3w2i: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal structure of re-oxidized form (60 min) of NADH-cytochrome b5 reductase from pig liver==
-<StructureSection load='3w2i' size='340' side='right' caption='[[3w2i]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
+<StructureSection load='3w2i' size='340' side='right'caption='[[3w2i]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
 == Structural highlights ==
-[[3w2i]] 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=3W2I OCA]. <br>
+<table><tr><td colspan='2'>[[3w2i]] 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=3W2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2I FirstGlance]. <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 id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
-<b>[[Related_structure|Related:]]</b> [[1ndh|1ndh]], [[3w2e|3w2e]], [[3w2f|3w2f]], [[3w2g|3w2g]], [[3w2h|3w2h]], [[3w5h|3w5h]]<br>
+<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>
-<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 id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3w2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2i OCA], [https://pdbe.org/3w2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2i RCSB], [https://www.ebi.ac.uk/pdbsum/3w2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2i ProSAT]</span></td></tr>
-<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2i RCSB], [http://www.ebi.ac.uk/pdbsum/3w2i PDBsum]</span><br>
+</table>
-== Publication Abstract from PubMed ==
+== Function ==
-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.
+[https://www.uniprot.org/uniprot/NB5R3_PIG NB5R3_PIG] Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]
-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>
+==See Also==
-== References ==
+*[[NADH-cytochrome b5 reductase|NADH-cytochrome b5 reductase]]
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cytochrome-b5 reductase]]
+[[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]]