7nb5 - Revision history

OCA at 09:46, 15 April 2026

2026-04-15T09:46:42Z

← Older revision		Revision as of 09:46, 15 April 2026
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	<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7nb5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.13Å</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]] 2.13Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U68:(4-nitrophenyl)+(2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'>U68</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U68:(4-nitrophenyl)+(2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'>U68</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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60 degrees C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the alpha/beta-hydrolase superfamily. The canonical alpha/beta-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.

	Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.,Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sanchez-Costa M, Hidalgo A, Berenguer J, Gonzalez-Siso MI, Cruces J, Rua ML, Hermoso JA Comput Struct Biotechnol J. 2021 Feb 10;19:1214-1232. doi:, 10.1016/j.csbj.2021.01.047. eCollection 2021. PMID:33680362<ref>PMID:33680362</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7nb5" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Uncultured bacterium]]~~
	[[Category: Hermoso JA]]		[[Category: Hermoso JA]]
	[[Category: Miguel-Ruano V]]		[[Category: Miguel-Ruano V]]
	[[Category: Rivera I]]		[[Category: Rivera I]]

OCA at 17:18, 29 November 2023

2023-11-29T17:18:29Z

← Older revision		Revision as of 17:18, 29 November 2023
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	<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7nb5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7nb5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=U68:(4~~-~~nitrophenyl)+(~~2~~~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'>U68</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]] 2.13Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[7at0\|7at0]], [[7at2\|7at2]], [[7at4\|7at4]], [[7atd\|7atd]], [[7atf\|7atf]], [[7auy\|7auy]], [[7av5\|7av5]], [[7at3\|7at3]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U68:(4-nitrophenyl)+(2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'>U68</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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Uncultivated~~ bacterium]]		[[Category: Uncultured bacterium]]
	[[Category: Hermoso~~, J A~~]]		[[Category: Hermoso JA]]
	[[Category: Miguel-Ruano, V]]		[[Category: Miguel-Ruano V]]
	[[Category: Rivera, I]]		[[Category: Rivera I]]
	~~[[Category: Esterase hormone-sensitive lipase metagenome library crystal structure]]~~
	~~[[Category: Hydrolase~~]]

OCA at 07:01, 17 March 2021

2021-03-17T07:01:19Z

← Older revision		Revision as of 07:01, 17 March 2021
Line 1:		Line 1:

	==Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester==		==Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester==
	<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]]' scene=''>		<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7nb5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>
	</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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U68:(4-nitrophenyl)+(2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate'>U68</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7at0\|7at0]], [[7at2\|7at2]], [[7at4\|7at4]], [[7atd\|7atd]], [[7atf\|7atf]], [[7auy\|7auy]], [[7av5\|7av5]], [[7at3\|7at3]]</div></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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60 degrees C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the alpha/beta-hydrolase superfamily. The canonical alpha/beta-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.

			Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.,Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sanchez-Costa M, Hidalgo A, Berenguer J, Gonzalez-Siso MI, Cruces J, Rua ML, Hermoso JA Comput Struct Biotechnol J. 2021 Feb 10;19:1214-1232. doi:, 10.1016/j.csbj.2021.01.047. eCollection 2021. PMID:33680362<ref>PMID:33680362</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7nb5" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hermoso JA]]		[[Category: Uncultivated bacterium]]
	[[Category: Miguel-Ruano V]]		[[Category: Hermoso, J A]]
	[[Category: Rivera I]]		[[Category: Miguel-Ruano, V]]
			[[Category: Rivera, I]]
			[[Category: Esterase hormone-sensitive lipase metagenome library crystal structure]]
			[[Category: Hydrolase]]

OCA at 14:47, 3 March 2021

2021-03-03T14:47:21Z

← Older revision		Revision as of 14:47, 3 March 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7nb5 is ~~ON HOLD~~		==Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester==
			<StructureSection load='7nb5' size='340' side='right'caption='[[7nb5]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NB5 FirstGlance]. <br>
	~~Description~~:		</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=7nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nb5 OCA], [https://pdbe.org/7nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nb5 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Hermoso JA]]
			[[Category: Miguel-Ruano V]]
			[[Category: Rivera I]]

OCA: Protected "7nb5" [edit=sysop:move=sysop]

2021-02-03T09:34:31Z

Protected "7nb5" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:34, 3 February 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7nb5 is ON HOLD Authors: Description: Category: Unreleased Structures

2021-02-03T09:34:29Z

New page: '''Unreleased structure''' The entry 7nb5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7nb5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]