4rzy - Revision history

OCA at 12:57, 1 March 2024

OCA — Fri, 01 Mar 2024 12:57:28 GMT

←Older revision		Revision as of 12:57, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_lacuscaerulensis_ITI-1157 Ruegeria lacuscaerulensis ITI-1157]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_lacuscaerulensis_ITI-1157 Ruegeria lacuscaerulensis ITI-1157]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.949Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [https://pdbe.org/4rzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [https://www.ebi.ac.uk/pdbsum/4rzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzy ProSAT]</span></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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [https://pdbe.org/4rzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [https://www.ebi.ac.uk/pdbsum/4rzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzy ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria, and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds, but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO4 3- and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Furthermore, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.
-
-	Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.,Wang P, Chen XL, Li CY, Gao X, Zhu DY, Xie BB, Qin QL, Zhang XY, Su HN, Zhou BC, Xun LY, Zhang YZ Mol Microbiol. 2015 Jul 8. doi: 10.1111/mmi.13119. PMID:26154071<ref>PMID:26154071</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rzy" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:36, 15 March 2023

OCA — Wed, 15 Mar 2023 10:36:50 GMT

←Older revision		Revision as of 10:36, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='4rzy' size='340' side='right'caption='[[4rzy]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4rzy' size='340' side='right'caption='[[4rzy]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rueli Rueli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_lacuscaerulensis_ITI-1157 Ruegeria lacuscaerulensis ITI-1157]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SL1157_2466 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644107 RUELI])~~</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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [https://pdbe.org/4rzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [https://www.ebi.ac.uk/pdbsum/4rzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzy 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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [~~http~~://pdbe.org/4rzy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rzy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzy ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rueli~~]]	+	[[Category: Ruegeria lacuscaerulensis ITI-1157]]
-	[[Category: Wang, P]]	+	[[Category: Wang P]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	~~[[Category: Dmsp lyase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metallopeptidase-like dmsp lyase~~]]	+

OCA at 10:31, 1 May 2019

OCA — Wed, 01 May 2019 10:31:07 GMT

←Older revision		Revision as of 10:31, 1 May 2019
Line 1:		Line 1:
		+
	==Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES==		==Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES==
-	<StructureSection load='4rzy' size='340' side='right' caption='[[4rzy]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='4rzy' size='340' side='right'caption='[[4rzy]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rueli Rueli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [http://pdbe.org/4rzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [http://www.ebi.ac.uk/pdbsum/4rzy PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SL1157_2466 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644107 RUELI])</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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [http://pdbe.org/4rzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [http://www.ebi.ac.uk/pdbsum/4rzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rueli]]
	[[Category: Wang, P]]		[[Category: Wang, P]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]

OCA at 23:39, 21 October 2015

OCA — Wed, 21 Oct 2015 23:39:55 GMT

←Older revision		Revision as of 23:39, 21 October 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [http://www.ebi.ac.uk/pdbsum/4rzy PDBsum]</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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [http://pdbe.org/4rzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [http://www.ebi.ac.uk/pdbsum/4rzy PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4rzy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:01, 5 August 2015

OCA — Wed, 05 Aug 2015 20:01:29 GMT

←Older revision		Revision as of 20:01, 5 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES==
		+	<StructureSection load='4rzy' size='340' side='right' caption='[[4rzy]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rzy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=4rzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rzy RCSB], [http://www.ebi.ac.uk/pdbsum/4rzy PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria, and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds, but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO4 3- and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Furthermore, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.

-	~~The entry 4rzy is ON HOLD until Paper Publication~~	+	Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.,Wang P, Chen XL, Li CY, Gao X, Zhu DY, Xie BB, Qin QL, Zhang XY, Su HN, Zhou BC, Xun LY, Zhang YZ Mol Microbiol. 2015 Jul 8. doi: 10.1111/mmi.13119. PMID:26154071<ref>PMID:26154071</ref>

-	~~Authors: Zhang~~, Y.~~, Wang, P~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wang, P]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
-	[[Category: ~~Wang, P~~]]	+	[[Category: Dmsp lyase]]
		+	[[Category: Lyase]]
		+	[[Category: Metallopeptidase-like dmsp lyase]]

OCA at 12:49, 7 February 2015

OCA — Sat, 07 Feb 2015 12:49:23 GMT

←Older revision		Revision as of 12:49, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rzy is ON HOLD	+	The entry 4rzy is ON HOLD until Paper Publication

	Authors: Zhang, Y., Wang, P.		Authors: Zhang, Y., Wang, P.

OCA at 10:57, 14 January 2015

OCA — Wed, 14 Jan 2015 10:57:03 GMT

←Older revision		Revision as of 10:57, 14 January 2015
Line 3:		Line 3:
	The entry 4rzy is ON HOLD		The entry 4rzy is ON HOLD

-	Authors: ~~Yuzhong~~ Zhang , ~~Peng~~ Wang	+	Authors: Zhang, Y., Wang, P.

	Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES		Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Yuzhong~~ Zhang , ~~Peng~~ Wang]]	+	[[Category: Zhang, Y]]
		+	[[Category: Wang, P]]

OCA: Protected "4rzy" [edit=sysop:move=sysop]

OCA — Wed, 07 Jan 2015 13:49:18 GMT

Protected "4rzy" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:49, 7 January 2015

OCA: New page: '''Unreleased structure''' The entry 4rzy is ON HOLD Authors: Yuzhong Zhang , Peng Wang Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase...

OCA — Wed, 07 Jan 2015 13:49:17 GMT

New page: '''Unreleased structure''' The entry 4rzy is ON HOLD Authors: Yuzhong Zhang , Peng Wang Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase...

New page

'''Unreleased structure'''

The entry 4rzy is ON HOLD

Authors: Yuzhong Zhang , Peng Wang

Description: Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES
[[Category: Unreleased Structures]]
[[Category: Yuzhong Zhang , Peng Wang]]