PDBsum entry 1vdc

Oxidoreductase

PDB id: 1vdc

Contents

Protein chain

322 a.a. *

Ligands

SO4

FAD

Waters ×326

* Residue conservation analysis

PDB id:

1vdc

Name:

Oxidoreductase

Title:

Structure of NADPH dependent thioredoxin reductase

Structure:

NADPH dependent thioredoxin reductase. Chain: a. Synonym: ntr. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: atthiredb. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: pet

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.188 R-free: 0.243

Authors:

S.Dai,H.Eklund

Key ref:

S.Dai et al. (1996). Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution. J Mol Biol, 264, 1044-1057. PubMed id: 9000629 DOI: 10.1006/jmbi.1996.0695

Date:

22-Sep-96 Release date: 12-Mar-97

Protein chain

Q39243  (TRXB1_ARATH) -  Thioredoxin reductase 1, mitochondrial from Arabidopsis thaliana

Seq: 375 a.a.

Struc: 322 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

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

[thioredoxin]-dithiol + NADP(+) (Bound ligand (Het Group name = FAD) matches with 71.19% similarity) = [thioredoxin]-disulfide + NADPH + H(+)

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

Added reference

DOI no: 10.1006/jmbi.1996.0695

J Mol Biol 264:1044-1057 (1996)

PubMed id: 9000629

Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution.

S.Dai, M.Saarinen, S.Ramaswamy, Y.Meyer, J.P.Jacquot, H.Eklund.

ABSTRACT

Thioredoxin exists in all organisms and is responsible for the hydrogen transfer to important enzymes for ribonucleotide reduction and the reduction of methionine sulphoxide and sulphate. Thioredoxins have also been shown to regulate enzyme activity in plants and are also involved in the regulation of transcription factors and several other regulatory activities. Thioredoxin is reduced by the flavoenzyme thioredoxin reductase using NADPH. We have now determined the first structure of a eukaryotic thioredoxin reductase, from the plant Arabidopsis thaliana, at 2.5 A resolution. The dimeric A. thaliana thioredoxin reductase is structurally similar to that of the Escherichia coli enzyme, and most differences occur in the loops. Because the plant and E. coli enzymes have the same architecture, with the same dimeric structure and the same position of the redox active disulphide bond, a similar mechanism that involves very large domain rotations is likely for the two enzymes. The subunit is divided into two domains, one that binds FAD and one that binds NADPH. The relative positions of the domains in A. thaliana thioredoxin reductase differ from those of the E. coli reductase. When the FAD domains are superimposed, the NADPH domain of A. thaliana thioredoxin reductase must be rotated by 8 degrees to superimpose on the corresponding domain of the E. coli enzyme. The domain rotation we now observe is much smaller than necessary for the thioredoxin reduction cycle.

Selected figure(s)

Figure 5.
Figure 5. The active sites of A. thaliana with the location of the redox-active disulphide in contact with the isoalloxazine moiety of FAD.

Figure 7.
Figure 7. The Ramachandran plot shows that all residues are in allowed conformation: 88% of the residues are in most favoured regions and the remaining 12% of the residues in additional allowed regions.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 264, 1044-1057) copyright 1996.

Figures were selected by an automated process.