PDBsum entry 3d4m

Oxidoreductase

PDB id: 3d4m

Contents

Protein chain

109 a.a. *

Waters ×83

* Residue conservation analysis

PDB id:

3d4m

Name:

Oxidoreductase

Title:

Glutaredoxin 2 oxidized structure

Structure:

Glutaredoxin-2, mitochondrial. Chain: a. Synonym: thioltransferase, glutathione-dependent oxidoreductase 2. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: grx2, ttr, ttr1, ydr513w, d9719.17. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.05Å R-factor: 0.182 R-free: 0.219

Authors:

K.F.Discola,M.A.De Oliveira,J.A.Barcena,P.Porras,B.G.Guimaraes, L.E.S.Netto

Key ref:

K.F.Discola et al. (2009). Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae. J Mol Biol, 385, 889-901. PubMed id: 18992757 DOI: 10.1016/j.jmb.2008.10.055

Date:

14-May-08 Release date: 28-Oct-08

Protein chain

P17695  (GLRX2_YEAST) -  Glutaredoxin-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 143 a.a.

Struc: 109 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.11.1.9 - glutathione peroxidase.
• Reaction: 2 glutathione + H2O2 = glutathione disulfide + 2 H2O
• Cofactor: Se(2+)
• Enzyme class 3: E.C.2.5.1.18 - glutathione transferase.
• Reaction: RX + glutathione = an S-substituted glutathione + a halide anion + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.jmb.2008.10.055

J Mol Biol 385:889-901 (2009)

PubMed id: 18992757

Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae.

K.F.Discola, M.A.de Oliveira, J.R.Rosa Cussiol, G.Monteiro, J.A.Bárcena, P.Porras, C.A.Padilla, B.G.Guimarães, L.E.Netto.

ABSTRACT

Glutaredoxins (Grxs) are small (9-12 kDa) heat-stable proteins that are ubiquitously distributed. In Saccharomyces cerevisiae, seven Grx enzymes have been identified. Two of them (yGrx1 and yGrx2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Here, we show that yGrx2 has a specific activity 15 times higher than that of yGrx1, although these two oxidoreductases share 64% identity and 85% similarity with respect to their amino acid sequences. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that yGrx2 possesses a lower K(M) for glutathione and a higher turnover than yGrx1. To better comprehend these biochemical differences, the pK(a) of the N-terminal active-site cysteines (Cys27) of these two proteins and of the yGrx2-C30S mutant were determined. Since the pK(a) values of the yGrx1 and yGrx2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. Therefore, crystal structures of yGrx2 in the oxidized form and with a glutathionyl mixed disulfide were determined at resolutions of 2.05 and 1.91 A, respectively. Comparisons of yGrx2 structures with the recently determined structures of yGrx1 provided insights into their remarkable functional divergence. We hypothesize that the substitutions of Ser23 and Gln52 in yGrx1 by Ala23 and Glu52 in yGrx2 modify the capability of the active-site C-terminal cysteine to attack the mixed disulfide between the N-terminal active-site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between yGrx1 and yGrx2 may reflect variations in substrate specificity.

Selected figure(s)

Figure 5.
Fig. 5. Cartoon representation of the overall fold of yGrx1 and yGrx2 showing the structural alignment of yGrx1[GS] (α-carbon atoms in violet; PDB code 2JAC),^22 yGrx2[ox] (α-carbon atoms in gray) and yGrx2[GS] (α-carbon atoms in cyan). The GSH molecule bonded to the yGrx2-C30S mutant is shown in yellow.

Figure 8.
Fig. 8. Side-chain conformation of Ser30 in the structures of the C30S mutants of yGrx1^22 (gray) and yGrx2 (cyan) in their glutathionylated forms. It is clear that the distances from the Cys27 sulfur atoms (yellow) to the Ser30 oxygen atom (red) are very different between yGrx1 and yGrx2, indicating that the conformation of a Ser30 residue in yGrx2 is less favorable to attack the mixed disulfide.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 889-901) copyright 2009.

Figures were selected by the author.