6ndo - Revision history

OCA at 06:51, 11 October 2023

OCA — Wed, 11 Oct 2023 06:51:15 GMT

←Older revision		Revision as of 06:51, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>		<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Xanc8 Xanc8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._8004 Xanthomonas campestris pv. campestris str. 8004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NDO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</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]] 3.58Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~bphP, XC_4241 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=314565 XANC8])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [https://pdbe.org/6ndo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [https://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo 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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [https://pdbe.org/6ndo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [https://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>	+	[https://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xanc8~~]]	+	[[Category: Xanthomonas campestris pv. campestris str. 8004]]
-	[[Category: Bonomi~~, H R~~]]	+	[[Category: Bonomi HR]]
-	[[Category: Chavas, L]]	+	[[Category: Chavas L]]
-	[[Category: Conforte, V]]	+	[[Category: Conforte V]]
-	[[Category: Goldbaum~~, F A~~]]	+	[[Category: Goldbaum FA]]
-	[[Category: Klinke, S]]	+	[[Category: Klinke S]]
-	[[Category: Malamud, F]]	+	[[Category: Malamud F]]
-	[[Category: Otero~~, L H~~]]	+	[[Category: Otero LH]]
-	[[Category: Rinaldi, J]]	+	[[Category: Rinaldi J]]
-	[[Category: Sirigu, S]]	+	[[Category: Sirigu S]]
-	~~[[Category: Bacterial protein]]~~	+
-	~~[[Category: Photoreceptor]]~~	+
-	~~[[Category: Photosensor]]~~	+
-	~~[[Category: Phytochrome]]~~	+
-	~~[[Category: Phytopathogen]]~~	+
-	~~[[Category: Red/far-red light]]~~	+
-	~~[[Category: Signal transduction]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 03:41, 2 July 2021

OCA — Fri, 02 Jul 2021 03:41:49 GMT

←Older revision		Revision as of 03:41, 2 July 2021
Line 3:		Line 3:
	<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>		<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Xanc8 Xanc8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanc8 Xanc8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NDO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, XC_4241 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314565 XANC8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, XC_4241 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314565 XANC8])</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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [~~http~~://pdbe.org/6ndo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo 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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [https://pdbe.org/6ndo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [https://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>	+	[[https://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Red/far-red light-sensing bacteriophytochrome photoreceptor (BphP) pathways play key roles in bacterial physiology and ecology. These bilin-binding proteins photoswitch between two states, Pr (red absorbing) and Pfr (far-red absorbing). The isomerization of the chromophore and the downstream structural changes result in the light signal transduction. The agricultural pathogen Xanthomonas campestris pv. campestris (Xcc) code for a single bathy-like type BphP (XccBphP), previously shown to negatively regulate several light-mediated biological processes involved in virulence. Here, we generated three different full-length variants with single amino acid changes within its GAF domain that affect the XccBphP photocycle favouring its Pr state: L193Q, L193N and D199A. While D199A recombinant protein locks XccBphP in a Pr-like state, L193Q and L193N exhibit a significant enrichment of the Pr form in thermal equilibrium. The X-ray crystal structures of the three variants were solved, resembling the wild-type protein in the Pr state. Finally, we studied the effects of altering the XccBphP photocycle on the exopolysaccharide xanthan production and stomatal aperture assays as readouts of its bacterial signalling pathway. Null-mutant complementation assays show that the photoactive Pr-favoured XccBphP variants L193Q and L193N tend to negatively regulate xanthan production in vivo. In addition, our results indicate that strains expressing these variants also promote stomatal apertures in challenged plant epidermal peels, compared to wild-type Xcc. The findings presented in this work provide new evidence on the Pr state of XccBphP as a negative regulator of the virulence-associated mechanisms by light in Xcc.
		+
		+	Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms.,Conforte V, Otero LH, Toum L, Sirigu S, Antelo GT, Rinaldi J, Foscaldi S, Klinke S, Chavas LMG, Vojnov AA, Goldbaum FA, Malamud F, Bonomi HR FEBS J. 2021 Apr 17. doi: 10.1111/febs.15883. PMID:33864705<ref>PMID:33864705</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ndo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:12, 4 March 2020

OCA — Wed, 04 Mar 2020 07:12:28 GMT

←Older revision		Revision as of 07:12, 4 March 2020
Line 3:		Line 3:
	<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>		<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanc8 Xanc8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NDO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, XC_4241 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314565 XANC8])</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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [http://pdbe.org/6ndo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [http://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo 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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [http://pdbe.org/6ndo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [http://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo ProSAT]</span></td></tr>
	</table>		</table>
Line 14:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Xanc8]]
	[[Category: Bonomi, H R]]		[[Category: Bonomi, H R]]
	[[Category: Chavas, L]]		[[Category: Chavas, L]]

OCA at 07:43, 18 December 2019

OCA — Wed, 18 Dec 2019 07:43:51 GMT

←Older revision		Revision as of 07:43, 18 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ndo is ~~ON HOLD until Dec 14 2020~~	+	==Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant L193N from Xanthomonas campestris==
-		+	<StructureSection load='6ndo' size='340' side='right'caption='[[6ndo]], [[Resolution\|resolution]] 3.58Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ndo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NDO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ndo OCA], [http://pdbe.org/6ndo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ndo RCSB], [http://www.ebi.ac.uk/pdbsum/6ndo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ndo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bonomi, H R]]
		+	[[Category: Chavas, L]]
		+	[[Category: Conforte, V]]
		+	[[Category: Goldbaum, F A]]
		+	[[Category: Klinke, S]]
		+	[[Category: Malamud, F]]
		+	[[Category: Otero, L H]]
		+	[[Category: Rinaldi, J]]
		+	[[Category: Sirigu, S]]
		+	[[Category: Bacterial protein]]
		+	[[Category: Photoreceptor]]
		+	[[Category: Photosensor]]
		+	[[Category: Phytochrome]]
		+	[[Category: Phytopathogen]]
		+	[[Category: Red/far-red light]]
		+	[[Category: Signal transduction]]
		+	[[Category: Signaling protein]]

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

OCA — Wed, 26 Dec 2018 06:46:37 GMT

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

←Older revision

Revision as of 06:46, 26 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ndo is ON HOLD until Dec 14 2020 Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Dec 2018 06:46:36 GMT

New page: '''Unreleased structure''' The entry 6ndo is ON HOLD until Dec 14 2020 Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ndo is ON HOLD until Dec 14 2020

Authors:

Description:
[[Category: Unreleased Structures]]