5e27 - Revision history

OCA at 06:10, 5 July 2023

OCA — Wed, 05 Jul 2023 06:10:32 GMT

←Older revision		Revision as of 06:10, 5 July 2023
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	<StructureSection load='5e27' size='340' side='right'caption='[[5e27]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5e27' size='340' side='right'caption='[[5e27]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e27]] is a 2 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=5E27 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e27]] is a 2 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=5E27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E27 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~rpfB~~, ABI38_15460, BN1303_02209, ERS024750_01702, ERS024751_02059, ERS024758_02236, ERS024764_01503, ERS094182_03333, ERS124362_01696, ERS124821_03131, ERS124823_03398, ERS124824_03090, ERS124825_03322, ERS124826_03034, ERS124827_03238, ERS124828_02982, ERS124829_03081, ERS124830_03164, ERS124832_03150, IQ42_14370, IQ45_14195, IQ47_14175, IQ48_14250, IU12_14990, IU13_14360, IU15_14665, IU16_14305, IU21_14520, T209_14145 ([~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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]] 2.6Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [~~http~~://pdbe.org/5e27 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e27 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e27 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=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [https://pdbe.org/5e27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [https://www.ebi.ac.uk/pdbsum/5e27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e27 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPFB_MYCTU RPFB_MYCTU] Factor that stimulates resuscitation of dormant cells. Has peptidoglycan (PG) hydrolytic activity. Active in the pM concentration range. Has little to no effect on actively-growing cells. PG fragments could either directly activate the resuscitation pathway of dormant bacteria or serve as a substrate for endogenous Rpf, resulting in low molecular weight products with resuscitation activity.<ref>PMID:12410821</ref> <ref>PMID:12906837</ref> <ref>PMID:18463693</ref> <ref>PMID:20016836</ref> Reduces lag phase and enhances the growth of quiescent (1 month-old culture) M.tuberculosis; works best between 8 and 128 pM. Increases the number of bacteria that can be recovered from a 3 month-old culture. Stimulates growth of stationary phase M.bovis (a slowly-growing Mycobacterium) as well as M.smegmatis cells (a fast grower). Binds N,N',N''-triacetylchitotriose (tri-NAG). A fragment (residues 194-362) hydrolyzes an artificial lysozyme substrate 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside (MUF tri-NAG). By itself has little activity on cell wall, in combination with RipA is active against cell wall extracts from a number of Actinobacteria; this activity is inhibited by PBP1A (ponA1). Sequential gene disruption indicates RpfB and RpfE are higher than RpfD and RpfC in functional hierarchy.<ref>PMID:12410821</ref> <ref>PMID:12906837</ref> <ref>PMID:18463693</ref> <ref>PMID:20016836</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Berisio, R~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Romano, M]]~~	+	[[Category: Berisio R]]
-	~~[[Category: Ruggiero, A~~]]	+	[[Category: De Simone A]]
-	[[Category: Simone, A De]]	+	[[Category: Romano M]]
-	[[Category: ~~Squeglia, F~~]]	+	[[Category: Ruggiero A]]
-	[[Category: ~~Vitagliano, L~~]]	+	[[Category: Squeglia F]]
-	[[Category: ~~Cell adhesion~~]]	+	[[Category: Vitagliano L]]
-	[[Category: ~~Cell wall]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Tuberculosis~~]]	+

OCA at 06:40, 22 April 2020

OCA — Wed, 22 Apr 2020 06:40:39 GMT

←Older revision		Revision as of 06:40, 22 April 2020
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		+
	==The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains==		==The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains==
-	<StructureSection load='5e27' size='340' side='right' caption='[[5e27]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5e27' size='340' side='right'caption='[[5e27]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e27]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E27 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e27]] is a 2 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=5E27 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E27 FirstGlance]. <br>
-	</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=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [http://pdbe.org/5e27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [http://www.ebi.ac.uk/pdbsum/5e27 PDBsum]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpfB, ABI38_15460, BN1303_02209, ERS024750_01702, ERS024751_02059, ERS024758_02236, ERS024764_01503, ERS094182_03333, ERS124362_01696, ERS124821_03131, ERS124823_03398, ERS124824_03090, ERS124825_03322, ERS124826_03034, ERS124827_03238, ERS124828_02982, ERS124829_03081, ERS124830_03164, ERS124832_03150, IQ42_14370, IQ45_14195, IQ47_14175, IQ48_14250, IU12_14990, IU13_14360, IU15_14665, IU16_14305, IU21_14520, T209_14145 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [http://pdbe.org/5e27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [http://www.ebi.ac.uk/pdbsum/5e27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e27 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Berisio, R]]		[[Category: Berisio, R]]
	[[Category: Romano, M]]		[[Category: Romano, M]]

OCA at 19:01, 1 December 2015

OCA — Tue, 01 Dec 2015 19:01:07 GMT

←Older revision		Revision as of 19:01, 1 December 2015
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-	'''~~Unreleased~~ structure'''	+	==The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains==
		+	<StructureSection load='5e27' size='340' side='right' caption='[[5e27]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e27]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E27 FirstGlance]. <br>
		+	</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=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [http://pdbe.org/5e27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [http://www.ebi.ac.uk/pdbsum/5e27 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D). METHODS: The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies. RESULTS AND CONCLUSIONS: The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains. GENERAL SIGNIFICANCE: Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.

-	The ~~entry 5e27 is ON HOLD~~	+	The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains.,Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R Biochim Biophys Acta. 2015 Nov 5. pii: S0304-4165(15)00300-1. doi:, 10.1016/j.bbagen.2015.11.001. PMID:26549874<ref>PMID:26549874</ref>

-	~~Authors: Ruggiero~~, A.~~, Squeglia, F~~.~~, Romano, M., Vitagliano, L., De Simone, A., Berisio, R~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains~~	+	<div class="pdbe-citations 5e27" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Berisio, R]]
		+	[[Category: Romano, M]]
	[[Category: Ruggiero, A]]		[[Category: Ruggiero, A]]
		+	[[Category: Simone, A De]]
		+	[[Category: Squeglia, F]]
	[[Category: Vitagliano, L]]		[[Category: Vitagliano, L]]
-	[[Category: ~~Squeglia, F~~]]	+	[[Category: Cell adhesion]]
-	[[Category: ~~Romano, M~~]]	+	[[Category: Cell wall]]
-	[[Category: ~~Berisio, R~~]]	+	[[Category: Peptidoglycan]]
-	[[Category: ~~De Simone, A~~]]	+	[[Category: Tuberculosis]]

OCA: Protected "5e27" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2015 12:52:15 GMT

Protected "5e27" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:52, 7 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e27 is ON HOLD Authors: Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R. Description: The structure of Resuscita...

OCA — Wed, 07 Oct 2015 12:52:13 GMT

New page: '''Unreleased structure''' The entry 5e27 is ON HOLD Authors: Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R. Description: The structure of Resuscita...

New page

'''Unreleased structure'''

The entry 5e27 is ON HOLD

Authors: Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R.

Description: The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
[[Category: Unreleased Structures]]
[[Category: Ruggiero, A]]
[[Category: Vitagliano, L]]
[[Category: Squeglia, F]]
[[Category: Romano, M]]
[[Category: Berisio, R]]
[[Category: De Simone, A]]