5iwh - Revision history

OCA at 10:35, 6 September 2023

OCA — Wed, 06 Sep 2023 10:35:14 GMT

←Older revision		Revision as of 10:35, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5iwh' size='340' side='right'caption='[[5iwh]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='5iwh' size='340' side='right'caption='[[5iwh]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iwh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29905 Atcc 29905~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IWH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iwh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IWH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.101Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[4px8\|4px8]], [[4w4g\|4w4g]], [[4ypb\|4ypb]], [[4yzv\|4yzv]], [[4mct\|4mct]], [[4mcx\|4mcx]], [[5ixl\|5ixl]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">higB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])~~</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=5iwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwh OCA], [https://pdbe.org/5iwh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iwh RCSB], [https://www.ebi.ac.uk/pdbsum/5iwh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwh ProSAT]</span></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=5iwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwh OCA], [~~http~~://pdbe.org/5iwh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iwh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iwh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwh ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HIGB_PROVU HIGB_PROVU]] Toxic component of a type II toxin-antitoxin (TA) module (PubMed:19423702, PubMed:24257752, PubMed:8645296). A ribosome-associated translation-dependent mRNA interferase. Inhibits translation by sequence-specific cleavage of mRNA. Prefers either in-frame or out-of-frame 5'-AAA-3' codons (lysine). Cleaves also the first three AAAs of stretches of four or more A sequences. 20% of codons containing AA are cleaved and occassionally cuts even at a single A (PubMed:19423702).<ref>PMID:19423702</ref> <ref>PMID:24257752</ref>	+	[https://www.uniprot.org/uniprot/HIGB_PROVU HIGB_PROVU] Toxic component of a type II toxin-antitoxin (TA) module (PubMed:19423702, PubMed:24257752, PubMed:8645296). A ribosome-associated translation-dependent mRNA interferase. Inhibits translation by sequence-specific cleavage of mRNA. Prefers either in-frame or out-of-frame 5'-AAA-3' codons (lysine). Cleaves also the first three AAAs of stretches of four or more A sequences. 20% of codons containing AA are cleaved and occassionally cuts even at a single A (PubMed:19423702).<ref>PMID:19423702</ref> <ref>PMID:24257752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 29905]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dunham, C M~~]]	+	[[Category: Proteus vulgaris]]
-	[[Category: ~~Marquez, J~~]]	+	[[Category: Dunham CM]]
-	[[Category: ~~Miles, S~~ J]]	+	[[Category: Marquez J]]
-	[[Category: ~~Repack, A A~~]]	+	[[Category: Miles SJ]]
-	[[Category: ~~Schureck, M A~~]]	+	[[Category: Repack AA]]
-	[[Category: ~~Bacterial toxin]]~~	+	[[Category: Schureck MA]]
-	~~[[Category: Biofilm]]~~	+
-	~~[[Category: Cell metabolism]]~~	+
-	~~[[Category: Energy metabolism]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Microbial pathogenesis]]~~	+
-	~~[[Category: Stress response]]~~	+
-	~~[[Category: Stringent response]]~~	+
-	~~[[Category: Translation control~~]]	+

OCA at 07:19, 10 June 2020

OCA — Wed, 10 Jun 2020 07:19:57 GMT

←Older revision		Revision as of 07:19, 10 June 2020
Line 1:		Line 1:

	==Structure of P. vulgaris HigB toxin delta H92==		==Structure of P. vulgaris HigB toxin delta H92==
-	<StructureSection load='5iwh' size='340' side='right' caption='[[5iwh]], [[Resolution\|resolution]] 1.10Å' scene=''>	+	<StructureSection load='5iwh' size='340' side='right'caption='[[5iwh]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iwh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWH OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IWH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iwh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IWH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4px8\|4px8]], [[4w4g\|4w4g]], [[4ypb\|4ypb]], [[4yzv\|4yzv]], [[4mct\|4mct]], [[4mcx\|4mcx]], [[5ixl\|5ixl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4px8\|4px8]], [[4w4g\|4w4g]], [[4ypb\|4ypb]], [[4yzv\|4yzv]], [[4mct\|4mct]], [[4mcx\|4mcx]], [[5ixl\|5ixl]]</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=5iwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwh OCA], [http://pdbe.org/5iwh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwh RCSB], [http://www.ebi.ac.uk/pdbsum/5iwh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwh ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">higB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</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=5iwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwh OCA], [http://pdbe.org/5iwh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwh RCSB], [http://www.ebi.ac.uk/pdbsum/5iwh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 29905]]
		+	[[Category: Large Structures]]
	[[Category: Dunham, C M]]		[[Category: Dunham, C M]]
	[[Category: Marquez, J]]		[[Category: Marquez, J]]

