PDBsum entry 1l1l

Oxidoreductase

PDB id: 1l1l

Contents

Protein chains

717 a.a. *

Waters ×2875

* Residue conservation analysis

PDB id:

1l1l

Name:

Oxidoreductase

Title:

Crystal structure of b-12 dependent (class ii) ribonucleotide reductase

Structure:

Ribonucleoside triphosphate reductase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Lactobacillus leichmannii. Organism_taxid: 28039. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.223 R-free: 0.266

Authors:

M.D.Sintchak,G.Arjara,B.A.Kellogg,J.Stubbe,C.L.Drennan

Key ref:

M.D.Sintchak et al. (2002). The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Nat Struct Biol, 9, 293-300. PubMed id: 11875520 DOI: 10.1038/nsb774

Date:

18-Feb-02 Release date: 10-Apr-02

Protein chains

Q59490  (RTPR_LACLE) -  Adenosylcobalamin-dependent ribonucleoside-triphosphate reductase from Lactobacillus leichmannii

Seq: 739 a.a.

Struc: 717 a.a.

Enzyme reactions

• Enzyme class: E.C.1.17.4.2 - ribonucleoside-triphosphate reductase (thioredoxin).
• Reaction: a 2'-deoxyribonucleoside 5'-triphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-triphosphate + [thioredoxin]-dithiol
• Cofactor: Adenosylcob(III)alamin

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

reference

DOI no: 10.1038/nsb774

Nat Struct Biol 9:293-300 (2002)

PubMed id: 11875520

The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer.

M.D.Sintchak, G.Arjara, B.A.Kellogg, J.Stubbe, C.L.Drennan.

ABSTRACT

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides, an essential step in DNA biosynthesis and repair. Here we present the crystal structure of class II (coenzyme B12-dependent) ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii in the apo enzyme form and in complex with the B12 analog adeninylpentylcobalamin at 1.75 and 2.0 A resolution, respectively. This monomeric, allosterically regulated class II RNR retains all the key structural features associated with the catalytic and regulatory machinery of oligomeric RNRs. Surprisingly, the dimer interface responsible for effector binding in class I RNR is preserved through a single 130-residue insertion in the class II structure. Thus, L. leichmannii RNR is a paradigm for the simplest structural entity capable of ribonucleotide reduction, a reaction linking the RNA and DNA worlds.

Selected figure(s)

Figure 1.
Figure 1. General reaction catalyzed by ribonucleotide reductases. Each of the three well-characterized RNR classes uses a different metallocofactor to generate the thiyl radical (S ). For class II RNRs, the S (Cys 408 in L. leichmannii) is generated by AdoCbl carbon-cobalt (C -Co) bond homolysis. Hydrogen atom (red) abstraction from the substrate by the thiyl radical and the subsequent multiple step radical rearrangements result in the loss of the 2' hydroxyl group in the form of water. In class I and II RNRs, reducing equivalents for the reaction are provided by the oxidation of two Cys residues to a disulfide (Cys 119 -Cys 419 in L. leichmannii)35. In contrast, class III RNR obtains reducing equivalents by the oxidation of formate^36.

Figure 4.
Figure 4. B[12] bound to RNR. a, Chemical structures of adenosylcobalamin (AdoCbl, left panel) and adeninylpentylcobalamin (AdPentCbl, right panel). b, Difference (F[o] - F[c]) electron density at 2.0 Å resolution (2 contour) for AdPentCbl bound to L. leichmannii RTPR, calculated before the inclusion of any AdPentCbl atoms in the refinement. The orientation of AdPentCbl in (b) is the same as in (a). Figure prepared using Ribbons37.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 293-300) copyright 2002.

Figures were selected by an automated process.