5xzd - Revision history

OCA at 08:18, 22 November 2023

OCA — Wed, 22 Nov 2023 08:18:04 GMT

←Older revision		Revision as of 08:18, 22 November 2023
Line 1:		Line 1:

	==Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM==		==Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM==
-	<StructureSection load='5xzd' size='340' side='right' caption='[[5xzd]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5xzd' size='340' side='right'caption='[[5xzd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xzd]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rosni Rosni~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xzd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseovarius_nubinhibens_ISM Roseovarius nubinhibens ISM]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XZD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACY:ACETIC+ACID'>ACY</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ISM_05820 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=89187 ROSNI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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=5xzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzd OCA], [~~http~~://pdbe.org/5xzd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xzd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xzd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzd 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=5xzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzd OCA], [https://pdbe.org/5xzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xzd RCSB], [https://www.ebi.ac.uk/pdbsum/5xzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3SKA6_ROSNI A3SKA6_ROSNI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xzd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xzd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Enoyl-CoA hydratase 3D structures\|Enoyl-CoA hydratase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rosni~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cao, H Y~~]]	+	[[Category: Roseovarius nubinhibens ISM]]
-	[[Category: ~~Wang, P~~]]	+	[[Category: Cao HY]]
-	[[Category: ~~Zhang, Y Z~~]]	+	[[Category: Wang P]]
-	[[Category: ~~Acrylate]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Acryloyl-coa]]~~	+
-	~~[[Category: Hydratase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:22, 30 January 2019

OCA — Wed, 30 Jan 2019 09:22:57 GMT

←Older revision		Revision as of 09:22, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='5xzd' size='340' side='right' caption='[[5xzd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5xzd' size='340' side='right' caption='[[5xzd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xzd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xzd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rosni Rosni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ISM_05820 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89187 ROSNI])</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=5xzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzd OCA], [http://pdbe.org/5xzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzd RCSB], [http://www.ebi.ac.uk/pdbsum/5xzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzd 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=5xzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzd OCA], [http://pdbe.org/5xzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzd RCSB], [http://www.ebi.ac.uk/pdbsum/5xzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microbial cleavage of dimethylsulfoniopropionate (DMSP) producing dimethyl sulfide (DMS) and acrylate is an important step in global sulfur cycling. Acrylate is toxic for cells, and thus should be metabolized effectively for detoxification. There are two proposed pathways for acrylate metabolism in DMSP-catabolizing bacteria, the AcuN-AcuK pathway and the PrpE-AcuI pathway. AcuH is an acryloyl-CoA hydratase in DMSP-catabolizing bacteria and can catalyze the hydration of toxic acryloyl-CoA to produce 3-hydroxypropionyl-CoA (3-HP-CoA) in both the AcuN-AcuK pathway and the side path of the PrpE-AcuI pathway. However, the structure and catalytic mechanism of AcuH remain unknown. Here, we cloned a putative acuH gene from Roseovarius nubinhibens ISM, a typical DMSP-catabolizing bacterium, and expressed it (RdAcuH) in Escherichia coli. The activity of RdAcuH toward acryloyl-CoA was detected by liquid chromatography-mass spectrometry (LC-MS), which suggests that RdAcuH is a functional acryloyl-CoA hydratase. Then we solved the crystal structure of RdAcuH. Each asymmetric unit in the crystal of RdAcuH contains a dimer of trimers and each RdAcuH monomer contains an N-terminal domain (NTD) and a C-terminal domain (CTD). There are three active centers in each trimer and each active center is located between the NTD of a subunit and the CTD of the neighboring subunit. Site-directed mutagenesis analysis indicates that two highly conserved glutamates, Glu112 and Glu132, in the active center are essential for catalysis. Based on our results and previous research, we analyzed the catalytic mechanism of AcuH to hydrate acryloyl-CoA, in which Glu132 acts as the catalytic base. This study sheds light on the mechanism of acrylate detoxification in DMSP-catabolizing bacteria.
		+
		+	Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria.,Cao HY, Wang P, Xu F, Li PY, Xie BB, Qin QL, Zhang YZ, Li CY, Chen XL Front Microbiol. 2017 Oct 17;8:2034. doi: 10.3389/fmicb.2017.02034. eCollection, 2017. PMID:29089943<ref>PMID:29089943</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xzd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rosni]]
	[[Category: Cao, H Y]]		[[Category: Cao, H Y]]
	[[Category: Wang, P]]		[[Category: Wang, P]]

OCA at 07:29, 18 July 2018

OCA — Wed, 18 Jul 2018 07:29:07 GMT

←Older revision		Revision as of 07:29, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xzd is ~~ON HOLD until Paper Publication~~	+	==Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM==
-		+	<StructureSection load='5xzd' size='340' side='right' caption='[[5xzd]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Zhang~~, Y.Z., ~~Wang~~, P., ~~Cao~~, H.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xzd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZD FirstGlance]. <br>
-	~~Description: Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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=5xzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzd OCA], [http://pdbe.org/5xzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzd RCSB], [http://www.ebi.ac.uk/pdbsum/5xzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzd ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cao, H Y]]
	[[Category: Wang, P]]		[[Category: Wang, P]]
-	[[Category: Zhang, Y.Z]]	+	[[Category: Zhang, Y Z]]
-	[[Category: ~~Cao, H.Y~~]]	+	[[Category: Acrylate]]
		+	[[Category: Acryloyl-coa]]
		+	[[Category: Hydratase]]
		+	[[Category: Lyase]]

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

OCA — Wed, 27 Sep 2017 15:57:01 GMT

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

←Older revision

Revision as of 15:57, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xzd is ON HOLD until Paper Publication Authors: Zhang, Y.Z., Wang, P., Cao, H.Y. Description: Structure of acryloyl-CoA hydratase AcuH from Roseov...

OCA — Wed, 27 Sep 2017 15:56:59 GMT

New page: '''Unreleased structure''' The entry 5xzd is ON HOLD until Paper Publication Authors: Zhang, Y.Z., Wang, P., Cao, H.Y. Description: Structure of acryloyl-CoA hydratase AcuH from Roseov...

New page

'''Unreleased structure'''

The entry 5xzd is ON HOLD until Paper Publication

Authors: Zhang, Y.Z., Wang, P., Cao, H.Y.

Description: Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM
[[Category: Unreleased Structures]]
[[Category: Wang, P]]
[[Category: Zhang, Y.Z]]
[[Category: Cao, H.Y]]