 1:
		+
	==Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD==		==Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD==
	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://pdbe.org/3s55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s55 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3s55" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:54, 22 April 2015

OCA — Wed, 22 Apr 2015 06:54:34 GMT

←Older revision		Revision as of 06:54, 22 April 2015
Line 2:		Line 2:
	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_abscessus Mycobacterium abscessus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Myca9 Myca9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~36809 Mycobacterium abscessus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
		+
		+	Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: S1472-9792(14)20565-8. doi:, 10.1016/j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycobacterium abscessus~~]]	+	[[Category: Myca9]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ortholog]]		[[Category: Ortholog]]

OCA at 10:22, 19 December 2014

OCA — Fri, 19 Dec 2014 10:22:57 GMT

←Older revision		Revision as of 10:22, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3s55\| PDB=3s55 \| SCENE= }}~~	+	==Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD==
-	===Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD===	+	<StructureSection load='3s55' size='340' side='right' caption='[[3s55]], [[Resolution\|resolution]] 2.10Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_abscessus Mycobacterium abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S55 FirstGlance]. <br>
-	[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_abscessus Mycobacterium abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oec\|3oec]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_1408c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 Mycobacterium abscessus])</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=3s55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s55 RCSB], [http://www.ebi.ac.uk/pdbsum/3s55 PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium abscessus]]		[[Category: Mycobacterium abscessus]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: Ortholog]]		[[Category: Ortholog]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Sdr]]		[[Category: Sdr]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
-	[[Category: Structural genomic]]

OCA at 07:56, 16 May 2013

OCA — Thu, 16 May 2013 07:56:49 GMT

←Older revision		Revision as of 07:56, 16 May 2013
Line 1:		Line 1:
-	[[Image:3s55.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3s55", 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_3s55\| PDB=3s55 \| SCENE= }}		{{STRUCTURE_3s55\| PDB=3s55 \| SCENE= }}
-
	===Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD===		===Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD===
-

	==About this Structure==		==About this Structure==
Line 16:		Line 6:
	[[Category: Mycobacterium abscessus]]		[[Category: Mycobacterium abscessus]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Ortholog]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sdr]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+	[[Category: Structural genomic]]

OCA at 05:25, 8 June 2011

OCA — Wed, 08 Jun 2011 05:25:46 GMT

←Older revision		Revision as of 05:25, 8 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s55.jpg\|left\|200px]]

-	The ~~entry 3s55~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s55", 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_3s55\| PDB=3s55 \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD===

-	~~Description: Crystal structure of~~ a ~~putative short-~~chain ~~dehydrogenase~~/~~reductase~~ from Mycobacterium abscessus ~~bound to NAD~~	+
		+	==About this Structure==
		+	[[3s55]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_abscessus Mycobacterium abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S55 OCA].
		+	[[Category: Mycobacterium abscessus]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]

OCA: Protected "3s55" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2011 05:26:40 GMT

Protected "3s55" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 1 June 2011