5um2 - Revision history

OCA at 13:29, 4 October 2023

2023-10-04T13:29:42Z

←Older revision		Revision as of 13:29, 4 October 2023
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	<StructureSection load='5um2' size='340' side='right'caption='[[5um2]], [[Resolution\|resolution]] 1.14Å' scene=''>		<StructureSection load='5um2' size='340' side='right'caption='[[5um2]], [[Resolution\|resolution]] 1.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5um2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xanac Xanac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5um2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri_pv._citri_str._306 Xanthomonas citri pv. citri str. 306]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UM2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.14Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~sbp, XAC1017 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=190486 XANAC])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um2 OCA], [~~http~~://pdbe.org/5um2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5um2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5um2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5um2 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=5um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um2 OCA], [https://pdbe.org/5um2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5um2 RCSB], [https://www.ebi.ac.uk/pdbsum/5um2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5um2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8PNN7_XANAC Q8PNN7_XANAC]
	<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: ~~Xanac~~]]	+	[[Category: Xanthomonas citri pv. citri str. 306]]
-	[[Category: Balan, A]]	+	[[Category: Balan A]]
-	[[Category: Hyvonen, M]]	+	[[Category: Hyvonen M]]
-	[[Category: Pereira~~, C T]]~~	+	[[Category: Pereira CT]]
-	~~[[Category: Abc transporter]]~~	+
-	~~[[Category: Periplasmic domain]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:28, 17 April 2019

2019-04-17T06:28:09Z

←Older revision		Revision as of 06:28, 17 April 2019
Line 1:		Line 1:

	==Functional and structural characterization of a Sulfate-binding protein (Sbp) from Xanthomonas citri==		==Functional and structural characterization of a Sulfate-binding protein (Sbp) from Xanthomonas citri==
-	<StructureSection load='5um2' size='340' side='right' caption='[[5um2]], [[Resolution\|resolution]] 1.14Å' scene=''>	+	<StructureSection load='5um2' size='340' side='right'caption='[[5um2]], [[Resolution\|resolution]] 1.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5um2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5um2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sbp, XAC1017 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190486 XANAC])</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=5um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um2 OCA], [http://pdbe.org/5um2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5um2 RCSB], [http://www.ebi.ac.uk/pdbsum/5um2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5um2 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=5um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um2 OCA], [http://pdbe.org/5um2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5um2 RCSB], [http://www.ebi.ac.uk/pdbsum/5um2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5um2 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Xanac]]
	[[Category: Balan, A]]		[[Category: Balan, A]]
	[[Category: Hyvonen, M]]		[[Category: Hyvonen, M]]

OCA at 17:00, 20 October 2017

2017-10-20T17:00:07Z

←Older revision		Revision as of 17:00, 20 October 2017
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~BACKGROUND:~~ The ~~Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species~~ of ~~citrus plants where it causes canker disease. The adaptation to different habitats~~ is ~~related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur,~~ an ~~essential element for all organisms. In Escherichia coli~~, ~~the necessary sulfur can be obtained by a set of proteins~~ whose ~~genes belong to the cys regulon. Although the cys regulon proteins and their~~ importance ~~have~~ been ~~described in many other bacteria, there are no data related~~ to ~~these proteins~~ in X. citri ~~or in~~ the ~~Xanthomonas genus. The study~~ of the ~~relevance~~ of ~~these systems~~ in ~~these phytopathogenic bacteria that have distinct mechanisms of infection is one essential step toward understanding their physiology~~. In this work, we ~~used bioinformatics, molecular modeling and transcription analysis (RT-PCR) to identify and characterize~~ the ~~putative cys regulon genes in X. citri. RESULTS: We showed~~ that the ~~ATP Binding Cassette Transporter (ABC transporter) SbpCysUWA for sulfate uptake is conserved~~ in ~~X. citri~~ and ~~translated~~ in ~~presence~~ of sulfate~~. On the other hand~~, ~~differently from what is predicted in databases~~, ~~according molecular modeling~~ and ~~phylogenetic analysis, X. citri does not show a proper taurine transporter, but two different ABC systems related to~~ the ~~alkanesulfonate/sulfonate~~ transport ~~that were recently acquired~~ during ~~evolution~~. RT-~~PCR analysis evidenced that these genes and their putative transcriptional regulator CysB are rather transcripted in XAM1, a medium with defined concentration of~~ sulfate~~, than LB~~. ~~CONCLUSIONS: The presence of at least three distinct systems for sulfate~~ and ~~sulfonates assimilation in X. citri evidenced the importance of these compounds for the bacterium~~. The ~~transcription of genes involved~~ with ~~alkanesulfonate/sulfur compounds in XAM1 along to CysB suggests that despite the differences in the transporters~~, the ~~regulation~~ of ~~these systems might be similar to the described for E. coli~~. Altogether, ~~these~~ results ~~will serve as a foundation for further studies aimed to understanding~~ the ~~relevance~~ of ~~sulfur in growth, virulence and pathogenesis~~ of X. citri and ~~related bacteria~~.	+	The uptake and transport of sulfate in bacteria is mediated by an ATP-binding cassette transporter (ABC transporter) encoded by sbpcysUWA genes, whose importance has been widely demonstrated due to their relevance in cysteine synthesis and bacterial growth. In Xanthomonas citri, the causative agent of canker disease, the expression of components from this ABC transporter and others related to uptake of organic sulfur sources has been shown during in vitro growth cultures. In this work, based on gene reporter and proteomics analyses, we showed the activation of the promoter that controls the sbpcysUWA operon in vitro and in vivo and the expression of sulfate-binding protein (Sbp), a periplasmic-binding protein, indicating that this protein plays an important function during growth and that the transport system is active during Citrus sinensis infection. To characterize Sbp, we solved its three-dimensional structure bound to sulfate at 1.14 A resolution and performed biochemical and functional characterization. The results revealed that Sbp interacts with sulfate without structural changes, but the interaction induces a significant increasing of protein thermal stability. Altogether, the results presented in this study show the evidence of the functionality of the ABC transporter for sulfate in X. citri and its relevance during infection.

