3w2g - Revision history

OCA at 08:43, 20 March 2024

2024-03-20T08:43:37Z

←Older revision		Revision as of 08:43, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3w2g' size='340' side='right'caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='3w2g' size='340' side='right'caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.68Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CYB5R3, DIA1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9823 PIG])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Cytochrome~~-~~b5_reductase Cytochrome~~-~~b5 reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2]~~ </~~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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [https://pdbe.org/3w2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [https://www.ebi.ac.uk/pdbsum/3w2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2g 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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [https://pdbe.org/3w2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [https://www.ebi.ac.uk/pdbsum/3w2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]	+	[https://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.	+
-		+
-	Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer.,Yamada M, Tamada T, Takeda K, Matsumoto F, Ohno H, Kosugi M, Takaba K, Shoyama Y, Kimura S, Kuroki R, Miki K J Mol Biol. 2013 Nov 15;425(22):4295-306. doi: 10.1016/j.jmb.2013.06.010. Epub, 2013 Jul 2. PMID:23831226<ref>PMID:23831226</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3w2g" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[NADH-cytochrome b5 reductase\|NADH-cytochrome b5 reductase]]		*[[NADH-cytochrome b5 reductase\|NADH-cytochrome b5 reductase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cytochrome-b5 reductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Kimura, S]]	+	[[Category: Kimura S]]
-	[[Category: Kuroki, R]]	+	[[Category: Kuroki R]]
-	[[Category: Matsumoto, F]]	+	[[Category: Matsumoto F]]
-	[[Category: Miki, K]]	+	[[Category: Miki K]]
-	[[Category: Shoyama, Y]]	+	[[Category: Shoyama Y]]
-	[[Category: Tamada, T]]	+	[[Category: Tamada T]]
-	[[Category: Yamada, M]]	+	[[Category: Yamada M]]
-	~~[[Category: Cytochrome b5]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductase~~]]	+

OCA at 05:19, 3 August 2022

2022-08-03T05:19:44Z

←Older revision		Revision as of 05:19, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver==		==Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver==
-	<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='3w2g' size='340' side='right'caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W2G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [~~http~~://pdbe.org/3w2g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w2g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2g 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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [https://pdbe.org/3w2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [https://www.ebi.ac.uk/pdbsum/3w2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]	+	[[https://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3w2g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3w2g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NADH-cytochrome b5 reductase\|NADH-cytochrome b5 reductase]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Cytochrome-b5 reductase]]		[[Category: Cytochrome-b5 reductase]]
		+	[[Category: Large Structures]]
	[[Category: Pig]]		[[Category: Pig]]
	[[Category: Kimura, S]]		[[Category: Kimura, S]]

OCA at 15:05, 5 August 2016

2016-08-05T15:05:33Z

←Older revision		Revision as of 15:05, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver==		==Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver==
	<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://pdbe.org/3w2g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3w2g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:29, 25 December 2014

2014-12-25T03:29:30Z

←Older revision		Revision as of 03:29, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>	+	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W2G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.~~7.1~~.2 2.7.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</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=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer.,Yamada M, Tamada T, Takeda K, Matsumoto F, Ohno H, Kosugi M, Takaba K, Shoyama Y, Kimura S, Kuroki R, Miki K J Mol Biol. 2013 Nov 15;425(22):4295-306. doi: 10.1016/j.jmb.2013.06.010. Epub, 2013 Jul 2. PMID:23831226<ref>PMID:23831226</ref>		Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer.,Yamada M, Tamada T, Takeda K, Matsumoto F, Ohno H, Kosugi M, Takaba K, Shoyama Y, Kimura S, Kuroki R, Miki K J Mol Biol. 2013 Nov 15;425(22):4295-306. doi: 10.1016/j.jmb.2013.06.010. Epub, 2013 Jul 2. PMID:23831226<ref>PMID:23831226</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Cytochrome-b5 reductase]]		[[Category: Cytochrome-b5 reductase]]
	[[Category: Pig]]		[[Category: Pig]]
-	[[Category: Kimura, S.]]	+	[[Category: Kimura, S]]
-	[[Category: Kuroki, R.]]	+	[[Category: Kuroki, R]]
-	[[Category: Matsumoto, F.]]	+	[[Category: Matsumoto, F]]
-	[[Category: Miki, K.]]	+	[[Category: Miki, K]]
-	[[Category: Shoyama, Y.]]	+	[[Category: Shoyama, Y]]
-	[[Category: Tamada, T.]]	+	[[Category: Tamada, T]]
-	[[Category: Yamada, M.]]	+	[[Category: Yamada, M]]
	[[Category: Cytochrome b5]]		[[Category: Cytochrome b5]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]

