5xsd - Revision history

OCA at 10:20, 27 March 2024

OCA — Wed, 27 Mar 2024 10:20:13 GMT

←Older revision		Revision as of 10:20, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xsd' size='340' side='right'caption='[[5xsd]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5xsd' size='340' side='right'caption='[[5xsd]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XSD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_beijerinckii_NCIMB_8052 Clostridium beijerinckii NCIMB 8052]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XSD FirstGlance]. <br>
-	</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=5xsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsd OCA], [~~http~~://pdbe.org/5xsd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xsd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xsd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsd ProSAT]</span></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]] 2.5Å</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=5xsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsd OCA], [https://pdbe.org/5xsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xsd RCSB], [https://www.ebi.ac.uk/pdbsum/5xsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsd ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A6LW07_CLOB8 A6LW07_CLOB8]
-	d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose. The molecular mechanism underlying signal perception and integration of these processes remains elusive, however. Here we purified the N-terminal periplasmic domain of LytS (LytSN) in a complex with XylFII and determined the conformational structures of the complex in its d-xylose-free and d-xylose-bound forms. LytSN contains a four-helix bundle, and XylFII contains two Rossmann fold-like globular domains with a xylose-binding cleft between them. In the absence of d-xylose, LytSN and XylFII formed a heterodimer. Specific binding of d-xylose to the cleft of XylFII induced a large conformational change that closed the cleft and brought the globular domains closer together. This conformational change led to the formation of an active XylFII-LytSN heterotetramer. Mutations at the d-xylose binding site and the heterotetramer interface diminished heterotetramer formation and impaired the d-xylose-sensing function of XylFII-LytS. Based on these data, we propose a working model of XylFII-LytS that provides a molecular basis for d-xylose utilization and metabolic modification in bacteria.	+
-		+
-	Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria.,Li J, Wang C, Yang G, Sun Z, Guo H, Shao K, Gu Y, Jiang W, Zhang P Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):~~8235-8240. doi:, 10.1073~~/~~pnas.1620183114. Epub 2017 Jul 17. PMID:28716923<ref>PMID:28716923<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5xsd" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium beijerinckii NCIMB 8052]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li~~, J X~~]]	+	[[Category: Li JX]]
-	[[Category: Wang~~, C Y~~]]	+	[[Category: Wang CY]]
-	[[Category: Zhang, P]]	+	[[Category: Zhang P]]
-	~~[[Category: D-xylose uptake]]~~	+
-	~~[[Category: Histidine kinase]]~~	+
-	~~[[Category: Signal transmission across the membrane]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Two component system~~]]	+

OCA at 06:58, 14 October 2020

OCA — Wed, 14 Oct 2020 06:58:01 GMT

←Older revision		Revision as of 06:58, 14 October 2020
Line 1:		Line 1:

	==XylFII-LytSN complex mutant - D103A==		==XylFII-LytSN complex mutant - D103A==
-	<StructureSection load='5xsd' size='340' side='right' caption='[[5xsd]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5xsd' size='340' side='right'caption='[[5xsd]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XSD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XSD 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=5xsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsd OCA], [http://pdbe.org/5xsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsd RCSB], [http://www.ebi.ac.uk/pdbsum/5xsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsd ProSAT]</span></td></tr>	+	</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=5xsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsd OCA], [http://pdbe.org/5xsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsd RCSB], [http://www.ebi.ac.uk/pdbsum/5xsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Li, J X]]		[[Category: Li, J X]]
	[[Category: Wang, C Y]]		[[Category: Wang, C Y]]

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

OCA — Fri, 04 Aug 2017 04:11:33 GMT

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

←Older revision

Revision as of 04:11, 4 August 2017

OCA: New page: ==XylFII-LytSN complex mutant - D103A== == Structural highlights ...

OCA — Fri, 04 Aug 2017 04:11:31 GMT

New page: ==XylFII-LytSN complex mutant - D103A== <StructureSection load='5xsd' size='340' side='right' caption='5xsd, resolution 2.50Å' scene=''> == Structural highlights ...

New page

==XylFII-LytSN complex mutant - D103A==
<StructureSection load='5xsd' size='340' side='right' caption='[[5xsd]], [[Resolution|resolution]] 2.50Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5xsd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XSD 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=5xsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsd OCA], [http://pdbe.org/5xsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsd RCSB], [http://www.ebi.ac.uk/pdbsum/5xsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsd ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose. The molecular mechanism underlying signal perception and integration of these processes remains elusive, however. Here we purified the N-terminal periplasmic domain of LytS (LytSN) in a complex with XylFII and determined the conformational structures of the complex in its d-xylose-free and d-xylose-bound forms. LytSN contains a four-helix bundle, and XylFII contains two Rossmann fold-like globular domains with a xylose-binding cleft between them. In the absence of d-xylose, LytSN and XylFII formed a heterodimer. Specific binding of d-xylose to the cleft of XylFII induced a large conformational change that closed the cleft and brought the globular domains closer together. This conformational change led to the formation of an active XylFII-LytSN heterotetramer. Mutations at the d-xylose binding site and the heterotetramer interface diminished heterotetramer formation and impaired the d-xylose-sensing function of XylFII-LytS. Based on these data, we propose a working model of XylFII-LytS that provides a molecular basis for d-xylose utilization and metabolic modification in bacteria.

Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria.,Li J, Wang C, Yang G, Sun Z, Guo H, Shao K, Gu Y, Jiang W, Zhang P Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8235-8240. doi:, 10.1073/pnas.1620183114. Epub 2017 Jul 17. PMID:28716923<ref>PMID:28716923</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xsd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Li, J X]]
[[Category: Wang, C Y]]
[[Category: Zhang, P]]
[[Category: D-xylose uptake]]
[[Category: Histidine kinase]]
[[Category: Signal transmission across the membrane]]
[[Category: Sugar binding protein]]
[[Category: Two component system]]