PDBsum entry 2cvs

Oxidoreductase

PDB id: 2cvs

Contents

Protein chain

657 a.a. *

Waters ×181

* Residue conservation analysis

PDB id:

2cvs

Name:

Oxidoreductase

Title:

Structures of yeast ribonucleotide reductase i

Structure:

Ribonucleoside-diphosphate reductase large chain 1. Chain: a. Synonym: ribonucleotide reductase i. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.60Å R-factor: 0.211 R-free: 0.267

Authors:

H.Xu,C.Faber,T.Uchiki,J.W.Fairman,J.Racca,C.Dealwis

Key ref:

H.Xu et al. (2006). Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. Proc Natl Acad Sci U S A, 103, 4022-4027. PubMed id: 16537479 DOI: 10.1073/pnas.0600443103

Date:

14-Jun-05 Release date: 07-Mar-06

Protein chain

P21524  (RIR1_YEAST) -  Ribonucleoside-diphosphate reductase large chain 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 888 a.a.

Struc: 657 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.0600443103

Proc Natl Acad Sci U S A 103:4022-4027 (2006)

PubMed id: 16537479

Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation.

H.Xu, C.Faber, T.Uchiki, J.W.Fairman, J.Racca, C.Dealwis.

ABSTRACT

Ribonucleotide reductase catalyzes a crucial step in de novo DNA synthesis and is allosterically controlled by relative levels of dNTPs to maintain a balanced pool of deoxynucleoside triphosphates in the cell. In eukaryotes, the enzyme comprises a heterooligomer of alpha(2) and beta(2) subunits. The alpha subunit, Rnr1, contains catalytic and regulatory sites. Here, we report the only x-ray structures of the eukaryotic alpha subunit of ribonucleotide reductase from Saccharomyces cerevisiae. The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. These are Class I structures with the only fully ordered catalytic sites, including loop 2, a stretch of polypeptide that spans specificity and catalytic sites, conferring specificity. Binding of specificity effector rearranges loop 2; in our structures, this rearrangement moves P294, a residue unique to eukaryotes, out of the catalytic site, accommodating substrate binding. Substrate binding further rearranges loop 2. Cross-talk, by which effector binding regulates substrate preference, occurs largely through R293 and Q288 of loop 2, which are analogous to residues in Thermotoga maritima that mediate cross-talk. However loop-2 conformations and residue-substrate interactions differ substantially between yeast and T. maritima. In most effector-substrate complexes, water molecules help mediate substrate-loop 2 interactions. Finally, the substrate ribose binds with its 3' hydroxyl closer than its 2' hydroxyl to C218 of the catalytic redox pair. We also see a conserved water molecule at the catalytic site in all our structures, near the ribose 2' hydroxyl.

Selected figure(s)

Figure 1.
Fig. 1. Structure of Rnr1. (A) The dimer of apo Rnr1. Rnr1 monomers are yellow and green; dGTP (violet) and ADP (blue) from the cognate complex are shown in the specificity and catalytic sites. The three-helix insert and C-terminal insert are red and blue, respectively. (B) 1.0 2F[o]–F[c] electron density for effector (blue density), loop 2 (red density), and substrate (green density) for the dGTP–ADP complex.

Figure 3.
Fig. 3. Specificity-site interactions. (A) Loop-2 rearrangements. Substrate (Left) and loop 2 and effector (Right) are shown for AMPPNP–UDP (yellow). Loop 2 is shown for apo (black), AMPPNP only (gray), and AMPPNP–CDP (orange). P294 is shown for apo and AMPPNP only. Q288 and R293 are shown for AMPPNP–CDP and AMPPNP–UDP. C spheres are shown for Q288, R293, and P294 in all structures. (B–E) Specificity effector binding. Colors of secondary structure cartoons are as in Fig. 2. Loop-1 carbons are yellow; Loop-2 carbons, light blue; other interacting atoms are colored as in Fig. 2, except effector carbons, which are green. (B) Stereoview of dGTP–ADP. (C) Stereoview of TTP–GDP. (D) Stereoview of AMPPNP–CDP. (E) Stereoview of AMPPNP–UDP.

Figures were selected by the author.

Author's comment

First eukaryotic ribonucleotide reductase I structure explains dNTP regulation.
Chris Dealwis