5doo - Revision history

OCA at 21:53, 28 June 2023

2023-06-28T21:53:08Z

←Older revision		Revision as of 21:53, 28 June 2023
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	<StructureSection load='5doo' size='340' side='right'caption='[[5doo]], [[Resolution\|resolution]] 3.13Å' scene=''>		<StructureSection load='5doo' size='340' side='right'caption='[[5doo]], [[Resolution\|resolution]] 3.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5doo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ricty Ricty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DOO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5doo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rickettsia_typhi_str._Wilmington Rickettsia typhi str. Wilmington]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DOO 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]] 3.133Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5dpl\|5dpl]], [[5dpd\|5dpd]], [[5do0\|5do0]], [[5dnk\|5dnk]]</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">RT0101 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=257363 RICTY])~~</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=5doo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5doo OCA], [https://pdbe.org/5doo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5doo RCSB], [https://www.ebi.ac.uk/pdbsum/5doo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5doo 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=5doo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5doo OCA], [~~http~~://pdbe.org/5doo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5doo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5doo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5doo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q68XQ5_RICTY Q68XQ5_RICTY]
	<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: ~~Ricty~~]]	+	[[Category: Rickettsia typhi str. Wilmington]]
-	[[Category: Abeykoon, A]]	+	[[Category: Abeykoon A]]
-	[[Category: Buchanan~~, S K~~]]	+	[[Category: Buchanan SK]]
-	[[Category: He, Y]]	+	[[Category: He Y]]
-	[[Category: Noinaj, N]]	+	[[Category: Noinaj N]]
-	[[Category: Yang~~, D C]]~~	+	[[Category: Yang DC]]
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Sam binding protein]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:12, 8 April 2020

2020-04-08T08:12:38Z

←Older revision		Revision as of 08:12, 8 April 2020
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	==The structure of PKMT2 from Rickettsia typhi==		==The structure of PKMT2 from Rickettsia typhi==
-	<StructureSection load='5doo' size='340' side='right' caption='[[5doo]], [[Resolution\|resolution]] 3.13Å' scene=''>	+	<StructureSection load='5doo' size='340' side='right'caption='[[5doo]], [[Resolution\|resolution]] 3.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5doo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DOO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5doo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ricty Ricty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DOO 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dpl\|5dpl]], [[5dpd\|5dpd]], [[5do0\|5do0]], [[5dnk\|5dnk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dpl\|5dpl]], [[5dpd\|5dpd]], [[5do0\|5do0]], [[5dnk\|5dnk]]</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=5doo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5doo OCA], [http://pdbe.org/5doo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5doo RCSB], [http://www.ebi.ac.uk/pdbsum/5doo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5doo ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RT0101 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=257363 RICTY])</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=5doo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5doo OCA], [http://pdbe.org/5doo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5doo RCSB], [http://www.ebi.ac.uk/pdbsum/5doo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5doo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ricty]]
	[[Category: Abeykoon, A]]		[[Category: Abeykoon, A]]
	[[Category: Buchanan, S K]]		[[Category: Buchanan, S K]]

OCA at 16:02, 10 August 2016

2016-08-10T16:02:52Z

←Older revision		Revision as of 16:02, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5doo is ~~ON HOLD until Paper~~ Publication	+	==The structure of PKMT2 from Rickettsia typhi==
		+	<StructureSection load='5doo' size='340' side='right' caption='[[5doo]], [[Resolution\|resolution]] 3.13Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5doo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DOO 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dpl\|5dpl]], [[5dpd\|5dpd]], [[5do0\|5do0]], [[5dnk\|5dnk]]</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=5doo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5doo OCA], [http://pdbe.org/5doo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5doo RCSB], [http://www.ebi.ac.uk/pdbsum/5doo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5doo ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rickettsia belong to a family of Gram-negative obligate-intracellular infectious bacteria that are the causative agents of typhus and spotted fever. Outer membrane protein B (OmpB) occurs in all rickettsial species, serves as a protective envelope, mediates host cell adhesion and invasion, and is a major immunodominant antigen. OmpBs from virulent strains contain multiple trimethylated lysine residues, while avirulent strain contains mainly monomethyllysine. Two protein lysine methyltransferases that catalyze methylation of recombinant OmpB at multiple sites with varying sequences have been identified and overexpressed. PKMT1 catalyzes predominantly monomethylation, while PKMT2 catalyzes mainly trimethylation. Rickettsial PKMT1 and PKMT2 are unusual in that their primary substrate appears to be limited to OmpB and both are capable of methylating multiple lysyl residues with broad sequence specificity. Here we report the crystal structures of PKMT1 from R. prowazekii and PKMT2 from R. typhi, both the apo-form and in complex with its cofactor AdoMet or AdoHcy. The structure of PKMT1 in complex with AdoHcy is solved to a resolution of 1.9 A. Both enzymes are dimeric, with each monomer containing an AdoMet binding domain with a core Rossmann fold, a dimerization domain, a middle domain, a C-terminal domain, and a centrally located open cavity. Based on the crystal structures, residues involved in catalysis, cofactor binding and substrate interactions were examined using site-directed mutagenesis followed by steady-state kinetic analysis to ascertain their catalytic functions in solution. Together, our data reveal new structural and mechanistic insights on how rickettsial methyltransferases catalyze OmpB methylation.

-	~~Authors: Noinaj, N~~., Abeykoon, A., He, Y., ~~Yang~~, ~~D.C.~~, Buchanan, S.K.	+	Structural Insights into Substrate Recognition and Catalysis in OmpB by Protein Lysine Methyltransferases from Rickettsia.,Abeykoon AH, Noinaj N, Choi BE, Wise L, He Y, Chao CC, Wang G, Gucek M, Ching WM, Chock PB, Buchanan SK, Yang DC J Biol Chem. 2016 Jul 29. pii: jbc.M116.723460. PMID:27474738<ref>PMID:27474738</ref>

-	~~Description: The structure~~ of ~~PKMT2 from Rickettsia typhi~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Buchanan,~~ S.~~K]]~~	+	<div class="pdbe-citations 5doo" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Yang, D.C]]~~	+	== References ==
-	~~[[Category: He, Y]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Abeykoon, A]]		[[Category: Abeykoon, A]]
		+	[[Category: Buchanan, S K]]
		+	[[Category: He, Y]]
	[[Category: Noinaj, N]]		[[Category: Noinaj, N]]
		+	[[Category: Yang, D C]]
		+	[[Category: Methylation]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Sam binding protein]]
		+	[[Category: Transferase]]

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

2015-09-30T13:17:29Z

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

←Older revision

Revision as of 13:17, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5doo is ON HOLD until Paper Publication Authors: Noinaj, N., Abeykoon, A., He, Y., Yang, D.C., Buchanan, S.K. Description: The structure of PKMT2 f...

2015-09-30T13:17:28Z

New page: '''Unreleased structure''' The entry 5doo is ON HOLD until Paper Publication Authors: Noinaj, N., Abeykoon, A., He, Y., Yang, D.C., Buchanan, S.K. Description: The structure of PKMT2 f...

New page

'''Unreleased structure'''

The entry 5doo is ON HOLD until Paper Publication

Authors: Noinaj, N., Abeykoon, A., He, Y., Yang, D.C., Buchanan, S.K.

Description: The structure of PKMT2 from Rickettsia typhi
[[Category: Unreleased Structures]]
[[Category: Buchanan, S.K]]
[[Category: Yang, D.C]]
[[Category: He, Y]]
[[Category: Abeykoon, A]]
[[Category: Noinaj, N]]