3w2f: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of oxidation intermediate (10 min) of NADH-cytochrome b5 reductase from pig liver== | ==Crystal structure of oxidation intermediate (10 min) of NADH-cytochrome b5 reductase from pig liver== | ||
<StructureSection load='3w2f' size='340' side='right' caption='[[3w2f]], [[Resolution|resolution]] 1.76Å' scene=''> | <StructureSection load='3w2f' size='340' side='right'caption='[[3w2f]], [[Resolution|resolution]] 1.76Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3w2f]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3w2f]] 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=3W2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2F 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]], [[3w2g|3w2g]], [[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]], [[3w2g|3w2g]], [[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 ([ | <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'>[ | <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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3w2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2f OCA], [https://pdbe.org/3w2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2f RCSB], [https://www.ebi.ac.uk/pdbsum/3w2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2f 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.[:] | ||
<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 3w2f" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3w2f" 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]] | ||
Revision as of 08:19, 3 August 2022
Crystal structure of oxidation intermediate (10 min) of NADH-cytochrome b5 reductase from pig liverCrystal structure of oxidation intermediate (10 min) of NADH-cytochrome b5 reductase from pig liver
Structural highlights
Function[NB5R3_PIG] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:] Publication Abstract from PubMedNADH-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||