3hfa - Revision history

OCA at 07:21, 6 September 2023

2023-09-06T07:21:06Z

←Older revision		Revision as of 07:21, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3hfa' size='340' side='right'caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3hfa' size='340' side='right'caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HFA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</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]] 2.504Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3h6i\|3h6i]]~~, [[~~3h6f~~\|~~3h6f~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MT2170, prcB, Rv2110c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1]~~ </~~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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [https://pdbe.org/3hfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [https://www.ebi.ac.uk/pdbsum/3hfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hfa 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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [https://pdbe.org/3hfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [https://www.ebi.ac.uk/pdbsum/3hfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hfa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~PSB_MYCTO PSB_MYCTO]~~] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. ~~[[https://www~~.~~uniprot~~.~~org/uniprot/PSA_MYCTO PSA_MYCTO]] Component~~ of the proteasome ~~core~~, ~~a large protease complex with broad specificity involved~~ in ~~protein~~ degradation.~~[HAMAP-Rule~~:~~MF_00289]~~	+	[https://www.uniprot.org/uniprot/PSA_MYCTU PSA_MYCTU] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Proteasome endopeptidase complex]]
-	[[Category: Li, D]]
-	[[Category: Li, H]]
-	[[Category: Hydrolase]]
-	[[Category: Mutant]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Open gate~~]]	+	[[Category: Li D]]
-	[[Category: ~~Proteasome]]~~	+	[[Category: Li H]]
-	~~[[Category: Proteasome endopeptidase~~]]	+

OCA at 12:46, 23 March 2022

2022-03-23T12:46:23Z

←Older revision		Revision as of 12:46, 23 March 2022
Line 3:		Line 3:
	<StructureSection load='3hfa' size='340' side='right'caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3hfa' size='340' side='right'caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HFA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3h6i\|3h6i]], [[3h6f\|3h6f]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2170, prcB, Rv2110c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), prcA, Rv2109c ([~~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">MT2170, prcB, Rv2110c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [~~http~~://pdbe.org/3hfa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hfa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hfa 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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [https://pdbe.org/3hfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [https://www.ebi.ac.uk/pdbsum/3hfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hfa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PSB_MYCTO PSB_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. [[~~http~~://www.uniprot.org/uniprot/PSA_MYCTO PSA_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.[HAMAP-Rule:MF_00289]	+	[[https://www.uniprot.org/uniprot/PSB_MYCTO PSB_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. [[https://www.uniprot.org/uniprot/PSA_MYCTO PSA_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.[HAMAP-Rule:MF_00289]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Proteasome\|Proteasome]]	+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:18, 24 July 2019

2019-07-24T08:18:47Z

←Older revision		Revision as of 08:18, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant==		==Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant==
-	<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3hfa' size='340' side='right'caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
Line 38:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
	[[Category: Li, D]]		[[Category: Li, D]]

OCA at 07:39, 12 December 2018

2018-12-12T07:39:58Z

←Older revision		Revision as of 07:39, 12 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant==		==Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant==
	<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), prcA, Rv2109c ([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">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://pdbe.org/3hfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa 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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://pdbe.org/3hfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hfa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hf/3hfa_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hf/3hfa_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 22:11, 7 February 2016

2016-02-07T22:11:20Z

←Older revision		Revision as of 22:11, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis]), prcA, Rv2109c ([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">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa 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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://pdbe.org/3hfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~PSB_MYCTU PSB_MYCTU~~]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref> [[http://www.uniprot.org/uniprot/~~PSA_MYCTU PSA_MYCTU~~]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:~~16468985</ref> <ref>PMID:18059281</ref>~~	+	[[http://www.uniprot.org/uniprot/PSB_MYCTO PSB_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. [[http://www.uniprot.org/uniprot/PSA_MYCTO PSA_MYCTO]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.[HAMAP-Rule:MF_00289]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	<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=3hfa ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3hfa" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
	[[Category: Li, D]]		[[Category: Li, D]]
Line 42:		Line 42:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutant]]		[[Category: Mutant]]
		+	[[Category: Mycobacterium tuberculosis]]
	[[Category: Open gate]]		[[Category: Open gate]]
	[[Category: Proteasome]]		[[Category: Proteasome]]
	[[Category: Proteasome endopeptidase]]		[[Category: Proteasome endopeptidase]]

