5CNT

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to UDP and dATP at 3.25 Angstroms resolution

Summary for 5CNT

• Entry DOI: 10.2210/pdb5cnt/pdb
• Related: 5CNS 5CNU 5CNV
• Descriptor: Ribonucleoside-diphosphate reductase 1 subunit alpha, Ribonucleoside-diphosphate reductase 1 subunit beta, URIDINE-5'-DIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: allostery, substrate specificity, ribonucleotide reductase, nucleotide metabolism, oxidoreductase
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 8
• Total formula weight: 525431.82

Authors

Chen, P.Y.-T.,Zimanyi, C.M.,Funk, M.A.,Drennan, C.L. (deposition date: 2015-07-18, release date: 2016-01-20, Last modification date: 2023-09-27)

Primary citation

Zimanyi, C.M.,Chen, P.Y.,Kang, G.,Funk, M.A.,Drennan, C.L.
Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
Elife, 5:e07141-e07141, 2016

PubMed Abstract: Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR 'reads' the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

PubMed: 26754917
DOI: 10.7554/eLife.07141

Experimental method

X-RAY DIFFRACTION (3.25 Å)