PDBsum entry 3djg

Oxidoreductase

PDB id: 3djg

Contents

Protein chain

461 a.a. *

Ligands

FAD

NDP

Waters ×512

* Residue conservation analysis

PDB id:

3djg

Name:

Oxidoreductase

Title:

Catalytic cycle of human glutathione reductase near 1 a resolution

Structure:

Glutathione reductase. Chain: x. Fragment: unp residues 45 to 522. Synonym: grase, gr. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gsr, glur, grd1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.145 R-free: 0.186

Authors:

D.S.Berkholz,H.R.Faber,S.N.Savvides,P.A.Karplus

Key ref:

D.S.Berkholz et al. (2008). Catalytic cycle of human glutathione reductase near 1 A resolution. J Mol Biol, 382, 371-384. PubMed id: 18638483 DOI: 10.1016/j.jmb.2008.06.083

Date:

23-Jun-08 Release date: 05-Aug-08

Protein chain

P00390  (GSHR_HUMAN) -  Glutathione reductase, mitochondrial from Homo sapiens

Seq: 522 a.a.

Struc: 461 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.1.7 - glutathione-disulfide reductase.
• Reaction: 2 glutathione + NADP⁺ = glutathione disulfide + NADPH + H⁺

2 × glutathione + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = glutathione disulfide + NADPH + 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.2008.06.083

J Mol Biol 382:371-384 (2008)

PubMed id: 18638483

Catalytic cycle of human glutathione reductase near 1 A resolution.

D.S.Berkholz, H.R.Faber, S.N.Savvides, P.A.Karplus.

ABSTRACT

Efficient enzyme catalysis depends on exquisite details of structure beyond those resolvable in typical medium- and high-resolution crystallographic analyses. Here we report synchrotron-based cryocrystallographic studies of natural substrate complexes of the flavoenzyme human glutathione reductase (GR) at nominal resolutions between 1.1 and 0.95 A that reveal new aspects of its mechanism. Compression in the active site causes overlapping van der Waals radii and distortion in the nicotinamide ring of the NADPH substrate, which enhances catalysis via stereoelectronic effects. The bound NADPH and redox-active disulfide are positioned optimally on opposite sides of the flavin for a 1,2-addition across a flavin double bond. The new structures extend earlier observations to reveal that the redox-active disulfide loop in GR is an extreme case of sequential peptide bonds systematically deviating from planarity--a net deviation of 53 degrees across five residues. But this apparent strain is not a factor in catalysis, as it is present in both oxidized and reduced structures. Intriguingly, the flavin bond lengths in oxidized GR are intermediate between those expected for oxidized and reduced flavin, but we present evidence that this may not be due to the protein environment but instead due to partial synchrotron reduction of the flavin by the synchrotron beam. Finally, of more general relevance, we present evidence that the structures of synchrotron-reduced disulfide bonds cannot generally be used as reliable models for naturally reduced disulfide bonds.

Selected figure(s)

Figure 7.
Fig. 7. Nicotinamide distortion and ribose conformation favor catalysis. (a) The schematic shows the planes of the nicotinamide and flavin (solid black lines). The hypothesized partial boat is shown as a solid red line. Pyramidalization at the nicotinamide N1 places the lone pair on the flavin side, where it (i) entropically favors the productive boat conformation to form, and (ii) repels the hydride to be transferred (dashed red line). (b) The ribose conformation relative to the nicotinamide stabilizes the electron-deficient NADP^+ ring orbitals via hyperconjugative electron donation from the ribose. The glycosidic C–O bond position parallel with the nicotinamide ring also favors NADP^+ over NADPH (see Results and Discussion).

Figure 8.
Fig. 8. Stereoelectronic control in nicotinamide–flavin interaction. (a) A side view with the flavin N5–C4a bond in the plane of the paper and (b) a view down the flavin N5–C4a bond together show the optimal geometry for concerted 1,2-addition across the double bond. Compression in the form of shorter-than-van-der-Waals interactions is also shown in (a).

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 382, 371-384) copyright 2008.

Figures were selected by an automated process.