PDBsum entry 3w2e

Oxidoreductase

PDB id: 3w2e

Contents

Protein chain

271 a.a.

Ligands

FAD

NAD

Waters ×140

PDB id:

3w2e

Name:

Oxidoreductase

Title:

Crystal structure of oxidation intermediate (20 min) of nadh- cytochrome b5 reductase from pig liver

Structure:

Nadh-cytochrome b5 reductase 3. Chain: a. Synonym: b5r, cytochrome b5 reductase, diaphorase-1. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: cyb5r3, dia1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.179 R-free: 0.213

Authors:

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

Key ref:

M.Yamada et al. (2013). Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer. J Mol Biol, 425, 4295-4306. PubMed id: 23831226 DOI: 10.1016/j.jmb.2013.06.010

Date:

28-Nov-12 Release date: 17-Jul-13

Protein chain

P83686  (NB5R3_PIG) -  NADH-cytochrome b5 reductase 3 (Fragment) from Sus scrofa

Seq: 272 a.a.

Struc: 271 a.a.

Enzyme reactions

• Enzyme class: E.C.1.6.2.2 - cytochrome-b5 reductase.
• Reaction: 2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD⁺ + H⁺

2 × Fe(III)-[cytochrome b5] + NADH (Bound ligand (Het Group name = NAD) corresponds exactly) = 2 × Fe(II)-[cytochrome b5] + NAD(+) + H(+)

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2013.06.010

J Mol Biol 425:4295-4306 (2013)

PubMed id: 23831226

Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer.

M.Yamada, T.Tamada, K.Takeda, F.Matsumoto, H.Ohno, M.Kosugi, K.Takaba, Y.Shoyama, S.Kimura, R.Kuroki, K.Miki.

ABSTRACT

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 1.68Å 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 0.78Å 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.