6thf - Revision history

OCA at 13:02, 24 January 2024

2024-01-24T13:02:22Z

←Older revision		Revision as of 13:02, 24 January 2024
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	<StructureSection load='6thf' size='340' side='right'caption='[[6thf]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='6thf' size='340' side='right'caption='[[6thf]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6thf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bras3 Bras3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6THF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6THF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6thf]] 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=6THF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6THF 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=MES:2~~-~~(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.47Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nirK, BRAO375_4030011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~566679 BRAS3])</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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/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'>[https://proteopedia.org/fgij/fg.htm?mol=6thf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6thf OCA], [https://pdbe.org/6thf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6thf RCSB], [https://www.ebi.ac.uk/pdbsum/6thf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6thf 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=6thf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6thf OCA], [~~http~~://pdbe.org/6thf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6thf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6thf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6thf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bras3~~]]	+	[[Category: Bradyrhizobium sp. ORS 375]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antonyuk~~, S V~~]]	+	[[Category: Antonyuk SV]]
-	[[Category: Eady~~, R R~~]]	+	[[Category: Eady RR]]
-	[[Category: Garratt~~, R C~~]]	+	[[Category: Garratt RC]]
-	[[Category: Hasnain~~, S S~~]]	+	[[Category: Hasnain SS]]
-	[[Category: Sasaki, D]]	+	[[Category: Sasaki D]]
-	[[Category: Watanabe~~, T F]]~~	+	[[Category: Watanabe TF]]
-	~~[[Category: Bradyrhizobium sp. ors 375]]~~	+
-	~~[[Category: Copper-containing nitrite reductase]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Two-domain~~]]	+

OCA at 06:00, 20 January 2021

2021-01-20T06:00:19Z

←Older revision		Revision as of 06:00, 20 January 2021
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	==Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375==		==Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375==
-	<StructureSection load='6thf' size='340' side='right'caption='[[6thf]]' scene=''>	+	<StructureSection load='6thf' size='340' side='right'caption='[[6thf]], [[Resolution\|resolution]] 1.47Å' 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=6THF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6THF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6thf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bras3 Bras3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6THF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6THF FirstGlance]. <br>
-	</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=6thf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6thf OCA], [http://pdbe.org/6thf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6thf RCSB], [http://www.ebi.ac.uk/pdbsum/6thf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6thf 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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, BRAO375_4030011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=566679 BRAS3])</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://proteopedia.org/fgij/fg.htm?mol=6thf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6thf OCA], [http://pdbe.org/6thf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6thf RCSB], [http://www.ebi.ac.uk/pdbsum/6thf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6thf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cu-containing nitrite reductases that convert NO2 (-) to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4-domain CuNiR that has both cytochrome and cupredoxin domains fused at the N-terminus and the other, a classical 2-domain CuNiR (Br(2D) NiR). We report the first enzymatic studies of a novel 4-domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3- and 2-domain variants, and Br(2D) NiR revealing up to ~500-fold difference in catalytic efficiency in comparison with classical 2-domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self-contained donor-acceptor system, we demonstrate that 4-domain BrNiR utilises N-terminal tethering for down-regulating enzymatic activity instead. Both Br(2D) NiR, as well as engineered 2-domain variant of BrNiR (Delta(Cytc-Cup) BrNiR), have 3 to 5 % NiR activity compared to the well-characterized 2-domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Delta(Cytc-Cup) BrNiR and Br(2D) NiR with classical 2-domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally-occurring 4-domain CuNiR and its engineered 3- and 2-domain variants.The reverse protein engineering approach utilized here provides has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes.
		+
		+	Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction.,Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS FEBS J. 2020 Apr 7. doi: 10.1111/febs.15324. PMID:32255260<ref>PMID:32255260</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6thf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bras3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antonyuk SV]]	+	[[Category: Antonyuk, S V]]
-	[[Category: Eady RR]]	+	[[Category: Eady, R R]]
-	[[Category: Garratt RC]]	+	[[Category: Garratt, R C]]
-	[[Category: Hasnain SS]]	+	[[Category: Hasnain, S S]]
-	[[Category: Sasaki D]]	+	[[Category: Sasaki, D]]
-	[[Category: Watanabe TF]]	+	[[Category: Watanabe, T F]]
		+	[[Category: Bradyrhizobium sp. ors 375]]
		+	[[Category: Copper-containing nitrite reductase]]
		+	[[Category: Electron transfer]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Two-domain]]

OCA at 05:44, 22 April 2020

2020-04-22T05:44:49Z

←Older revision		Revision as of 05:44, 22 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6thf is ~~ON HOLD~~	+	==Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375==
-		+	<StructureSection load='6thf' size='340' side='right'caption='[[6thf]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6THF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6THF FirstGlance]. <br>
-	~~Description~~:	+	</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=6thf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6thf OCA], [http://pdbe.org/6thf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6thf RCSB], [http://www.ebi.ac.uk/pdbsum/6thf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6thf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Antonyuk SV]]
		+	[[Category: Eady RR]]
		+	[[Category: Garratt RC]]
		+	[[Category: Hasnain SS]]
		+	[[Category: Sasaki D]]
		+	[[Category: Watanabe TF]]

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

2019-11-27T05:17:20Z

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

←Older revision

Revision as of 05:17, 27 November 2019

OCA: New page: '''Unreleased structure''' The entry 6thf is ON HOLD Authors: Description: Category: Unreleased Structures

2019-11-27T05:17:18Z

New page: '''Unreleased structure''' The entry 6thf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6thf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]