PDBsum entry 6tqx

Oxidoreductase

PDB id: 6tqx

Contents

Protein chains

285 a.a.

Ligands

SO4 ×6

Waters ×250

PDB id:

6tqx

Name:

Oxidoreductase

Title:

Crystal structure of apo (metal-free) ribonucleotide reductase nrdf l61g variant from bacillus anthracis

Structure:

Ribonucleoside-diphosphate reductase subunit beta. Chain: a, b. Engineered: yes. Other_details: l61g variant

Source:

Bacillus anthracis. Organism_taxid: 1392. Variant: pxo1-/pxo2- deficient. Gene: nrdf, gbaa_1372. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell_line: rosetta 2

Resolution:

2.05Å R-factor: 0.170 R-free: 0.207

Authors:

K.Grave,M.Hogbom

Key ref:

K.Grāve et al. (2020). The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron. J Biol Inorg Chem, 25, 571-582. PubMed id: 32296998 DOI: 10.1007/s00775-020-01782-3

Date:

17-Dec-19 Release date: 15-Apr-20

Protein chains

Q81TB4  (Q81TB4_BACAN) -  Ribonucleoside-diphosphate reductase subunit beta from Bacillus anthracis

Seq: 322 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/s00775-020-01782-3

J Biol Inorg Chem 25:571-582 (2020)

PubMed id: 32296998

The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.

K.Grāve, J.J.Griese, G.Berggren, M.D.Bennett, M.Högbom.

ABSTRACT

Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn^II and Fe^II in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving-Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation.