PDBsum entry 1pm2

Oxidoreductase

PDB id: 1pm2

Contents

Protein chains

339 a.a. *

Metals

_HG ×14

_MN ×4

Waters ×439

* Residue conservation analysis

PDB id:

1pm2

Name:

Oxidoreductase

Title:

Crystal structure of manganese substituted r2-d84e (d84e mutant of the r2 subunit of e. Coli ribonucleotide reductase)

Structure:

Ribonucleoside-diphosphate reductase 1 beta chain. Chain: a, b. Synonym: ribonucleotide reductase 1, b2 protein, r2 protein. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: rir2. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.185 R-free: 0.215

Authors:

W.C.Voegtli,M.Sommerhalter,J.Baldwin,L.Saleh,J.M.Bollinger Jr., A.C.Rosenzweig

Key ref:

W.C.Voegtli et al. (2003). Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2. J Am Chem Soc, 125, 15822-15830. PubMed id: 14677973 DOI: 10.1021/ja0370387

Date:

09-Jun-03 Release date: 13-Jan-04

Protein chains

P69924  (RIR2_ECOLI) -  Ribonucleoside-diphosphate reductase 1 subunit beta from Escherichia coli (strain K12)

Seq: 376 a.a.

Struc: 339 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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: 10.1021/ja0370387

J Am Chem Soc 125:15822-15830 (2003)

PubMed id: 14677973

Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2.

W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger, A.C.Rosenzweig.

ABSTRACT

The R2 subunit of Escherichia coli ribonucleotide reductase contains a dinuclear iron center that generates a catalytically essential stable tyrosyl radical by one electron oxidation of a nearby tyrosine residue. After acquisition of Fe(II) ions by the apo protein, the resulting diiron(II) center reacts with O(2) to initiate formation of the radical. Knowledge of the structure of the reactant diiron(II) form of R2 is a prerequisite for a detailed understanding of the O(2) activation mechanism. Whereas kinetic and spectroscopic studies of the reaction have generally been conducted at pH 7.6 with reactant produced by the addition of Fe(II) ions to the apo protein, the available crystal structures of diferrous R2 have been obtained by chemical or photoreduction of the oxidized diiron(III) protein at pH 5-6. To address this discrepancy, we have generated the diiron(II) states of wildtype R2 (R2-wt), R2-D84E, and R2-D84E/W48F by infusion of Fe(II) ions into crystals of the apo proteins at neutral pH. The structures of diferrous R2-wt and R2-D48E determined from these crystals reveal diiron(II) centers with active site geometries that differ significantly from those observed in either chemically or photoreduced crystals. Structures of R2-wt and R2-D48E/W48F determined at both neutral and low pH are very similar, suggesting that the differences are not due solely to pH effects. The structures of these "ferrous soaked" forms are more consistent with circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopic data and provide alternate starting points for consideration of possible O(2) activation mechanisms.