6kly - Revision history

OCA at 10:43, 27 March 2024

OCA — Wed, 27 Mar 2024 10:43:20 GMT

←Older revision		Revision as of 10:43, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6kly' size='340' side='right'caption='[[6kly]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='6kly' size='340' side='right'caption='[[6kly]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kly]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"xanthomonas_citri"_(hasse_1915)_dowson_1939 "xanthomonas~~ citri~~" (hasse 1915) dowson 1939~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4eln 4eln]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kly]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri Xanthomonas citri]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4eln 4eln]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KLY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6k93\|6k93]], [[6k94\|6k94]]</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]] 2.01Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">XopAI, XAC3230 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=346 "Xanthomonas citri" (Hasse 1915) Dowson 1939])~~</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=6kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kly OCA], [https://pdbe.org/6kly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kly RCSB], [https://www.ebi.ac.uk/pdbsum/6kly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kly 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=6kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kly OCA], [~~http~~://pdbe.org/6kly PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kly RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kly PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kly ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0U5GCU5_XANCI A0A0U5GCU5_XANCI]
-	Plant pathogens secrete proteins called effectors into the cells of their host to modulate the host immune response against colonization. Effectors can either modify or arrest host target proteins to sabotage the signaling pathway, and therefore are considered potential drug targets for crop disease control. In earlier research, the Xanthomonas type III effector XopAI was predicted to be a member of the arginine-specific mono-ADP-ribosyltransferase family. However, the crystal structure of XopAI revealed an altered active site that is unsuitable to bind the cofactor NAD+, but with the capability to capture an arginine-containing peptide from XopAI itself. The arginine peptide consists of residues 60 through 69 of XopAI, and residue 62 (R62) is key to determining the protein-peptide interaction. The crystal structure and the molecular dynamics simulation results indicate that specific arginine recognition is mediated by hydrogen bonds provided by the backbone oxygen atoms from residues W154, T155, and T156, and a salt bridge provided by the E265 sidechain. In addition, a protruding loop of XopAI adopts dynamic conformations in response to arginine peptide binding and is probably involved in target protein recognition. These data suggest that XopAI binds to its target protein by the peptide-binding ability, and therefore, it promotes disease progression. Our findings reveal an unexpected and intriguing function of XopAI and pave the way for further investigation on the role of XopAI in pathogen invasion.	+
-		+
-	Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein.,Liu JH, Yang JY, Hsu DW, Lai YH, Li YP, Tsai YR, Hou MH Int J Mol Sci. 2019 Oct 14;20(20). pii: ~~ijms20205085. doi: 10.3390~~/~~ijms20205085. PMID:31615004<ref>PMID:31615004<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6kly" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chiu, S W~~]]	+	[[Category: Xanthomonas citri]]
-	[[Category: ~~Lin, H~~]]	+	[[Category: Chiu SW]]
-	[[Category: ~~Liu, J~~ H]]	+	[[Category: Lin H]]
-	[[Category: ~~Wu,~~ J ~~E]]~~	+	[[Category: Liu J-H]]
-	~~[[Category: Yang, J Y]]~~	+	[[Category: Wu JE]]
-	~~[[Category: Cell invasion]]~~	+	[[Category: Yang JY]]
-	~~[[Category: Mono~~-~~adp-ribosyltransferase fold~~]]	+
-	[[Category: ~~Peptide-binding domain~~]]	+
-	[[Category: ~~Type iii effector]]~~	+
-	~~[[Category: Xanthomonas axonopodis pv. citri~~]]	+