OCA at 18:33, 24 December 2014

2014-12-24T18:33:22Z

←Older revision		Revision as of 18:33, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]), prcA, Rv2109c ([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">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa 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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSB_MYCTU PSB_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref> [[http://www.uniprot.org/uniprot/PSA_MYCTU PSA_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
-	[[Category: Li, D.]]	+	[[Category: Li, D]]
-	[[Category: Li, H.]]	+	[[Category: Li, H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutant]]		[[Category: Mutant]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Open gate]]		[[Category: Open gate]]
	[[Category: Proteasome]]		[[Category: Proteasome]]
	[[Category: Proteasome endopeptidase]]		[[Category: Proteasome endopeptidase]]

OCA at 12:11, 29 September 2014

2014-09-29T12:11:45Z

←Older revision		Revision as of 12:11, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3hfa.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant==
		+	<StructureSection load='3hfa' size='340' side='right' caption='[[3hfa]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hfa]] is a 28 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=3HFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HFA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3h6i\|3h6i]], [[3h6f\|3h6f]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2170, prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]), prcA, Rv2109c ([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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3hfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hfa RCSB], [http://www.ebi.ac.uk/pdbsum/3hfa 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/hf/3hfa_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 ==
		+	Many anti-infectives inhibit the synthesis of bacterial proteins, but none selectively inhibits their degradation. Most anti-infectives kill replicating pathogens, but few preferentially kill pathogens that have been forced into a non-replicating state by conditions in the host. To explore these alternative approaches we sought selective inhibitors of the proteasome of Mycobacterium tuberculosis. Given that the proteasome structure is extensively conserved, it is not surprising that inhibitors of all chemical classes tested have blocked both eukaryotic and prokaryotic proteasomes, and no inhibitor has proved substantially more potent on proteasomes of pathogens than of their hosts. Here we show that certain oxathiazol-2-one compounds kill non-replicating M. tuberculosis and act as selective suicide-substrate inhibitors of the M. tuberculosis proteasome by cyclocarbonylating its active site threonine. Major conformational changes protect the inhibitor-enzyme intermediate from hydrolysis, allowing formation of an oxazolidin-2-one and preventing regeneration of active protease. Residues outside the active site whose hydrogen bonds stabilize the critical loop before and after it moves are extensively non-conserved. This may account for the ability of oxathiazol-2-one compounds to inhibit the mycobacterial proteasome potently and irreversibly while largely sparing the human homologue.

-	~~{{STRUCTURE_3hfa\| PDB=3hfa \| SCENE= }}~~	+	Inhibitors selective for mycobacterial versus human proteasomes.,Lin G, Li D, de Carvalho LP, Deng H, Tao H, Vogt G, Wu K, Schneider J, Chidawanyika T, Warren JD, Li H, Nathan C Nature. 2009 Oct 1;461(7264):621-6. Epub 2009 Sep 16. PMID:19759536<ref>PMID:19759536</ref>

-	~~===Crystal Structure~~ of ~~Mycobacterium Tuberculosis Proteasome open-gate mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19759536}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3hfa]] is a 28 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=3HFA OCA].~~	+

	==See Also==		==See Also==
	*[[Proteasome\|Proteasome]]		*[[Proteasome\|Proteasome]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019759536<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]

OCA at 08:00, 20 October 2012

2012-10-20T08:00:16Z

←Older revision		Revision as of 08:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3hfa]] is a 28 chain structure ~~of [[Proteasome]]~~ 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=3HFA OCA].	+	[[3hfa]] is a 28 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=3HFA OCA].

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

OCA at 18:08, 25 July 2012

2012-07-25T18:08:44Z

←Older revision		Revision as of 18:08, 25 July 2012
Line 1:		Line 1:
	[[Image:3hfa.png\|left\|200px]]		[[Image:3hfa.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hfa", 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_3hfa\| PDB=3hfa \| SCENE= }}		{{STRUCTURE_3hfa\| PDB=3hfa \| SCENE= }}

	===Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant===		===Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19759536}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19759536 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19759536}}		{{ABSTRACT_PUBMED_19759536}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Proteasome]]	+	*[[Proteasome\|Proteasome]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19759536~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019759536</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
	[[Category: Li, D.]]		[[Category: Li, D.]]
	[[Category: Li, H.]]		[[Category: Li, H.]]
-	[[Category: Crystallography]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutant]]		[[Category: Mutant]]
Line 37:		Line 25:
	[[Category: Proteasome]]		[[Category: Proteasome]]
	[[Category: Proteasome endopeptidase]]		[[Category: Proteasome endopeptidase]]
-	[[Category: X-ray]]

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

2010-12-26T21:00:37Z

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

←Older revision

Revision as of 21:00, 26 December 2010