PDBsum entry 6f6h

Oxidoreductase

PDB id: 6f6h

Contents

Protein chains

285 a.a.

Ligands

PLM ×2

Metals

_MN ×2

MN3 ×2

_FE ×2

Waters ×148

PDB id:

6f6h

Name:

Oxidoreductase

Title:

R2-like ligand-binding oxidase v72l mutant with aerobically reconstituted mn/fe cofactor

Structure:

Ribonucleotide reductase small subunit. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Geobacillus kaustophilus (strain hta426). Organism_taxid: 235909. Strain: hta426. Gene: gk2771. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.76Å R-factor: 0.185 R-free: 0.235

Authors:

J.J.Griese,M.Hogbom

Key ref:

J.J.Griese et al. (2018). Ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem, 23, 879-886. PubMed id: 29946980 DOI: 10.1007/s00775-018-1583-3

Date:

05-Dec-17 Release date: 04-Jul-18

Protein chains

Q5KW80  (Q5KW80_GEOKA) -  R2-like ligand binding oxidase from Geobacillus kaustophilus (strain HTA426)

Seq: 302 a.a.

Struc: 285 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.17.4.1 - ribonucleoside-diphosphate reductase.
• Reaction: a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-diphosphate + [thioredoxin]-dithiol
• Cofactor: Fe(3+) or adenosylcob(III)alamin or Mn(2+)

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

reference

DOI no: 10.1007/s00775-018-1583-3

J Biol Inorg Chem 23:879-886 (2018)

PubMed id: 29946980

Ether cross-link formation in the R2-like ligand-binding oxidase.

J.J.Griese, R.M.M.Branca, V.Srinivas, M.Högbom.

ABSTRACT

R2-like ligand-binding oxidases contain a dinuclear metal cofactor which can consist either of two iron ions or one manganese and one iron ion, but the heterodinuclear Mn/Fe cofactor is the preferred assembly in the presence of Mn^II and Fe^II in vitro. We have previously shown that both types of cofactor are capable of catalyzing formation of a tyrosine-valine ether cross-link in the protein scaffold. Here we demonstrate that Mn/Fe centers catalyze cross-link formation more efficiently than Fe/Fe centers, indicating that the heterodinuclear cofactor is the biologically relevant one. We further explore the chemical potential of the Mn/Fe cofactor by introducing mutations at the cross-linking valine residue. We find that cross-link formation is possible also to the tertiary beta-carbon in an isoleucine, but not to the secondary beta-carbon or tertiary gamma-carbon in a leucine, nor to the primary beta-carbon of an alanine. These results illustrate that the reactivity of the cofactor is highly specific and directed.