4pmx - Revision history

OCA at 00:45, 28 December 2023

2023-12-28T00:45:41Z

← Older revision		Revision as of 00:45, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.304Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [https://pdbe.org/4pmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [https://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx 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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [https://pdbe.org/4pmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [https://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:19, 8 February 2023

2023-02-08T07:19:44Z

← Older revision		Revision as of 07:19, 8 February 2023
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	<StructureSection load='4pmx' size='340' side='right'caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4pmx' size='340' side='right'caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xynB, XAC4254 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [https://pdbe.org/4pmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [https://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx 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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [~~http~~://pdbe.org/4pmx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8PET6_XANAC Q8PET6_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: Martins~~, V P.M~~]]		[[Category: Martins VPM]]
	[[Category: Murakami~~, M T~~]]		[[Category: Murakami MT]]
	[[Category: Ruller, R]]		[[Category: Ruller R]]
	[[Category: Santos~~, C R~~]]		[[Category: Santos CR]]
	[[Category: Zanphorlin~~, L M]]~~		[[Category: Zanphorlin LM]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Xylanase~~]]

OCA at 06:16, 17 April 2019

2019-04-17T06:16:27Z

← Older revision		Revision as of 06:16, 17 April 2019
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	==Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form==		==Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form==
	<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4pmx' size='340' side='right'caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Xanac]]		[[Category: Xanac]]
	[[Category: Martins, V P.M]]		[[Category: Martins, V P.M]]

OCA at 12:27, 7 November 2018

2018-11-07T12:27:57Z

← Older revision		Revision as of 12:27, 7 November 2018
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	<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pmx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pmx]] 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=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xynB, XAC4254 ([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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://pdbe.org/4pmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx 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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://pdbe.org/4pmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Xanac]]
	[[Category: Martins, V P.M]]		[[Category: Martins, V P.M]]
	[[Category: Murakami, M T]]		[[Category: Murakami, M T]]

OCA at 11:53, 11 August 2016

2016-08-11T11:53:41Z

← Older revision		Revision as of 11:53, 11 August 2016
Line 1:		Line 1:

	==Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form==		==Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form==
	<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
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	<table><tr><td colspan='2'>[[4pmx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pmx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx 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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://pdbe.org/4pmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pmx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4pmx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:17, 26 November 2014

2014-11-26T06:17:15Z

← Older revision		Revision as of 06:17, 26 November 2014
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Martins, V P.M.]]		[[Category: Martins, V P.M]]
	[[Category: Murakami, M T.]]		[[Category: Murakami, M T]]
	[[Category: Ruller, R.]]		[[Category: Ruller, R]]
	[[Category: Santos, C R.]]		[[Category: Santos, C R]]
	[[Category: Zanphorlin, L M.]]		[[Category: Zanphorlin, L M]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Xylanase]]		[[Category: Xylanase]]

OCA at 08:55, 20 October 2014

2014-10-20T08:55:18Z

← Older revision		Revision as of 08:55, 20 October 2014
Line 1:		Line 1:
	==~~Structure~~ of ~~a novel bacterial~~ xylanase in the native form==		==Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form==
	<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	<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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx 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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx PDBsum]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Xanthomonas pathogens attack a variety of economically-relevant plants and their xylan CUT system (Carbohydrate Utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, XynA and XynB, which influence biofilm formation and virulence by molecular mechanisms still elusive. Herein, we demonstrated that XynA is a rare reducing-end xylose-releasing exo-oligoxylanase and not an endo-beta-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the beta7-alpha7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-beta-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB showed to be a classical endo-beta-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell-wall barrier providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.

			Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens.,Santos CR, Hoffmam ZB, Martins VP, Zanphorlin LM, Assis LH, Honorato RV, Oliveira PS, Ruller R, Murakami MT J Biol Chem. 2014 Sep 29. pii: jbc.M114.605105. PMID:25266726<ref>PMID:25266726</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:52, 8 October 2014

2014-10-08T07:52:24Z

← Older revision		Revision as of 07:52, 8 October 2014
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	'''~~Unreleased structure~~'''		==Structure of a novel bacterial xylanase in the native form==
			<StructureSection load='4pmx' size='340' side='right' caption='[[4pmx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	~~The entry~~ 4pmx is ~~ON HOLD until Paper Publication~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4pmx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PMX FirstGlance]. <br>
	~~Authors~~: ~~Santos~~, C.R., Martins, V.P.M., ~~Zanphorlin, L.~~M., Ruller, R., ~~Murakami~~, M.T.		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4pmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pmx RCSB], [http://www.ebi.ac.uk/pdbsum/4pmx PDBsum]</span></td></tr>
	~~Description~~:		</table>
			__TOC__
			</StructureSection>
			[[Category: Martins, V P.M.]]
			[[Category: Murakami, M T.]]
			[[Category: Ruller, R.]]
			[[Category: Santos, C R.]]
			[[Category: Zanphorlin, L M.]]
			[[Category: Hydrolase]]
			[[Category: Xylanase]]

OCA at 07:28, 13 August 2014

2014-08-13T07:28:03Z

← Older revision		Revision as of 07:28, 13 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4pmx is ON HOLD		The entry 4pmx is ON HOLD until Paper Publication

	Authors: Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.		Authors: Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.

	Description:		Description:

OCA at 00:59, 7 August 2014

2014-08-07T00:59:58Z

← Older revision		Revision as of 00:59, 7 August 2014
Line 3:		Line 3:
	The entry 4pmx is ON HOLD		The entry 4pmx is ON HOLD

	Authors: Santos, C.R., Martins, V.P.M., Zanphorlin.L.M., Ruller, R., Murakami, M.T.		Authors: Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.

	Description:		Description: