Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis

Hannah R. Rose, Ailiena O. Maggiolo, Molly J. McBride, Gavin M. Palowitch, Maria Eirini Pandelia, Katherine M. Davis, Neela H. Yennawar, Amie K. Boal

Research output: Contribution to journalArticle

1 Citation (Scopus)

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 II 2 cluster by free superoxide to yield a metal-based Mn III Mn IV 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.

Original languageEnglish (US)
Pages (from-to)1845-1860
Number of pages16
JournalBiochemistry
Volume58
Issue number14
DOIs
StatePublished - Apr 9 2019

Fingerprint

Ribonucleotide Reductases
Biosynthesis
Flavobacterium
Catalytic Domain
Actinobacillus
Enzymes
Nucleotides
Catalysis
Oxidants
Superoxides
Cones
Conservation
Proteins
Adenosine Triphosphate
Crystal structure
Metals
Chemical activation
X-Rays
Association reactions
X rays

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

Rose, Hannah R. ; Maggiolo, Ailiena O. ; McBride, Molly J. ; Palowitch, Gavin M. ; Pandelia, Maria Eirini ; Davis, Katherine M. ; Yennawar, Neela H. ; Boal, Amie K. / Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. In: Biochemistry. 2019 ; Vol. 58, No. 14. pp. 1845-1860.
@article{b76d02587f38401cae448779c28d2a2e,
title = "Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis",
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 II 2 cluster by free superoxide to yield a metal-based Mn III Mn IV 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.",
author = "Rose, {Hannah R.} and Maggiolo, {Ailiena O.} and McBride, {Molly J.} and Palowitch, {Gavin M.} and Pandelia, {Maria Eirini} and Davis, {Katherine M.} and Yennawar, {Neela H.} and Boal, {Amie K.}",
year = "2019",
month = "4",
day = "9",
doi = "10.1021/acs.biochem.8b01252",
language = "English (US)",
volume = "58",
pages = "1845--1860",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "14",

}

Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. / Rose, Hannah R.; Maggiolo, Ailiena O.; McBride, Molly J.; Palowitch, Gavin M.; Pandelia, Maria Eirini; Davis, Katherine M.; Yennawar, Neela H.; Boal, Amie K.

In: Biochemistry, Vol. 58, No. 14, 09.04.2019, p. 1845-1860.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis

AU - Rose, Hannah R.

AU - Maggiolo, Ailiena O.

AU - McBride, Molly J.

AU - Palowitch, Gavin M.

AU - Pandelia, Maria Eirini

AU - Davis, Katherine M.

AU - Yennawar, Neela H.

AU - Boal, Amie K.

PY - 2019/4/9

Y1 - 2019/4/9

N2 - 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 II 2 cluster by free superoxide to yield a metal-based Mn III Mn IV 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.

AB - 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 II 2 cluster by free superoxide to yield a metal-based Mn III Mn IV 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.

UR - http://www.scopus.com/inward/record.url?scp=85063376839&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85063376839&partnerID=8YFLogxK

U2 - 10.1021/acs.biochem.8b01252

DO - 10.1021/acs.biochem.8b01252

M3 - Article

C2 - 30855138

AN - SCOPUS:85063376839

VL - 58

SP - 1845

EP - 1860

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 14

ER -