OCA at 15:21, 26 July 2016

OCA — Tue, 26 Jul 2016 15:21:54 GMT

←Older revision		Revision as of 15:21, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5iwh is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of P. vulgaris HigB toxin delta H92==
		+	<StructureSection load='5iwh' size='340' side='right' caption='[[5iwh]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5iwh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IWH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4px8\|4px8]], [[4w4g\|4w4g]], [[4ypb\|4ypb]], [[4yzv\|4yzv]], [[4mct\|4mct]], [[4mcx\|4mcx]], [[5ixl\|5ixl]]</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=5iwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwh OCA], [http://pdbe.org/5iwh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwh RCSB], [http://www.ebi.ac.uk/pdbsum/5iwh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwh ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HIGB_PROVU HIGB_PROVU]] Toxic component of a type II toxin-antitoxin (TA) module (PubMed:19423702, PubMed:24257752, PubMed:8645296). A ribosome-associated translation-dependent mRNA interferase. Inhibits translation by sequence-specific cleavage of mRNA. Prefers either in-frame or out-of-frame 5'-AAA-3' codons (lysine). Cleaves also the first three AAAs of stretches of four or more A sequences. 20% of codons containing AA are cleaved and occassionally cuts even at a single A (PubMed:19423702).<ref>PMID:19423702</ref> <ref>PMID:24257752</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteria encode multiple type II toxin-antitoxin modules that cleave ribosome-bound mRNAs in response to stress. All ribosome-dependent toxin family members structurally characterized to date adopt similar microbial RNase architectures despite possessing low sequence identities. Therefore, determining which residues are catalytically important in this specialized RNase family has been a challenge in the field. Structural studies of RelE and YoeB toxins bound to the ribosome provided significant insights but biochemical experiments with RelE were required to clearly demonstrate which residues are critical for acid-base catalysis of mRNA cleavage. Here, we solved an X-ray crystal structure of the wild-type, ribosome-dependent toxin HigB bound to the ribosome revealing potential catalytic residues proximal to the mRNA substrate. Using cell-based and biochemical assays, we further determined that HigB residues His54, Asp90, Tyr91 and His92 are critical for activity in vivo, while HigB H54A and Y91A variants have the largest effect on mRNA cleavage in vitro Comparison of X-ray crystal structures of two catalytically inactive HigB variants with 70S-HigB bound structures reveal that HigB active site residues undergo conformational rearrangements likely required for recognition of its mRNA substrate. These data support the emerging concept that ribosome-dependent toxins have diverse modes of mRNA recognition.

-	~~Authors~~:	+	Mechanism of endonuclease cleavage by the HigB toxin.,Schureck MA, Repack A, Miles SJ, Marquez J, Dunham CM Nucleic Acids Res. 2016 Jul 4. pii: gkw598. PMID:27378776<ref>PMID:27378776</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5iwh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dunham, C M]]
		+	[[Category: Marquez, J]]
		+	[[Category: Miles, S J]]
		+	[[Category: Repack, A A]]
		+	[[Category: Schureck, M A]]
		+	[[Category: Bacterial toxin]]
		+	[[Category: Biofilm]]
		+	[[Category: Cell metabolism]]
		+	[[Category: Energy metabolism]]
		+	[[Category: Hydrolase]]
		+	[[Category: Microbial pathogenesis]]
		+	[[Category: Stress response]]
		+	[[Category: Stringent response]]
		+	[[Category: Translation control]]

OCA at 14:49, 15 May 2016

OCA — Sun, 15 May 2016 14:49:15 GMT

←Older revision		Revision as of 14:49, 15 May 2016
Line 3:		Line 3:
	The entry 5iwh is ON HOLD until Paper Publication		The entry 5iwh is ON HOLD until Paper Publication

-	Authors: ~~Schureck, M.A., Repack, A.A., Miles, S.J., Marquez, J., Dunham, C.M.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Marquez, J]]
-	[[Category: Repack, A.A]]
-	[[Category: Miles, S.J]]
-	[[Category: Schureck, M.A]]
-	[[Category: Dunham, C.M]]

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

OCA — Wed, 11 May 2016 01:04:10 GMT

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

←Older revision

Revision as of 01:04, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5iwh is ON HOLD until Paper Publication Authors: Schureck, M.A., Repack, A.A., Miles, S.J., Marquez, J., Dunham, C.M. Description: [[Category: Unr...

OCA — Wed, 11 May 2016 01:04:09 GMT

New page: '''Unreleased structure''' The entry 5iwh is ON HOLD until Paper Publication Authors: Schureck, M.A., Repack, A.A., Miles, S.J., Marquez, J., Dunham, C.M. Description: [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5iwh is ON HOLD until Paper Publication

Authors: Schureck, M.A., Repack, A.A., Miles, S.J., Marquez, J., Dunham, C.M.

Description:
[[Category: Unreleased Structures]]
[[Category: Marquez, J]]
[[Category: Repack, A.A]]
[[Category: Miles, S.J]]
[[Category: Schureck, M.A]]
[[Category: Dunham, C.M]]