PDBsum entry 2vm2

Oxidoreductase

PDB id: 2vm2

Contents

Protein chains

110 a.a. *

Waters ×544

* Residue conservation analysis

PDB id:

2vm2

Name:

Oxidoreductase

Title:

Crystal structure of barley thioredoxin h isoform 1 crystallized using peg as precipitant

Structure:

Thioredoxin h isoform 1.. Chain: a, b, c, d. Synonym: thioredoxin. Engineered: yes

Source:

Hordeum vulgare var. Distichum. Two-rowed barley. Organism_taxid: 112509. Variant: barke. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta.

Resolution:

1.80Å R-factor: 0.198 R-free: 0.249

Authors:

K.Maeda,P.Hagglund,C.Finnie,B.Svensson,A.Henriksen

Key ref:

K.Maeda et al. (2008). Crystal structures of barley thioredoxin h isoforms HvTrxh1 and HvTrxh2 reveal features involved in protein recognition and possibly in discriminating the isoform specificity. Protein Sci, 17, 1015-1024. PubMed id: 18424513 DOI: 10.1110/ps.083460308

Date:

21-Jan-08 Release date: 29-Apr-08

Protein chains

Q7XZK3  (Q7XZK3_HORVV) -  Thioredoxin from Hordeum vulgare subsp. vulgare

Seq: 118 a.a.

Struc: 110 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.1.9 - thioredoxin-disulfide reductase (NADPH).
• Reaction: [thioredoxin]-dithiol + NADP⁺ = [thioredoxin]-disulfide + NADPH + H⁺

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

Added reference

DOI no: 10.1110/ps.083460308

Protein Sci 17:1015-1024 (2008)

PubMed id: 18424513

Crystal structures of barley thioredoxin h isoforms HvTrxh1 and HvTrxh2 reveal features involved in protein recognition and possibly in discriminating the isoform specificity.

K.Maeda, P.Hägglund, C.Finnie, B.Svensson, A.Henriksen.

ABSTRACT

H-type thioredoxins (Trxs) constitute a particularly large Trx sub-group in higher plants. Here, the crystal structures are determined for the two barley Trx h isoforms, HvTrxh1 and HvTrxh2, in the partially radiation-reduced state to resolutions of 1.7 A, and for HvTrxh2 in the oxidized state to 2.0 A. The two Trxs have a sequence identity of 51% and highly similar fold and active-site architecture. Interestingly, the four independent molecules in the crystals of HvTrxh1 form two relatively large and essentially identical protein-protein interfaces. In each interface, a loop segment of one HvTrxh1 molecule is positioned along a shallow hydrophobic groove at the primary nucleophile Cys40 of another HvTrxh1 molecule. The association mode can serve as a model for the target protein recognition by Trx, as it brings the Met82 Cgamma atom (gamma position as a disulfide sulfur) of the bound loop segment in the proximity of the Cys40 thiol. The interaction involves three characteristic backbone-backbone hydrogen bonds in an antiparallel beta-sheet-like arrangement, similar to the arrangement observed in the structure of an engineered, covalently bound complex between Trx and a substrate protein, as reported by Maeda et al. in an earlier paper. The occurrence of an intermolecular salt bridge between Glu80 of the bound loop segment and Arg101 near the hydrophobic groove suggests that charge complementarity plays a role in the specificity of Trx. In HvTrxh2, isoleucine corresponds to this arginine, which emphasizes the potential for specificity differences between the coexisting barley Trx isoforms.

Selected figure(s)

Figure 2.
Figure 2. Active-site architecture of HvTrxh1 (A) and HvTrxh2 (B). Carbon, nitrogen, oxygen, and sulfur atoms are colored green, blue, red, and yellow, respectively. The 2F [o]–F [c] electron density maps are presented as a gray isosurface mesh at the 1.0 level. The water molecule buried in the internal cavity is shown as a sphere and is modeled in two alternative positions in HvTrxh1. For the HvTrxh2 structure, Cys46 and Cys49 are shown only in the reduced conformations, although they are also modeled in the oxidized conformations.

Figure 3.
Figure 3. Radiation disruption of the active-site disulfide in HvTrxh2. Stereo images of HvTrxh2[OX] (A) and HvTrxh2[RED2], 80% reduced (B), showing a close-up view of segment Cys46–Cys49. The 2F [o]–F [c] electron density maps are shown as gray isosurface mesh at the 1.0 level. (C) HvTrxh2[RED1] with the 1/V | F(h)[RED1] – F(h)[RED2] | e^i ^RED2(h) e ^–2 i(h – r) difference electron density contoured at the 7 level. Significant negative (red) density represents areas where the HvTrxh2[RED2] structure has a higher level of electron density than the HvTrxh2[RED1] structure, and positive (green) electron density, the opposite. For HvTrxh2[RED1] and HvTrxh2[RED2] structures, Cys46 and Cys49 are modeled and shown in two alternative conformations (for oxidized and reduced states).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2008, 17, 1015-1024) copyright 2008.

Figures were selected by an automated process.