5ytn - Revision history

OCA at 10:25, 27 March 2024

OCA — Wed, 27 Mar 2024 10:25:07 GMT

←Older revision		Revision as of 10:25, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5ytn' size='340' side='right'caption='[[5ytn]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5ytn' size='340' side='right'caption='[[5ytn]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YTN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YTN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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]] 1.75Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytn OCA], [~~http~~://pdbe.org/5ytn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ytn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ytn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytn 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=5ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytn OCA], [https://pdbe.org/5ytn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ytn RCSB], [https://www.ebi.ac.uk/pdbsum/5ytn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytn ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A1W6VP04_GEOTD A0A1W6VP04_GEOTD]
-	Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO2(-)) to nitric oxide (NO) and the two-electron reduction of dioxygen (O2) to hydrogen peroxide (H2O2). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.	+
-		+
-	Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.,Fukuda Y, Matsusaki T, Tse KM, Mizohata E, Murphy MEP, Inoue T Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):~~769-777. doi:, 10.1107~~/~~S2059798318010082. Epub 2018 Jul 24. PMID:30082512<ref>PMID:30082512<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ytn" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]		*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacillus thermodenitrificans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukuda, Y]]	+	[[Category: Fukuda Y]]
-	[[Category: Inoue, T]]	+	[[Category: Inoue T]]
-	[[Category: Matsusaki, T]]	+	[[Category: Matsusaki T]]
-	[[Category: Mizohata, E]]	+	[[Category: Mizohata E]]
-	[[Category: Murphy~~, M E.P~~]]	+	[[Category: Murphy MEP]]
-	[[Category: Tse~~, K M]]~~	+	[[Category: Tse KM]]
-	~~[[Category: Copper]]~~	+
-	~~[[Category: Nitrite reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:27, 21 October 2020

OCA — Wed, 21 Oct 2020 09:27:38 GMT

←Older revision		Revision as of 09:27, 21 October 2020
Line 1:		Line 1:

	==C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide==		==C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide==
-	<StructureSection load='5ytn' size='340' side='right' caption='[[5ytn]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5ytn' size='340' side='right'caption='[[5ytn]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YTN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YTN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=5ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytn OCA], [http://pdbe.org/5ytn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytn RCSB], [http://www.ebi.ac.uk/pdbsum/5ytn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytn ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytn OCA], [http://pdbe.org/5ytn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytn RCSB], [http://www.ebi.ac.uk/pdbsum/5ytn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5ytn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ytn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fukuda, Y]]		[[Category: Fukuda, Y]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]

OCA at 06:00, 22 August 2018

OCA — Wed, 22 Aug 2018 06:00:24 GMT

←Older revision		Revision as of 06:00, 22 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ytn is ~~ON HOLD until Paper~~ Publication	+	==C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide==
		+	<StructureSection load='5ytn' size='340' side='right' caption='[[5ytn]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ytn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=5ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytn OCA], [http://pdbe.org/5ytn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytn RCSB], [http://www.ebi.ac.uk/pdbsum/5ytn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytn ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO2(-)) to nitric oxide (NO) and the two-electron reduction of dioxygen (O2) to hydrogen peroxide (H2O2). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.

-	~~Authors: Fukuda~~, Y., Matsusaki, T., Tse~~, K.M.~~, Mizohata, E., Murphy, M.E.P.~~, Inoue, T~~.	+	Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.,Fukuda Y, Matsusaki T, Tse KM, Mizohata E, Murphy MEP, Inoue T Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):769-777. doi:, 10.1107/S2059798318010082. Epub 2018 Jul 24. PMID:30082512<ref>PMID:30082512</ref>

-	~~Description: C135A mutant~~ of ~~copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Tse, K~~.~~M]]~~	+	<div class="pdbe-citations 5ytn" style="background-color:#fffaf0;"></div>
-	~~[[Category: Murphy, M~~.E.~~P]]~~	+	== References ==
-	~~[[Category~~: ~~Mizohata, E]]~~	+	<references/>
-	~~[[Category: Inoue, T]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Fukuda, Y]]		[[Category: Fukuda, Y]]
		+	[[Category: Inoue, T]]
	[[Category: Matsusaki, T]]		[[Category: Matsusaki, T]]
		+	[[Category: Mizohata, E]]
		+	[[Category: Murphy, M E.P]]
		+	[[Category: Tse, K M]]
		+	[[Category: Copper]]
		+	[[Category: Nitrite reductase]]
		+	[[Category: Oxidoreductase]]

OCA at 04:03, 6 June 2018

OCA — Wed, 06 Jun 2018 04:03:56 GMT

←Older revision		Revision as of 04:03, 6 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ytn is ON HOLD	+	The entry 5ytn is ON HOLD until Paper Publication

	Authors: Fukuda, Y., Matsusaki, T., Tse, K.M., Mizohata, E., Murphy, M.E.P., Inoue, T.		Authors: Fukuda, Y., Matsusaki, T., Tse, K.M., Mizohata, E., Murphy, M.E.P., Inoue, T.

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

OCA — Wed, 29 Nov 2017 04:57:45 GMT

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

←Older revision

Revision as of 04:57, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ytn is ON HOLD Authors: Fukuda, Y., Matsusaki, T., Tse, K.M., Mizohata, E., Murphy, M.E.P., Inoue, T. Description: C135A mutant of copper-containi...

OCA — Wed, 29 Nov 2017 04:57:44 GMT

New page: '''Unreleased structure''' The entry 5ytn is ON HOLD Authors: Fukuda, Y., Matsusaki, T., Tse, K.M., Mizohata, E., Murphy, M.E.P., Inoue, T. Description: C135A mutant of copper-containi...

New page

'''Unreleased structure'''

The entry 5ytn is ON HOLD

Authors: Fukuda, Y., Matsusaki, T., Tse, K.M., Mizohata, E., Murphy, M.E.P., Inoue, T.

Description: C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide
[[Category: Unreleased Structures]]
[[Category: Tse, K.M]]
[[Category: Murphy, M.E.P]]
[[Category: Mizohata, E]]
[[Category: Inoue, T]]
[[Category: Fukuda, Y]]
[[Category: Matsusaki, T]]