6DQW

Flavobacterium johnsoniae class Id ribonucleotide reductase alpha subuint

Summary for 6DQW

• Entry DOI: 10.2210/pdb6dqw/pdb
• Descriptor: Ribonucleoside-diphosphate reductase, alpha chain (2 entities in total)
• Functional Keywords: ribonucleotide reductase, alpha subunit, nucleotide metabolism, oxidoreductase
• Biological source: Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (Cytophaga johnsonae)
• Total number of polymer chains: 4
• Total formula weight: 263615.41

Authors

Maggiolo, A.O.,Boal, A.K. (deposition date: 2018-06-11, release date: 2019-04-17, Last modification date: 2023-10-11)

Primary citation

Rose, H.R.,Maggiolo, A.O.,McBride, M.J.,Palowitch, G.M.,Pandelia, M.E.,Davis, K.M.,Yennawar, N.H.,Boal, A.K.
Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.
Biochemistry, 58:1845-1860, 2019

PubMed Abstract: Class I ribonucleotide reductases (RNRs) share a common mechanism of nucleotide reduction in a catalytic α subunit. All RNRs initiate catalysis with a thiyl radical, generated in class I enzymes by a metallocofactor in a separate β subunit. Class Id RNRs use a simple mechanism of cofactor activation involving oxidation of a Mn cluster by free superoxide to yield a metal-based MnMn oxidant. This simple cofactor assembly pathway suggests that class Id RNRs may be representative of the evolutionary precursors to more complex class Ia-c enzymes. X-ray crystal structures of two class Id α proteins from Flavobacterium johnsoniae ( Fj) and Actinobacillus ureae ( Au) reveal that this subunit is distinctly small. The enzyme completely lacks common N-terminal ATP-cone allosteric motifs that regulate overall activity, a process that normally occurs by dATP-induced formation of inhibitory quaternary structures to prevent productive β subunit association. Class Id RNR activity is insensitive to dATP in the Fj and Au enzymes evaluated here, as expected. However, the class Id α protein from Fj adopts higher-order structures, detected crystallographically and in solution. The Au enzyme does not exhibit these quaternary forms. Our study reveals structural similarity between bacterial class Id and eukaryotic class Ia α subunits in conservation of an internal auxiliary domain. Our findings with the Fj enzyme illustrate that nucleotide-independent higher-order quaternary structures can form in simple RNRs with truncated or missing allosteric motifs.

PubMed: 30855138
DOI: 10.1021/acs.biochem.8b01252

Experimental method

X-RAY DIFFRACTION (2.6 Å)