6bas - Revision history

OCA at 14:37, 4 October 2023

2023-10-04T14:37:12Z

← Older revision		Revision as of 14:37, 4 October 2023
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	<StructureSection load='6bas' size='340' side='right'caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>		<StructureSection load='6bas' size='340' side='right'caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BAS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BAS 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.194Å</td></tr>
	~~<tr~~ id~~='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class~~="~~sblockDat~~">[[~~6bar~~\|~~6bar~~]]</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"~~>rodA, TTHA1241 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~300852 THET8])</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=6bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bas OCA], [https://pdbe.org/6bas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bas RCSB], [https://www.ebi.ac.uk/pdbsum/6bas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bas ProSAT]</span></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Peptidoglycan_glycosyltransferase Peptidoglycan glycosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.129 2.4.1.129]~~ </~~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=6bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bas OCA], [~~http~~://pdbe.org/6bas PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bas RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bas PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bas ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/Q5SIX3_THET8 Q5SIX3_THET8]] Peptidoglycan polymerase that is essential for cell wall elongation.[HAMAP-Rule:MF_02079]		[https://www.uniprot.org/uniprot/Q5SIX3_THET8 Q5SIX3_THET8] Peptidoglycan polymerase that is essential for cell wall elongation.[HAMAP-Rule:MF_02079]
	<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: ~~Peptidoglycan glycosyltransferase]]~~		[[Category: Thermus thermophilus HB8]]
	~~[[Category: Thet8~~]]		[[Category: Bernhardt TG]]
	[[Category: Bernhardt~~, T G~~]]		[[Category: Brock K]]
	[[Category: Brock, K]]		[[Category: Dobihal G]]
	[[Category: Dobihal, G]]		[[Category: Green AG]]
	[[Category: Green~~, A G~~]]		[[Category: Hopf TA]]
	[[Category: Hopf~~, T A~~]]		[[Category: Kruse AC]]
	[[Category: Kruse~~, A C~~]]		[[Category: Marks DS]]
	[[Category: Marks~~, D S~~]]		[[Category: Meeske AJ]]
	[[Category: Meeske~~, A J~~]]		[[Category: Rohs PDA]]
	[[Category: Rohs~~, P D.A~~]]		[[Category: Rudner DZ]]
	[[Category: Rudner~~, D Z~~]]		[[Category: Sjodt M]]
	[[Category: Sjodt, M]]
	~~[[Category: Elongasome]]~~
	~~[[Category: Shape elogation division and sporulation]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transmembrane protein~~]]

OCA at 17:44, 11 December 2019

2019-12-11T17:44:37Z

← Older revision		Revision as of 17:44, 11 December 2019
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	==Crystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)==		==Crystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)==
	<StructureSection load='6bas' size='340' side='right' caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>		<StructureSection load='6bas' size='340' side='right'caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BAS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BAS FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6bas" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bas" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Glycosyltransferase 3D structures\|Glycosyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Peptidoglycan glycosyltransferase]]		[[Category: Peptidoglycan glycosyltransferase]]
	[[Category: Thet8]]		[[Category: Thet8]]

OCA at 14:16, 11 April 2018

2018-04-11T14:16:30Z

← Older revision		Revision as of 14:16, 11 April 2018
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	<StructureSection load='6bas' size='340' side='right' caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>		<StructureSection load='6bas' size='340' side='right' caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BAS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BAS 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"><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">[[6bar\|6bar]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6bar\|6bar]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rodA, TTHA1241 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidoglycan_glycosyltransferase Peptidoglycan glycosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.129 2.4.1.129] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidoglycan_glycosyltransferase Peptidoglycan glycosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.129 2.4.1.129] </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=6bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bas OCA], [http://pdbe.org/6bas PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bas RCSB], [http://www.ebi.ac.uk/pdbsum/6bas PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bas 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=6bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bas OCA], [http://pdbe.org/6bas PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bas RCSB], [http://www.ebi.ac.uk/pdbsum/6bas PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bas ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q5SIX3_THET8 Q5SIX3_THET8]] Peptidoglycan polymerase that is essential for cell wall elongation.[HAMAP-Rule:MF_02079]		[[http://www.uniprot.org/uniprot/Q5SIX3_THET8 Q5SIX3_THET8]] Peptidoglycan polymerase that is essential for cell wall elongation.[HAMAP-Rule:MF_02079]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The shape, elongation, division and sporulation (SEDS) proteins are a large family of ubiquitous and essential transmembrane enzymes with critical roles in bacterial cell wall biology. The exact function of SEDS proteins was for a long time poorly understood, but recent work has revealed that the prototypical SEDS family member RodA is a peptidoglycan polymerase-a role previously attributed exclusively to members of the penicillin-binding protein family. This discovery has made RodA and other SEDS proteins promising targets for the development of next-generation antibiotics. However, little is known regarding the molecular basis of SEDS activity, and no structural data are available for RodA or any homologue thereof. Here we report the crystal structure of Thermus thermophilus RodA at a resolution of 2.9 A, determined using evolutionary covariance-based fold prediction to enable molecular replacement. The structure reveals a ten-pass transmembrane fold with large extracellular loops, one of which is partially disordered. The protein contains a highly conserved cavity in the transmembrane domain, reminiscent of ligand-binding sites in transmembrane receptors. Mutagenesis experiments in Bacillus subtilis and Escherichia coli show that perturbation of this cavity abolishes RodA function both in vitro and in vivo, indicating that this cavity is catalytically essential. These results provide a framework for understanding bacterial cell wall synthesis and SEDS protein function.

			Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.,Sjodt M, Brock K, Dobihal G, Rohs PDA, Green AG, Hopf TA, Meeske AJ, Srisuknimit V, Kahne D, Walker S, Marks DS, Bernhardt TG, Rudner DZ, Kruse AC Nature. 2018 Apr 5;556(7699):118-121. doi: 10.1038/nature25985. Epub 2018 Mar 28. PMID:29590088<ref>PMID:29590088</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6bas" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Peptidoglycan glycosyltransferase]]		[[Category: Peptidoglycan glycosyltransferase]]
			[[Category: Thet8]]
	[[Category: Bernhardt, T G]]		[[Category: Bernhardt, T G]]
	[[Category: Brock, K]]		[[Category: Brock, K]]

OCA at 06:37, 28 March 2018

2018-03-28T06:37:17Z

← Older revision		Revision as of 06:37, 28 March 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6bas is ~~ON HOLD~~		==Crystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)==
			<StructureSection load='6bas' size='340' side='right' caption='[[6bas]], [[Resolution\|resolution]] 3.19Å' scene=''>
	~~Authors~~: ~~Sjodt~~, M.~~, Brock, K~~.~~, Dobihal, G~~.~~, Rohs, P~~.D.A.~~, Green, A~~.G.~~, Hopf, T~~.A.~~, Meeske, A~~.J., ~~Marks, D~~.S., ~~Bernhardt~~, T.G., ~~Rudner, D~~.Z., ~~Kruse, A~~.C.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6bas]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BAS FirstGlance]. <br>
	~~Description: Crystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)~~		</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>
	[[~~Category~~: ~~Unreleased Structures~~]]		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6bar\|6bar]]</td></tr>
	[[Category: ~~Rohs, P.D.A~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidoglycan_glycosyltransferase Peptidoglycan glycosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.129 2.4.1.129] </span></td></tr>
	[[Category: ~~Meeske~~, ~~A.J~~]]		<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=6bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bas OCA], [http://pdbe.org/6bas PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bas RCSB], [http://www.ebi.ac.uk/pdbsum/6bas PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bas ProSAT]</span></td></tr>
	[[Category: ~~Green~~, ~~A.G~~]]		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q5SIX3_THET8 Q5SIX3_THET8]] Peptidoglycan polymerase that is essential for cell wall elongation.[HAMAP-Rule:MF_02079]
			__TOC__
			</StructureSection>
			[[Category: Peptidoglycan glycosyltransferase]]
			[[Category: Bernhardt, T G]]
			[[Category: Brock, K]]
	[[Category: Dobihal, G]]		[[Category: Dobihal, G]]
			[[Category: Green, A G]]
			[[Category: Hopf, T A]]
			[[Category: Kruse, A C]]
			[[Category: Marks, D S]]
			[[Category: Meeske, A J]]
			[[Category: Rohs, P D.A]]
			[[Category: Rudner, D Z]]
	[[Category: Sjodt, M]]		[[Category: Sjodt, M]]
	[[Category: ~~Marks, D.S~~]]		[[Category: Elongasome]]
	[[Category: ~~Brock, K~~]]		[[Category: Shape elogation division and sporulation]]
	[[Category: ~~Kruse, A.C~~]]		[[Category: Transferase]]
	[[Category: ~~Bernhardt, T.G]]~~		[[Category: Transmembrane protein]]
	~~[[Category: Hopf, T.A]]~~
	~~[[Category: Rudner, D.Z~~]]

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

2017-10-25T05:49:20Z

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

← Older revision	Revision as of 05:49, 25 October 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6bas is ON HOLD Authors: Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Marks, D.S., Bernhardt, T.G., Rudne...

2017-10-25T05:49:19Z

New page: '''Unreleased structure''' The entry 6bas is ON HOLD Authors: Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Marks, D.S., Bernhardt, T.G., Rudne...

New page

'''Unreleased structure'''

The entry 6bas is ON HOLD

Authors: Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Marks, D.S., Bernhardt, T.G., Rudner, D.Z., Kruse, A.C.

Description: Crystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)
[[Category: Unreleased Structures]]
[[Category: Rohs, P.D.A]]
[[Category: Meeske, A.J]]
[[Category: Green, A.G]]
[[Category: Dobihal, G]]
[[Category: Sjodt, M]]
[[Category: Marks, D.S]]
[[Category: Brock, K]]
[[Category: Kruse, A.C]]
[[Category: Bernhardt, T.G]]
[[Category: Hopf, T.A]]
[[Category: Rudner, D.Z]]