OCA at 20:52, 24 January 2018

2018-01-24T20:52:30Z

←Older revision		Revision as of 20:52, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5xky' size='340' side='right' caption='[[5xky]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5xky' size='340' side='right' caption='[[5xky]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xky]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_bereziniae_niph_3 Acinetobacter bereziniae niph 3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xkx\|5xkx]], [[5xkz\|5xkz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xkx\|5xkx]], [[5xkz\|5xkz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F963_02809 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1217651 Acinetobacter bereziniae NIPH 3])</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=5xky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xky OCA], [http://pdbe.org/5xky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xky RCSB], [http://www.ebi.ac.uk/pdbsum/5xky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xky 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=5xky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xky OCA], [http://pdbe.org/5xky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xky RCSB], [http://www.ebi.ac.uk/pdbsum/5xky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xky ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The marine osmolyte dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Bacterial DMSP lyases cleave DMSP, producing acrylate and dimethyl sulfide (DMS), a climate-active gas with roles in global sulfur cycling and atmospheric chemistry. DddY is the only known periplasmic DMSP lyase and is present in beta-, gamma-, delta- and epsilon-proteobacteria. Unlike other known DMSP lyases, DddY has not been classified into a protein superfamily, and its structure and catalytic mechanism are unknown. Here, we determined the crystal structure of DddY from the gamma-proteobacterium Acinetobacter bereziniae originally isolated from human clinical specimens. This structure revealed that DddY contains a cap domain and a catalytic domain with a Zn(2+) bound at its active site. We also observed that the DddY catalytic domain adopts a typical beta-barrel fold and contains two conserved cupin motifs. Therefore, we concluded that DddY should belong to the cupin superfamily. Using structural and mutational analyses, we identified key residues involved in Zn(2+) coordination, DMSP binding and the catalysis of DMSP cleavage, enabling elucidation of the catalytic mechanism, in which the residue Tyr271 of DddY acts as a general base to attack DMSP. Moreover, sequence analysis suggested that this proposed mechanism is common to DddY proteins from beta-, gamma-, delta- and epsilon-proteobacteria. The DddY structure and proposed catalytic mechanism provide a better understanding of how DMSP is catabolized to generate the important climate-active gas DMS.
		+
		+	Mechanistic Insights into Dimethylsulfoniopropionate Lyase DddY, a New Member of the Cupin Superfamily.,Li CY, Zhang D, Chen XL, Wang P, Shi WL, Li PY, Zhang XY, Qin QL, Todd JD, Zhang YZ J Mol Biol. 2017 Dec 8;429(24):3850-3862. doi: 10.1016/j.jmb.2017.10.022. Epub, 2017 Oct 26. PMID:29106934<ref>PMID:29106934</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xky" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acinetobacter bereziniae niph 3]]
	[[Category: Li, C Y]]		[[Category: Li, C Y]]
	[[Category: Zhang, Y Z]]		[[Category: Zhang, Y Z]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 06:32, 1 November 2017

2017-11-01T06:32:54Z

←Older revision		Revision as of 06:32, 1 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xky is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of DddY Se derivative==
-		+	<StructureSection load='5xky' size='340' side='right' caption='[[5xky]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xky]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKY FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xkx\|5xkx]], [[5xkz\|5xkz]]</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=5xky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xky OCA], [http://pdbe.org/5xky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xky RCSB], [http://www.ebi.ac.uk/pdbsum/5xky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xky ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, C Y]]
		+	[[Category: Zhang, Y Z]]
		+	[[Category: Lyase]]

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

2017-05-17T14:54:44Z

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

←Older revision

Revision as of 14:54, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xky is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-05-17T14:54:43Z

New page: '''Unreleased structure''' The entry 5xky is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xky is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

5xky - Revision history

OCA at 20:52, 24 January 2018

OCA at 06:32, 1 November 2017

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

OCA: New page: '''Unreleased structure''' The entry 5xky is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures