PDBsum entry 5ci3

Oxidoreductase

PDB id: 5ci3

Contents

Protein chain

349 a.a.

Ligands

FEO

SO4 ×4

Waters ×209

PDB id:

5ci3

Name:

Oxidoreductase

Title:

Ribonucleotide reductase y122 2,3,5-f3y variant

Structure:

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

Source:

Escherichia coli o157:h7. Organism_taxid: 83334. Gene: nrdb, ftsb, z3491, ecs3118. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.40Å R-factor: 0.168 R-free: 0.212

Authors:

M.A.Funk,C.L.Drennan

Key ref:

P.H.Oyala et al. (2016). Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J Am Chem Soc, 138, 7951-7964. PubMed id: 27276098 DOI: 10.1021/jacs.6b03605

Date:

10-Jul-15 Release date: 13-Jul-16

Protein chain

P69925  (RIR2_ECO57) -  Ribonucleoside-diphosphate reductase 1 subunit beta from Escherichia coli O157:H7

Seq: 376 a.a.

Struc: 349 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: 10.1021/jacs.6b03605

J Am Chem Soc 138:7951-7964 (2016)

PubMed id: 27276098

Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example.

P.H.Oyala, K.R.Ravichandran, M.A.Funk, P.A.Stucky, T.A.Stich, C.L.Drennan, R.D.Britt, J.Stubbe.

ABSTRACT

Fluorinated tyrosines (FnY's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. FnY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe(2+), and O2 to produce ∼1 Y·/β2 and ∼3 Fe(3+)/β2. The FnY· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each FnY·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the (19)F nucleus provide unique signatures of each FnY· that are readily distinguishable from unlabeled Y·'s. The variability of the abiotic FnY pKa's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y·'s in catalysis and to investigate the importance and identity of hopping Y·'s within redox active proteins proposed to protect them from uncoupled radical chemistry.