PDBsum entry 4tve

Isomerase

PDB id: 4tve

Contents

Protein chain

263 a.a.

Waters ×351

PDB id:

4tve

Name:

Isomerase

Title:

Structure of the first two thioredoxin domains of naumovozyma dairenensis eps1p

Structure:

Naumovozyma dairenensis eps1p. Chain: a. Fragment: unp residues 32-294. Engineered: yes

Source:

Naumovozyma dairenensis. Organism_taxid: 1071378. Strain: atcc 10597 / bcrc 20456 / cbs 421 / nbrc 0211 / nrrl y- 12639. Gene: ndai0b01070, ndai_0b01070. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.176 R-free: 0.212

Authors:

F.Deborah,S.Biran

Key ref:

S.Biran et al. (2014). The Eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino acid motifs but not their functional geometries. Plos One, 9, e113431. PubMed id: 25437863 DOI: 10.1371/journal.pone.0113431

Date:

26-Jun-14 Release date: 17-Dec-14

Protein chain

G0W5T0  (G0W5T0_NAUDC) -  Thioredoxin domain-containing protein from Naumovozyma dairenensis (strain ATCC 10597 / BCRC 20456 / CBS 421 / NBRC 0211 / NRRL Y-12639)

Seq: 695 a.a.

Struc: 263 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.4.3.1 - Deleted entry.

DOI no: 10.1371/journal.pone.0113431

Plos One 9:e113431 (2014)

PubMed id: 25437863

The Eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino acid motifs but not their functional geometries.

S.Biran, Y.Gat, D.Fass.

ABSTRACT

The widespread thioredoxin superfamily enzymes typically share the following features: a characteristic α-β fold, the presence of a Cys-X-X-Cys (or Cys-X-X-Ser) redox-active motif, and a proline in the cis configuration abutting the redox-active site in the tertiary structure. The Cys-X-X-Cys motif is at the solvent-exposed amino terminus of an α-helix, allowing the first cysteine to engage in nucleophilic attack on substrates, or substrates to attack the Cys-X-X-Cys disulfide, depending on whether the enzyme functions to reduce, isomerize, or oxidize its targets. We report here the X-ray crystal structure of an enzyme that breaks many of our assumptions regarding the sequence-structure relationship of thioredoxin superfamily proteins. The yeast Protein Disulfide Isomerase family member Eps1p has Cys-X-X-Cys motifs and proline residues at the appropriate primary structural positions in its first two predicted thioredoxin-fold domains. However, crystal structures show that the Cys-X-X-Cys of the second domain is buried and that the adjacent proline is in the trans, rather than the cis isomer. In these configurations, neither the "active-site" disulfide nor the backbone carbonyl preceding the proline is available to interact with substrate. The Eps1p structures thus expand the documented diversity of the PDI oxidoreductase family and demonstrate that conserved sequence motifs in common folds do not guarantee structural or functional conservation.