4xi8 - Revision history

OCA at 07:45, 27 September 2023

OCA — Wed, 27 Sep 2023 07:45:59 GMT

←Older revision		Revision as of 07:45, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bartonella_clarridgeiae_73 Bartonella clarridgeiae 73]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bartonella_clarridgeiae_73 Bartonella clarridgeiae 73]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.95Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [https://pdbe.org/4xi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [https://pdbe.org/4xi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:54, 14 June 2023

OCA — Wed, 14 Jun 2023 11:54:32 GMT

←Older revision		Revision as of 11:54, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='4xi8' size='340' side='right'caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='4xi8' size='340' side='right'caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Barc7 Barc7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bartonella_clarridgeiae_73 Bartonella clarridgeiae 73]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BARCL_0262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=696125 BARC7])</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [https://pdbe.org/4xi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [https://pdbe.org/4xi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E6YGF5_BARC7 E6YGF5_BARC7]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Barc7~~]]	+	[[Category: Bartonella clarridgeiae 73]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Structural genomic]]
-	[[Category: Bartonella clarridgeiae]]
-	[[Category: Bep5]]
-	[[Category: Protein binding]]
-	[[Category: Ssgcid]]
-	[[Category: Virb-translocated bartonella effector protein]]

OCA at 09:01, 8 September 2021

OCA — Wed, 08 Sep 2021 09:01:29 GMT

←Older revision		Revision as of 09:01, 8 September 2021
Line 1:		Line 1:

	==Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae==		==Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae==
-	<StructureSection load='4xi8' size='340' side='right' caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>	+	<StructureSection load='4xi8' size='340' side='right'caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Barc7 Barc7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Barc7 Barc7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BARCL_0262 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=696125 BARC7])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BARCL_0262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=696125 BARC7])</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [~~http~~://pdbe.org/4xi8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [https://pdbe.org/4xi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these, Bartonella effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three Bartonella lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The beta-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure-function analyses of the highly versatile FIC domains.
		+
		+	Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module.,Schirmer T, de Beer TAP, Tamegger S, Harms A, Dietz N, Dranow DM, Edwards TE, Myler PJ, Phan I, Dehio C Microorganisms. 2021 Jul 31;9(8). pii: microorganisms9081645. doi:, 10.3390/microorganisms9081645. PMID:34442725<ref>PMID:34442725</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xi8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Barc7]]		[[Category: Barc7]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Bartonella clarridgeiae]]		[[Category: Bartonella clarridgeiae]]

OCA at 09:34, 22 November 2017

OCA — Wed, 22 Nov 2017 09:34:39 GMT

←Older revision		Revision as of 09:34, 22 November 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae==		==Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae==
	<StructureSection load='4xi8' size='340' side='right' caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='4xi8' size='340' side='right' caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Barc7 Barc7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [http://pdbe.org/4xi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xi8 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BARCL_0262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=696125 BARC7])</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [http://pdbe.org/4xi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xi8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xi8 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Barc7]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Bartonella clarridgeiae]]		[[Category: Bartonella clarridgeiae]]

OCA at 20:22, 13 January 2016

OCA — Wed, 13 Jan 2016 20:22:47 GMT

←Older revision		Revision as of 20:22, 13 January 2016
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae==
-		+	<StructureSection load='4xi8' size='340' side='right' caption='[[4xi8]], [[Resolution\|resolution]] 2.95Å' scene=''>
-	~~The entry 4xi8 is ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xi8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XI8 FirstGlance]. <br>
-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4xi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xi8 OCA], [http://pdbe.org/4xi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xi8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xi8 PDBsum]</span></td></tr>
-	~~Description:~~ Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
-	[[Category: ~~Seattle~~ Structural ~~Genomics Center For Infectious Disease (~~Ssgcid)]]	+	</StructureSection>
		+	[[Category: Structural genomic]]
		+	[[Category: Bartonella clarridgeiae]]
		+	[[Category: Bep5]]
		+	[[Category: Protein binding]]
		+	[[Category: Ssgcid]]
		+	[[Category: Virb-translocated bartonella effector protein]]

OCA at 15:53, 21 January 2015

OCA — Wed, 21 Jan 2015 15:53:11 GMT

←Older revision		Revision as of 15:53, 21 January 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xi8 is ON HOLD	+	The entry 4xi8 is ON HOLD until Paper Publication

-	Authors: Seattle Structural Genomics Center for Infectious Disease	+	Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

-	Description: Crystal Structure of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae	+	Description: Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Seattle Structural Genomics Center For Infectious Disease]]	+	[[Category: Seattle Structural Genomics Center For Infectious Disease (Ssgcid)]]

OCA: Protected "4xi8" [edit=sysop:move=sysop]

OCA — Wed, 14 Jan 2015 12:45:40 GMT

Protected "4xi8" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 14 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xi8 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease Description: Crystal Structure of Bep5 protein (VirB-translocate...

OCA — Wed, 14 Jan 2015 12:45:39 GMT

New page: '''Unreleased structure''' The entry 4xi8 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease Description: Crystal Structure of Bep5 protein (VirB-translocate...

New page

'''Unreleased structure'''

The entry 4xi8 is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease

Description: Crystal Structure of Bep5 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae
[[Category: Unreleased Structures]]
[[Category: Seattle Structural Genomics Center For Infectious Disease]]