7zcq - Revision history

OCA at 13:31, 1 February 2024

OCA — Thu, 01 Feb 2024 13:31:02 GMT

←Older revision		Revision as of 13:31, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7zcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._ORS_375 Bradyrhizobium sp. ORS 375]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZCQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[7zcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._ORS_375 Bradyrhizobium sp. ORS 375]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZCQ 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=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</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]] 1.35Å</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=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7zcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zcq OCA], [https://pdbe.org/7zcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zcq RCSB], [https://www.ebi.ac.uk/pdbsum/7zcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zcq 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=7zcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zcq OCA], [https://pdbe.org/7zcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zcq RCSB], [https://www.ebi.ac.uk/pdbsum/7zcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zcq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/H0SLX7_BRAS3 H0SLX7_BRAS3]]	+	[https://www.uniprot.org/uniprot/H0SLX7_BRAS3 H0SLX7_BRAS3]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7zcq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7zcq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:24, 8 September 2022

OCA — Thu, 08 Sep 2022 03:24:59 GMT

←Older revision		Revision as of 03:24, 8 September 2022
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	==Nitrite-bound MSOX movie series dataset 25 (20 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - NO/water intermediate==		==Nitrite-bound MSOX movie series dataset 25 (20 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - NO/water intermediate==
-	<StructureSection load='7zcq' size='340' side='right'caption='[[7zcq]]' scene=''>	+	<StructureSection load='7zcq' size='340' side='right'caption='[[7zcq]], [[Resolution\|resolution]] 1.35Å' 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=7ZCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._ORS_375 Bradyrhizobium sp. ORS 375]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZCQ 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=7zcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zcq OCA], [https://pdbe.org/7zcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zcq RCSB], [https://www.ebi.ac.uk/pdbsum/7zcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zcq 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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7zcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zcq OCA], [https://pdbe.org/7zcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zcq RCSB], [https://www.ebi.ac.uk/pdbsum/7zcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zcq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/H0SLX7_BRAS3 H0SLX7_BRAS3]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br(2D)NiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site ( approximately 20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.
		+
		+	Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.,Rose SL, Baba S, Okumura H, Antonyuk SV, Sasaki D, Hedison TM, Shanmugam M, Heyes DJ, Scrutton NS, Kumasaka T, Tosha T, Eady RR, Yamamoto M, Hasnain SS Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2205664119. doi:, 10.1073/pnas.2205664119. Epub 2022 Jul 21. PMID:35862453<ref>PMID:35862453</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7zcq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bradyrhizobium sp. ORS 375]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Antonyuk SV]]		[[Category: Antonyuk SV]]

OCA at 04:55, 3 August 2022

OCA — Wed, 03 Aug 2022 04:55:28 GMT

←Older revision		Revision as of 04:55, 3 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7zcq is ~~ON HOLD until Paper Publication~~	+	==Nitrite-bound MSOX movie series dataset 25 (20 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - NO/water intermediate==
-		+	<StructureSection load='7zcq' size='340' side='right'caption='[[7zcq]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZCQ 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=7zcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zcq OCA], [https://pdbe.org/7zcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zcq RCSB], [https://www.ebi.ac.uk/pdbsum/7zcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zcq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Antonyuk SV]]
		+	[[Category: Baba S]]
		+	[[Category: Eady RR]]
		+	[[Category: Hasnain SS]]
		+	[[Category: Kumasaka T]]
		+	[[Category: Okumura H]]
		+	[[Category: Rose SL]]
		+	[[Category: Sasaki D]]
		+	[[Category: Tosha T]]
		+	[[Category: Yamamoto M]]

OCA at 05:01, 12 May 2022

OCA — Thu, 12 May 2022 05:01:59 GMT

←Older revision		Revision as of 05:01, 12 May 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zcq is ON HOLD	+	The entry 7zcq is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 06 Apr 2022 09:22:56 GMT

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

←Older revision

Revision as of 09:22, 6 April 2022

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

OCA — Wed, 06 Apr 2022 09:22:55 GMT

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

New page

'''Unreleased structure'''

The entry 7zcq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]