OCA at 09:34, 30 October 2019

OCA — Wed, 30 Oct 2019 09:34:04 GMT

←Older revision		Revision as of 09:34, 30 October 2019
Line 3:		Line 3:
	<StructureSection load='6kly' size='340' side='right'caption='[[6kly]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='6kly' size='340' side='right'caption='[[6kly]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kly]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4eln 4eln]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kly]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"xanthomonas_citri"_(hasse_1915)_dowson_1939 "xanthomonas citri" (hasse 1915) dowson 1939]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4eln 4eln]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KLY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6k93\|6k93]], [[6k94\|6k94]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6k93\|6k93]], [[6k94\|6k94]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XopAI, XAC3230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=346 "Xanthomonas citri" (Hasse 1915) Dowson 1939])</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=6kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kly OCA], [http://pdbe.org/6kly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kly RCSB], [http://www.ebi.ac.uk/pdbsum/6kly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kly 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=6kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kly OCA], [http://pdbe.org/6kly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kly RCSB], [http://www.ebi.ac.uk/pdbsum/6kly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kly ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant pathogens secrete proteins called effectors into the cells of their host to modulate the host immune response against colonization. Effectors can either modify or arrest host target proteins to sabotage the signaling pathway, and therefore are considered potential drug targets for crop disease control. In earlier research, the Xanthomonas type III effector XopAI was predicted to be a member of the arginine-specific mono-ADP-ribosyltransferase family. However, the crystal structure of XopAI revealed an altered active site that is unsuitable to bind the cofactor NAD+, but with the capability to capture an arginine-containing peptide from XopAI itself. The arginine peptide consists of residues 60 through 69 of XopAI, and residue 62 (R62) is key to determining the protein-peptide interaction. The crystal structure and the molecular dynamics simulation results indicate that specific arginine recognition is mediated by hydrogen bonds provided by the backbone oxygen atoms from residues W154, T155, and T156, and a salt bridge provided by the E265 sidechain. In addition, a protruding loop of XopAI adopts dynamic conformations in response to arginine peptide binding and is probably involved in target protein recognition. These data suggest that XopAI binds to its target protein by the peptide-binding ability, and therefore, it promotes disease progression. Our findings reveal an unexpected and intriguing function of XopAI and pave the way for further investigation on the role of XopAI in pathogen invasion.
		+
		+	Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein.,Liu JH, Yang JY, Hsu DW, Lai YH, Li YP, Tsai YR, Hou MH Int J Mol Sci. 2019 Oct 14;20(20). pii: ijms20205085. doi: 10.3390/ijms20205085. PMID:31615004<ref>PMID:31615004</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kly" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:44, 21 August 2019

OCA — Wed, 21 Aug 2019 05:44:40 GMT

←Older revision		Revision as of 05:44, 21 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6kly is ON HOLD~~	+	==Crystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri in space group P43212==
-		+	<StructureSection load='6kly' size='340' side='right'caption='[[6kly]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~Authors: Liu, J.-H., Wu, J.E., Lin, H., Chiu, S.W., Yang, J.Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6kly]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4eln 4eln]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KLY FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri in space group P43212	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6k93\|6k93]], [[6k94\|6k94]]</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=6kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kly OCA], [http://pdbe.org/6kly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kly RCSB], [http://www.ebi.ac.uk/pdbsum/6kly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kly ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Liu~~, J.-H]]	+	</table>
-	[[Category: Wu, ~~J.E~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chiu, S W]]
	[[Category: Lin, H]]		[[Category: Lin, H]]
-	[[Category: ~~Chiu~~, ~~S.W~~]]	+	[[Category: Liu, J H]]
-	[[Category: Yang, J.Y]]	+	[[Category: Wu, J E]]
		+	[[Category: Yang, J Y]]
		+	[[Category: Cell invasion]]
		+	[[Category: Mono-adp-ribosyltransferase fold]]
		+	[[Category: Peptide-binding domain]]
		+	[[Category: Type iii effector]]
		+	[[Category: Xanthomonas axonopodis pv. citri]]

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

OCA — Wed, 07 Aug 2019 04:10:25 GMT

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

←Older revision

Revision as of 04:10, 7 August 2019

OCA: New page: '''Unreleased structure''' The entry 6kly is ON HOLD Authors: Liu, J.-H., Wu, J.E., Lin, H., Chiu, S.W., Yang, J.Y. Description: Crystal structure of the type III effector XopAI from X...

OCA — Wed, 07 Aug 2019 04:10:24 GMT

New page: '''Unreleased structure''' The entry 6kly is ON HOLD Authors: Liu, J.-H., Wu, J.E., Lin, H., Chiu, S.W., Yang, J.Y. Description: Crystal structure of the type III effector XopAI from X...

New page

'''Unreleased structure'''

The entry 6kly is ON HOLD

Authors: Liu, J.-H., Wu, J.E., Lin, H., Chiu, S.W., Yang, J.Y.

Description: Crystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri in space group P43212
[[Category: Unreleased Structures]]
[[Category: Liu, J.-H]]
[[Category: Wu, J.E]]
[[Category: Lin, H]]
[[Category: Chiu, S.W]]
[[Category: Yang, J.Y]]