PDBsum entry 4hr0

Oxidoreductase

PDB id: 4hr0

Contents

Protein chain

286 a.a.

Ligands

PLM

Metals

MN3

_FE

_MN

_NA

Waters ×98

PDB id:

4hr0

Name:

Oxidoreductase

Title:

R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor

Structure:

Ribonuleotide reductase small subunit. Chain: a. Synonym: r2-like ligand-binding oxidase. Engineered: yes

Source:

Geobacillus kaustophilus. Organism_taxid: 235909. Strain: hta246. Gene: gk2771. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.167 R-free: 0.196

Authors:

J.J.Griese,M.Hogbom

Key ref:

J.J.Griese et al. (2013). Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein. Proc Natl Acad Sci U S A, 110, 17189-17194. PubMed id: 24101498 DOI: 10.1073/pnas.1304368110

Date:

26-Oct-12 Release date: 16-Oct-13

Protein chain

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

Seq: 302 a.a.

Struc: 286 a.a.

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: 10.1073/pnas.1304368110

Proc Natl Acad Sci U S A 110:17189-17194 (2013)

PubMed id: 24101498

Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein.

J.J.Griese, K.Roos, N.Cox, H.S.Shafaat, R.M.Branca, J.Lehtiö, A.Gräslund, W.Lubitz, P.E.Siegbahn, M.Högbom.

ABSTRACT

Although metallocofactors are ubiquitous in enzyme catalysis, how metal binding specificity arises remains poorly understood, especially in the case of metals with similar primary ligand preferences such as manganese and iron. The biochemical selection of manganese over iron presents a particularly intricate problem because manganese is generally present in cells at a lower concentration than iron, while also having a lower predicted complex stability according to the Irving-Williams series (Mn(II) < Fe(II) < Ni(II) < Co(II) < Cu(II) > Zn(II)). Here we show that a heterodinuclear Mn/Fe cofactor with the same primary protein ligands in both metal sites self-assembles from Mn(II) and Fe(II) in vitro, thus diverging from the Irving-Williams series without requiring auxiliary factors such as metallochaperones. Crystallographic, spectroscopic, and computational data demonstrate that one of the two metal sites preferentially binds Fe(II) over Mn(II) as expected, whereas the other site is nonspecific, binding equal amounts of both metals in the absence of oxygen. Oxygen exposure results in further accumulation of the Mn/Fe cofactor, indicating that cofactor assembly is at least a two-step process governed by both the intrinsic metal specificity of the protein scaffold and additional effects exerted during oxygen binding or activation. We further show that the mixed-metal cofactor catalyzes a two-electron oxidation of the protein scaffold, yielding a tyrosine-valine ether cross-link. Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate.