6DQX image
Entry Detail
PDB ID:
6DQX
Keywords:
Title:
Actinobacillus ureae class Id ribonucleotide reductase alpha subunit
Biological Source:
PDB Version:
Deposition Date:
2018-06-11
Release Date:
2019-04-17
Method Details:
Experimental Method:
Resolution:
1.76 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 42 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Ribonucleoside-diphosphate reductase, alpha chain
Chain IDs:A
Chain Length:574
Number of Molecules:1
Biological Source:Actinobacillus ureae ATCC 25976
Primary Citation
Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.
Biochemistry 58 1845 1860 (2019)
PMID: 30855138 DOI: 10.1021/acs.biochem.8b01252

Abstact

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 MnII2 cluster by free superoxide to yield a metal-based MnIIIMnIV 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.

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