6a55 - Revision history

OCA at 09:18, 22 November 2023

2023-11-22T09:18:45Z

←Older revision		Revision as of 09:18, 22 November 2023
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	<StructureSection load='6a55' size='340' side='right'caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6a55' size='340' side='right'caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Candidatus_pelagibacter_ubique_htcc1062~~ Candidatus ~~pelagibacter~~ ubique ~~htcc1062~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Pelagibacter_ubique_HTCC1062 Candidatus Pelagibacter ubique HTCC1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A55 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.6Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAR11_0394 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=335992 Candidatus Pelagibacter ubique HTCC1062])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6a55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a55 OCA], [~~http~~://pdbe.org/6a55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a55 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=6a55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a55 OCA], [https://pdbe.org/6a55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a55 RCSB], [https://www.ebi.ac.uk/pdbsum/6a55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a55 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4FNM4_PELUB Q4FNM4_PELUB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candidatus ~~pelagibacter~~ ubique ~~htcc1062~~]]	+	[[Category: Candidatus Pelagibacter ubique HTCC1062]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li~~, C Y~~]]	+	[[Category: Li CY]]
-	[[Category: Zhang~~, Y Z]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Dmsp lyase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:45, 24 April 2019

2019-04-24T07:45:09Z

←Older revision		Revision as of 07:45, 24 April 2019
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	==Crystal structure of DddK mutant Y122A==		==Crystal structure of DddK mutant Y122A==
-	<StructureSection load='6a55' size='340' side='right' caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='6a55' size='340' side='right'caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_pelagibacter_ubique_htcc1062 Candidatus pelagibacter ubique htcc1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A55 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_pelagibacter_ubique_htcc1062 Candidatus pelagibacter ubique htcc1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A55 FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Candidatus pelagibacter ubique htcc1062]]		[[Category: Candidatus pelagibacter ubique htcc1062]]
		+	[[Category: Large Structures]]
	[[Category: Li, C Y]]		[[Category: Li, C Y]]
	[[Category: Zhang, Y Z]]		[[Category: Zhang, Y Z]]
	[[Category: Dmsp lyase]]		[[Category: Dmsp lyase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 15:53, 27 February 2019

2019-02-27T15:53:13Z

←Older revision		Revision as of 15:53, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='6a55' size='340' side='right' caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6a55' size='340' side='right' caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_pelagibacter_ubique_htcc1062 Candidatus pelagibacter ubique htcc1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAR11_0394 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=335992 Candidatus Pelagibacter ubique HTCC1062])</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=6a55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a55 OCA], [http://pdbe.org/6a55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a55 RCSB], [http://www.ebi.ac.uk/pdbsum/6a55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a55 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=6a55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a55 OCA], [http://pdbe.org/6a55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a55 RCSB], [http://www.ebi.ac.uk/pdbsum/6a55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a55 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei, and thus may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria, many of which contain the DMSP lyase DddK and whose dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the beta-elimination reaction of DMSP. This Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its' neighboring His96. To further probe into this mechanism, we purified and characterized the same DddK protein from Pelagibacter ubique HTCC1062 and determined the crystal structures of wild type DddK, and mutants Y64A and Y122A, where the latter is complexed with DMSP. Structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its' deprotonation. Our data indicates an active water in the active site of DddK plays an important role in the deprotonation of Tyr64, and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding on DMS generation by SAR11 bacteria.Importance The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which forms cloud condensation nuclei that influence the reflectivity of clouds and thereby global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, many of which contain DMSP lyase DddK to cleave DMSP generating DMS. In this study, we revealed the catalytic mechanism of DddK based on structural analyses and mutational assays, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.
		+
		+	Structure-function analysis indicates that an active site water participates in dimethylsulfoniopropionate cleavage by DddK.,Peng M, Chen XL, Zhang D, Wang XJ, Wang N, Wang P, Todd JD, Zhang YZ, Li CY Appl Environ Microbiol. 2019 Feb 15. pii: AEM.03127-18. doi:, 10.1128/AEM.03127-18. PMID:30770407<ref>PMID:30770407</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a55" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candidatus pelagibacter ubique htcc1062]]
	[[Category: Li, C Y]]		[[Category: Li, C Y]]
	[[Category: Zhang, Y Z]]		[[Category: Zhang, Y Z]]
	[[Category: Dmsp lyase]]		[[Category: Dmsp lyase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 06:36, 21 February 2019

2019-02-21T06:36:21Z

←Older revision		Revision as of 06:36, 21 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a55 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of DddK mutant Y122A==
-		+	<StructureSection load='6a55' size='340' side='right' caption='[[6a55]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~: ~~Zhang~~, Y.Z., Li, C.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a55]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A55 FirstGlance]. <br>
-	~~Description: Crystal structure of DddK mutant Y122A~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6a55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a55 OCA], [http://pdbe.org/6a55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a55 RCSB], [http://www.ebi.ac.uk/pdbsum/6a55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a55 ProSAT]</span></td></tr>
-	[[Category: Zhang, Y.Z]]	+	</table>
-	[[Category: ~~Li, C.Y~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, C Y]]
		+	[[Category: Zhang, Y Z]]
		+	[[Category: Dmsp lyase]]
		+	[[Category: Lyase]]

OCA at 05:31, 4 July 2018

2018-07-04T05:31:51Z

←Older revision		Revision as of 05:31, 4 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a55 is ON HOLD	+	The entry 6a55 is ON HOLD until Paper Publication

	Authors: Zhang, Y.Z., Li, C.Y.		Authors: Zhang, Y.Z., Li, C.Y.

OCA: Protected "6a55" [edit=sysop:move=sysop]

2018-06-27T03:56:02Z

Protected "6a55" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:56, 27 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a55 is ON HOLD Authors: Zhang, Y.Z., Li, C.Y. Description: Crystal structure of DddK mutant Y122A Category: Unreleased Structures [[Category: ...

2018-06-27T03:56:00Z

New page: '''Unreleased structure''' The entry 6a55 is ON HOLD Authors: Zhang, Y.Z., Li, C.Y. Description: Crystal structure of DddK mutant Y122A Category: Unreleased Structures [[Category: ...

New page

'''Unreleased structure'''

The entry 6a55 is ON HOLD

Authors: Zhang, Y.Z., Li, C.Y.

Description: Crystal structure of DddK mutant Y122A
[[Category: Unreleased Structures]]
[[Category: Zhang, Y.Z]]
[[Category: Li, C.Y]]