5jfn - Revision history

OCA at 11:02, 6 September 2023

OCA — Wed, 06 Sep 2023 11:02:21 GMT

←Older revision		Revision as of 11:02, 6 September 2023
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	<StructureSection load='5jfn' size='340' side='right'caption='[[5jfn]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5jfn' size='340' side='right'caption='[[5jfn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jfn]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhopb Rhopb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JFN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jfn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_BisB18 Rhodopseudomonas palustris BisB18]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JFN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>~~, ~~<scene name='pdbligand=1VU:PROPIONYL+COENZYME+A'>1VU</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~6KM~~:~~S-PROPANOYL-L-CYSTEINE~~'>~~6KM~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=1VU:PROPIONYL+COENZYME+A'>1VU</scene>, <scene name='pdbligand=6KM:S-PROPANOYL-L-CYSTEINE'>6KM</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5jfl\|5jfl]]~~, ~~[[5jfm\|5jfm]]~~<~~/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=5jfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jfn OCA], [https://pdbe.org/5jfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jfn RCSB], [https://www.ebi.ac.uk/pdbsum/5jfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jfn ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">RPC_1174 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316056 RHOPB])~~</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=5jfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jfn OCA], [~~http~~://pdbe.org/5jfn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jfn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jfn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jfn ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q21A49_RHOPB Q21A49_RHOPB]
	<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: ~~Rhopb~~]]	+	[[Category: Rhodopseudomonas palustris BisB18]]
-	[[Category: Kerfeld~~, C A~~]]	+	[[Category: Kerfeld CA]]
-	[[Category: Sutter, M]]	+	[[Category: Sutter M]]
-	[[Category: Zarzycki, J]]	+	[[Category: Zarzycki J]]
-	~~[[Category: Acylating aldehyde dehydrogenase]]~~	+
-	~~[[Category: Bacterial microcompartment]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Propionylcysteine~~]]	+

OCA at 07:46, 10 June 2020

OCA — Wed, 10 Jun 2020 07:46:54 GMT

←Older revision		Revision as of 07:46, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated Cys330==		==Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated Cys330==
-	<StructureSection load='5jfn' size='340' side='right' caption='[[5jfn]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5jfn' size='340' side='right'caption='[[5jfn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jfn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JFN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhopb Rhopb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JFN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JFN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=1VU:PROPIONYL+COENZYME+A'>1VU</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=1VU:PROPIONYL+COENZYME+A'>1VU</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KM:S-PROPANOYL-L-CYSTEINE'>6KM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KM:S-PROPANOYL-L-CYSTEINE'>6KM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jfl\|5jfl]], [[5jfm\|5jfm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jfl\|5jfl]], [[5jfm\|5jfm]]</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=5jfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jfn OCA], [http://pdbe.org/5jfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jfn RCSB], [http://www.ebi.ac.uk/pdbsum/5jfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jfn ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPC_1174 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316056 RHOPB])</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=5jfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jfn OCA], [http://pdbe.org/5jfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jfn RCSB], [http://www.ebi.ac.uk/pdbsum/5jfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jfn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5jfn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jfn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rhopb]]
	[[Category: Kerfeld, C A]]		[[Category: Kerfeld, C A]]
	[[Category: Sutter, M]]		[[Category: Sutter, M]]

OCA at 09:34, 11 March 2017

OCA — Sat, 11 Mar 2017 09:34:43 GMT

←Older revision		Revision as of 09:34, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jfn is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated Cys330==
		+	<StructureSection load='5jfn' size='340' side='right' caption='[[5jfn]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jfn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JFN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=1VU:PROPIONYL+COENZYME+A'>1VU</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KM:S-PROPANOYL-L-CYSTEINE'>6KM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jfl\|5jfl]], [[5jfm\|5jfm]]</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=5jfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jfn OCA], [http://pdbe.org/5jfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jfn RCSB], [http://www.ebi.ac.uk/pdbsum/5jfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jfn ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO2-fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B12-dependent enzymes. Genes required to form BMCs are typically organized in gene clusters, which promoted their distribution across phyla by horizontal gene transfer. Recently, BMCs associated with glycyl radical enzymes (GREs) were discovered; these are widespread and comprise at least three functionally distinct types. Previously, we predicted one type of these GRE-associated microcompartments (GRMs) represents a B12-independent propanediol-utilizing BMC. Here we functionally and structurally characterize enzymes of the GRM of Rhodopseudomonas palustris BisB18 and demonstrate their concerted function in vitro. The GRM signature enzyme, the GRE, is a dedicated 1,2-propanediol dehydratase with a new type of intramolecular encapsulation peptide. It forms a complex with its activating enzyme and, in conjunction with an aldehyde dehydrogenase, converts 1,2-propanediol to propionyl-CoA. Notably, homologous GRMs are also encoded in pathogenic Escherichia coli strains. Our high-resolution crystal structures of the aldehyde dehydrogenase lead to a revised reaction mechanism. The successful in vitro reconstitution of a part of the GRM metabolism provides insights into the metabolic function and steps in the assembly of this BMC.

-	~~Authors~~:	+	In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.,Zarzycki J, Sutter M, Cortina NS, Erb TJ, Kerfeld CA Sci Rep. 2017 Feb 16;7:42757. doi: 10.1038/srep42757. PMID:28202954<ref>PMID:28202954</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jfn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kerfeld, C A]]
		+	[[Category: Sutter, M]]
		+	[[Category: Zarzycki, J]]
		+	[[Category: Acylating aldehyde dehydrogenase]]
		+	[[Category: Bacterial microcompartment]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Propionylcysteine]]

OCA at 15:21, 15 May 2016

OCA — Sun, 15 May 2016 15:21:59 GMT

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

-	The entry 5jfn is ON HOLD	+	The entry 5jfn is ON HOLD until Paper Publication

-	Authors: ~~Zarzycki, J., Sutter, M., Kerfeld, C.A.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sutter, M]]
-	[[Category: Kerfeld, C.A]]
-	[[Category: Zarzycki, J]]

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

OCA — Wed, 11 May 2016 01:58:34 GMT

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

←Older revision

Revision as of 01:58, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jfn is ON HOLD Authors: Zarzycki, J., Sutter, M., Kerfeld, C.A. Description: Category: Unreleased Structures Category: Sutter, M [[Catego...

OCA — Wed, 11 May 2016 01:58:33 GMT

New page: '''Unreleased structure''' The entry 5jfn is ON HOLD Authors: Zarzycki, J., Sutter, M., Kerfeld, C.A. Description: Category: Unreleased Structures Category: Sutter, M [[Catego...

New page

'''Unreleased structure'''

The entry 5jfn is ON HOLD

Authors: Zarzycki, J., Sutter, M., Kerfeld, C.A.

Description:
[[Category: Unreleased Structures]]
[[Category: Sutter, M]]
[[Category: Kerfeld, C.A]]
[[Category: Zarzycki, J]]