-	~~The sulfur/sulfonates transport systems in~~ Xanthomonas citri ~~pv. citri~~.,Pereira CT, ~~Moutran A~~, Fessel M, Balan A ~~BMC Genomics~~. ~~2015~~ Jul 14;16:~~524~~. doi: 10.~~1186~~/~~s12864~~-~~015~~-~~1736~~-5. PMID:~~26169280~~<ref>PMID:~~26169280~~</ref>	+	Sulfate-Binding Protein (Sbp) from Xanthomonas citri: Structure and Functional Insights.,Pereira CT, Roesler C, Faria JN, Fessel MR, Balan A Mol Plant Microbe Interact. 2017 Jul;30(7):578-588. doi:, 10.1094/MPMI-02-17-0032-R. Epub 2017 May 31. PMID:28562158<ref>PMID:28562158</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>

OCA at 14:05, 29 March 2017

2017-03-29T14:05:33Z

←Older revision		Revision as of 14:05, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5um2 is ~~ON HOLD~~	+	==Functional and structural characterization of a Sulfate-binding protein (Sbp) from Xanthomonas citri==
		+	<StructureSection load='5um2' size='340' side='right' caption='[[5um2]], [[Resolution\|resolution]] 1.14Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5um2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um2 OCA], [http://pdbe.org/5um2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5um2 RCSB], [http://www.ebi.ac.uk/pdbsum/5um2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5um2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essential element for all organisms. In Escherichia coli, the necessary sulfur can be obtained by a set of proteins whose genes belong to the cys regulon. Although the cys regulon proteins and their importance have been described in many other bacteria, there are no data related to these proteins in X. citri or in the Xanthomonas genus. The study of the relevance of these systems in these phytopathogenic bacteria that have distinct mechanisms of infection is one essential step toward understanding their physiology. In this work, we used bioinformatics, molecular modeling and transcription analysis (RT-PCR) to identify and characterize the putative cys regulon genes in X. citri. RESULTS: We showed that the ATP Binding Cassette Transporter (ABC transporter) SbpCysUWA for sulfate uptake is conserved in X. citri and translated in presence of sulfate. On the other hand, differently from what is predicted in databases, according molecular modeling and phylogenetic analysis, X. citri does not show a proper taurine transporter, but two different ABC systems related to the alkanesulfonate/sulfonate transport that were recently acquired during evolution. RT-PCR analysis evidenced that these genes and their putative transcriptional regulator CysB are rather transcripted in XAM1, a medium with defined concentration of sulfate, than LB. CONCLUSIONS: The presence of at least three distinct systems for sulfate and sulfonates assimilation in X. citri evidenced the importance of these compounds for the bacterium. The transcription of genes involved with alkanesulfonate/sulfur compounds in XAM1 along to CysB suggests that despite the differences in the transporters, the regulation of these systems might be similar to the described for E. coli. Altogether, these results will serve as a foundation for further studies aimed to understanding the relevance of sulfur in growth, virulence and pathogenesis of X. citri and related bacteria.

-	~~Authors: Pereira, C~~.T., ~~Hyvonen~~, M., Balan, A.	+	The sulfur/sulfonates transport systems in Xanthomonas citri pv. citri.,Pereira CT, Moutran A, Fessel M, Balan A BMC Genomics. 2015 Jul 14;16:524. doi: 10.1186/s12864-015-1736-5. PMID:26169280<ref>PMID:26169280</ref>

-	~~Description: Functional and structural characterization of~~ a ~~Sulfate-binding protein (Sbp) from Xanthomonas citri~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Hyvonen, M]]~~	+	<div class="pdbe-citations 5um2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Balan, A]]		[[Category: Balan, A]]
-	[[Category: Pereira, C.T]]	+	[[Category: Hyvonen, M]]
		+	[[Category: Pereira, C T]]
		+	[[Category: Abc transporter]]
		+	[[Category: Periplasmic domain]]
		+	[[Category: Transport protein]]

OCA at 19:10, 15 March 2017

2017-03-15T19:10:52Z

←Older revision		Revision as of 19:10, 15 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hyvonen, M]]		[[Category: Hyvonen, M]]
-	[[Category: Pereira, C.T]]
	[[Category: Balan, A]]		[[Category: Balan, A]]
		+	[[Category: Pereira, C.T]]

OCA: Protected "5um2" [edit=sysop:move=sysop]

2017-03-09T14:36:22Z

Protected "5um2" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:36, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5um2 is ON HOLD Authors: Pereira, C.T., Hyvonen, M., Balan, A. Description: Functional and structural characterization of a Sulfate-binding protein...

2017-03-09T14:36:20Z

New page: '''Unreleased structure''' The entry 5um2 is ON HOLD Authors: Pereira, C.T., Hyvonen, M., Balan, A. Description: Functional and structural characterization of a Sulfate-binding protein...

New page

'''Unreleased structure'''

The entry 5um2 is ON HOLD

Authors: Pereira, C.T., Hyvonen, M., Balan, A.

Description: Functional and structural characterization of a Sulfate-binding protein (Sbp) from Xanthomonas citri
[[Category: Unreleased Structures]]
[[Category: Hyvonen, M]]
[[Category: Pereira, C.T]]
[[Category: Balan, A]]