PDBsum entry 4w8c

Oxidoreductase

PDB id: 4w8c

Contents

Protein chains

134 a.a.

Ligands

GLY ×2

Waters ×115

PDB id:

4w8c

Name:

Oxidoreductase

Title:

Crystal structure of the helical domain deleted form msra from clostridium oremlandii

Structure:

Peptide methionine sulfoxide reductase msra. Chain: a, b. Fragment: unp residues 1-144. Synonym: protein-methionine-s-oxide reductase,peptide-methionine (s)- s-oxide reductase. Engineered: yes. Mutation: yes

Source:

Alkaliphilus oremlandii ohilas. Organism_taxid: 350688. Gene: msra, clos_1947. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.76Å R-factor: 0.229 R-free: 0.275

Authors:

E.H.Lee,K.Y.Hwang,H.-Y.Kim

Key ref:

E.H.Lee et al. (2015). Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii. Plos One, 10, e0117836. PubMed id: 25692691 DOI: 10.1371/journal.pone.0117836

Date:

23-Aug-14 Release date: 15-Jul-15

Protein chains

A8MI53  (A8MI53_ALKOO) -  Peptide methionine sulfoxide reductase MsrA from Alkaliphilus oremlandii (strain OhILAs)

Seq: 209 a.a.

Struc: 134 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.8.4.11 - peptide-methionine (S)-S-oxide reductase.
• Reaction:
  1. L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl- (S)-S-oxide-[protein] + [thioredoxin]-dithiol
  2. [thioredoxin]-disulfide + L-methionine + H2O = L-methionine (S)-S- oxide + [thioredoxin]-dithiol

[thioredoxin]-disulfide + L-methionine + H2O (Bound ligand (Het Group name = GLY) matches with 55.56% similarity) = L-methionine (S)-S- oxide + [thioredoxin]-dithiol

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

Added reference

DOI no: 10.1371/journal.pone.0117836

Plos One 10:e0117836 (2015)

PubMed id: 25692691

Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii.

E.H.Lee, K.Lee, K.Y.Hwang, H.Y.Kim.

ABSTRACT

We previously determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii (CoMsrA). The overall structure of CoMsrA is unusual, consisting of two domains, the N-terminal catalytic domain and the C-terminal distinct helical domain which is absent from other known MsrA structures. Deletion of the helical domain almost completely abolishes the catalytic activity of CoMsrA. In this study, we determined the crystal structure of the helical domain-deleted (ΔH-domain) form of CoMsrA at a resolution of 1.76 Å. The monomer structure is composed of the central rolled mixed β-sheet surrounded by α-helices. However, there are significant conformational changes in the N- and C-termini and loop regions of the ΔH-domain protein relative to the catalytic domain structure of full-length CoMsrA. The active site structure in the ΔH-domain protein completely collapses, thereby causing loss of catalytic activity of the protein. Interestingly, dimer structures are observed in the crystal formed by N-terminus swapping between two molecules. The ΔH-domain protein primarily exists as a dimer in solution, whereas the full-length CoMsrA exists as a monomer. Collectively, this study provides insight into the structural basis of the essential role of the helical domain of CoMsrA in its catalysis.