6qpa - Revision history

OCA at 12:05, 24 January 2024

OCA — Wed, 24 Jan 2024 12:05:29 GMT

←Older revision		Revision as of 12:05, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6qpa' size='340' side='right'caption='[[6qpa]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6qpa' size='340' side='right'caption='[[6qpa]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qpa]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QPA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qpa]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Halothiobacillus_neapolitanus_c2 Halothiobacillus neapolitanus c2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QPA 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=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Sulfur_oxygenase/reductase Sulfur oxygenase/reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.55 1.13.11.55]~~ </~~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=6qpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qpa OCA], [https://pdbe.org/6qpa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qpa RCSB], [https://www.ebi.ac.uk/pdbsum/6qpa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qpa 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=6qpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qpa OCA], [~~http~~://pdbe.org/6qpa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qpa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qpa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qpa ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/D0L035_HALNC D0L035_HALNC]
-	A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium Halothiobacillus neapolitanus (HnSOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The HnSOR purified from Escherichia coli after heterologous gene expression had a temperature range of activity of 10 to 99 degrees C with an optimum at 80 degrees C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the HnSOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile Acidianus ambivalens (AaSOR). The melting point of the HnSOR was approximately 20 degrees C lower than that of the AaSOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere.	+
-		+
-	The sulfur oxygenase reductase from the mesophilic bacterium Halothiobacillus neapolitanus is a highly active thermozyme.,Veith A, Botelho HM, Kindinger F, Gomes CM, Kletzin A J Bacteriol. 2012 Feb;194(3):~~677-85. doi: 10.1128~~/~~JB.06531-11. Epub 2011 Dec 2. PMID:22139503<ref>PMID:22139503<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6qpa" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halothiobacillus neapolitanus c2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Sulfur oxygenase/reductase]]~~	+	[[Category: Coelho R]]
-	[[Category: Coelho, R]]	+	[[Category: Frazao C]]
-	[[Category: Frazao, C]]	+	[[Category: Klezin A]]
-	[[Category: Klezin, A]]	+	[[Category: Poell U]]
-	[[Category: Poell, U]]	+	[[Category: Ruehl P]]
-	[[Category: Ruehl, P]]	+	[[Category: Veith A]]
-	[[Category: Veith, A]]	+
-	~~[[Category: 2-his-1-carboxylate facial triad]]~~	+
-	~~[[Category: Biogeochemical sulfur cycle]]~~	+
-	~~[[Category: Cysteine persulphuration]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sulfur oxygenase reductase~~]]	+

OCA at 09:46, 18 March 2020

OCA — Wed, 18 Mar 2020 09:46:02 GMT

←Older revision		Revision as of 09:46, 18 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qpa is ~~ON HOLD~~	+	==Halothiobacillus neapolitanus sulfur oxygenase reductase==
		+	<StructureSection load='6qpa' size='340' side='right'caption='[[6qpa]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qpa]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QPA 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=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sulfur_oxygenase/reductase Sulfur oxygenase/reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.55 1.13.11.55] </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=6qpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qpa OCA], [http://pdbe.org/6qpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qpa RCSB], [http://www.ebi.ac.uk/pdbsum/6qpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qpa ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium Halothiobacillus neapolitanus (HnSOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The HnSOR purified from Escherichia coli after heterologous gene expression had a temperature range of activity of 10 to 99 degrees C with an optimum at 80 degrees C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the HnSOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile Acidianus ambivalens (AaSOR). The melting point of the HnSOR was approximately 20 degrees C lower than that of the AaSOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere.

-	~~Authors: Frazao, C~~., ~~Klezin,~~ A., ~~Poell~~, U., ~~Veith~~, A.~~, Ruehl, P~~.~~, Coelho, R~~.	+	The sulfur oxygenase reductase from the mesophilic bacterium Halothiobacillus neapolitanus is a highly active thermozyme.,Veith A, Botelho HM, Kindinger F, Gomes CM, Kletzin A J Bacteriol. 2012 Feb;194(3):677-85. doi: 10.1128/JB.06531-11. Epub 2011 Dec 2. PMID:22139503<ref>PMID:22139503</ref>

-	~~Description: Halothiobacillus neapolitanus sulfur oxygenase reductase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Ruehl, P]]~~	+	<div class="pdbe-citations 6qpa" style="background-color:#fffaf0;"></div>
-	~~[[Category: Veith, A]]~~	+	== References ==
-	[[Category: ~~Klezin, A~~]]	+	<references/>
-	[[Category: ~~Frazao, C~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sulfur oxygenase/reductase]]
	[[Category: Coelho, R]]		[[Category: Coelho, R]]
		+	[[Category: Frazao, C]]
		+	[[Category: Klezin, A]]
	[[Category: Poell, U]]		[[Category: Poell, U]]
		+	[[Category: Ruehl, P]]
		+	[[Category: Veith, A]]
		+	[[Category: 2-his-1-carboxylate facial triad]]
		+	[[Category: Biogeochemical sulfur cycle]]
		+	[[Category: Cysteine persulphuration]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sulfur oxygenase reductase]]

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

OCA — Thu, 21 Feb 2019 05:26:37 GMT

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

←Older revision

Revision as of 05:26, 21 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qpa is ON HOLD Authors: Frazao, C., Klezin, A., Poell, U., Veith, A., Ruehl, P., Coelho, R. Description: Halothiobacillus neapolitanus sulfur oxyg...

OCA — Thu, 21 Feb 2019 05:26:36 GMT

New page: '''Unreleased structure''' The entry 6qpa is ON HOLD Authors: Frazao, C., Klezin, A., Poell, U., Veith, A., Ruehl, P., Coelho, R. Description: Halothiobacillus neapolitanus sulfur oxyg...

New page

'''Unreleased structure'''

The entry 6qpa is ON HOLD

Authors: Frazao, C., Klezin, A., Poell, U., Veith, A., Ruehl, P., Coelho, R.

Description: Halothiobacillus neapolitanus sulfur oxygenase reductase
[[Category: Unreleased Structures]]
[[Category: Ruehl, P]]
[[Category: Veith, A]]
[[Category: Klezin, A]]
[[Category: Frazao, C]]
[[Category: Coelho, R]]
[[Category: Poell, U]]