OCA at 09:35, 1 May 2014

2014-05-01T09:35:39Z

←Older revision		Revision as of 09:35, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>	+	<table><tr><td colspan='2'>[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>
-	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
-	<b>[[Related_structure\|Related:]]</b> [[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]<br>	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB5R3, DIA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.		NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.
Line 13:		Line 16:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:10, 30 April 2014

2014-04-30T10:10:22Z

←Older revision		Revision as of 10:10, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>		[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>
-	<b>Related:</b> [[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]<br>	+	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<b>[[Related_structure\|Related:]]</b> [[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2g RCSB], [http://www.ebi.ac.uk/pdbsum/3w2g PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.		NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.

OCA at 05:16, 30 April 2014

2014-04-30T05:16:29Z

←Older revision		Revision as of 05:16, 30 April 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3w2g\| PDB=3w2g \| SCENE= }}~~	+	==Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver==
-	===Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver===	+	<StructureSection load='3w2g' size='340' side='right' caption='[[3w2g]], [[Resolution\|resolution]] 1.68Å' scene=''>
		+	== Structural highlights ==
		+	[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA]. <br>
		+	<b>Related:</b> [[1ndh\|1ndh]], [[3w2e\|3w2e]], [[3w2f\|3w2f]], [[3w2h\|3w2h]], [[3w2i\|3w2i]], [[3w5h\|3w5h]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68A resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78A resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.

-	~~==Function==~~	+	Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer.,Yamada M, Tamada T, Takeda K, Matsumoto F, Ohno H, Kosugi M, Takaba K, Shoyama Y, Kimura S, Kuroki R, Miki K J Mol Biol. 2013 Nov 15;425(22):4295-306. doi: 10.1016/j.jmb.2013.06.010. Epub, 2013 Jul 2. PMID:23831226<ref>PMID:23831226</ref>
-	~~[[http~~:~~//www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation~~ of ~~fatty acids~~, ~~cholesterol biosynthesis~~, ~~drug metabolism~~, ~~and~~, ~~in erythrocyte~~, ~~methemoglobin reduction~~.[:]	+

-	==~~About this Structure~~==	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3w2g]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA].~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-b5 reductase]]		[[Category: Cytochrome-b5 reductase]]
-	[[Category: ~~Sus scrofa~~]]	+	[[Category: Pig]]
	[[Category: Kimura, S.]]		[[Category: Kimura, S.]]
	[[Category: Kuroki, R.]]		[[Category: Kuroki, R.]]

OCA at 05:01, 18 July 2013

2013-07-18T05:01:28Z

←Older revision		Revision as of 05:01, 18 July 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3w2g\| PDB=3w2g \| SCENE= }}
		+	===Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver===

-	~~The entry 3w2g is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG]] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]

-	~~Authors~~: ~~Yamada, M~~.~~, Tamada, T~~.~~, Matsumoto, F~~.~~, Shoyama, Y~~., Kimura, S., Kuroki, R., Miki, K.	+	==About this Structure==
-		+	[[3w2g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W2G OCA].
-	~~Description~~: ~~Crystal structure of fully reduced form of NADH-cytochrome~~ b5 ~~reductase from pig liver~~	+	[[Category: Cytochrome-b5 reductase]]
		+	[[Category: Sus scrofa]]
		+	[[Category: Kimura, S.]]
		+	[[Category: Kuroki, R.]]
		+	[[Category: Matsumoto, F.]]
		+	[[Category: Miki, K.]]
		+	[[Category: Shoyama, Y.]]
		+	[[Category: Tamada, T.]]
		+	[[Category: Yamada, M.]]
		+	[[Category: Cytochrome b5]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Reductase]]

OCA at 09:37, 13 March 2013

2013-03-13T09:37:28Z

←Older revision		Revision as of 09:37, 13 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3w2g is ON HOLD	+	The entry 3w2g is ON HOLD until Paper Publication

	Authors: Yamada, M., Tamada, T., Matsumoto, F., Shoyama, Y., Kimura, S., Kuroki, R., Miki, K.		Authors: Yamada, M., Tamada, T., Matsumoto, F., Shoyama, Y., Kimura, S., Kuroki, R., Miki, K.

	Description: Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver		Description: Crystal structure of fully reduced form of NADH-cytochrome b5 reductase from pig liver

OCA: Protected "3w2g" [edit=sysop:move=sysop]

2012-12-05T10:18:03Z

Protected "3w2g" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:18, 5 December 2012