The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase
Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, MnIII 2-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the MnII 2 form of NrdF is an important component in understanding O2-mediated f...
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| Published in | Biochemistry (Easton) Vol. 51; no. 18; pp. 3861 - 3871 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Chemical Society
08.05.2012
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0006-2960 1520-4995 1520-4995 |
| DOI | 10.1021/bi201925t |
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| Abstract | Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, MnIII 2-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the MnII 2 form of NrdF is an important component in understanding O2-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli MnII 2-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis MnII 2-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli MnII 2-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the MnII 2 cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for MnIII 2-Y• cofactor assembly in class Ib RNRs. |
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| AbstractList | Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn(III)(2)-Y(•), in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn(II)(2) form of NrdF is an important component in understanding O(2)-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn(II)(2)-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn(II)(2)-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn(II)(2)-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn(II)(2) cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn(III)(2)-Y(•) cofactor assembly in class Ib RNRs. Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mnᴵᴵᴵ₂-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mnᴵᴵ₂ form of NrdF is an important component in understanding O₂-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mnᴵᴵ₂-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mnᴵᴵ₂-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mnᴵᴵ₂-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mnᴵᴵ₂ cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mnᴵᴵᴵ₂-Y• cofactor assembly in class Ib RNRs. Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn{sub 2}{sup III}-Y{sm_bullet}, in their homodimeric NrdF ({beta}2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn{sub 2}{sup II} form of NrdF is an important component in understanding O{sub 2}-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn{sub 2}{sup II}-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 {angstrom} resolution crystal structure of Bacillus subtilis Mn{sub 2}{sup II}-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the {beta}2 dimer are distinct from those observed in E. coli Mn{sub 2}{sup II}-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn{sub 2}{sup II} cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn{sub 2}{sup III}-Y{sm_bullet} cofactor assembly in class Ib RNRs. Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn III 2 -Y•, in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn II 2 form of NrdF is an important component in understanding O 2 -mediated formation of the active metallocofactor, a subject of much interest since a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn II 2 -NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn II 2 -NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus genera. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn II 2 -NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn II 2 cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn III 2 -Y• cofactor assembly in class Ib RNRs. Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn(III)(2)-Y(•), in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn(II)(2) form of NrdF is an important component in understanding O(2)-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn(II)(2)-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn(II)(2)-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn(II)(2)-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn(II)(2) cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn(III)(2)-Y(•) cofactor assembly in class Ib RNRs.Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn(III)(2)-Y(•), in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn(II)(2) form of NrdF is an important component in understanding O(2)-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn(II)(2)-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis Mn(II)(2)-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli Mn(II)(2)-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn(II)(2) cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn(III)(2)-Y(•) cofactor assembly in class Ib RNRs. Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, MnIII 2-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the MnII 2 form of NrdF is an important component in understanding O2-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli MnII 2-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 Å resolution crystal structure of Bacillus subtilis MnII 2-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the β2 dimer are distinct from those observed in E. coli MnII 2-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the MnII 2 cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for MnIII 2-Y• cofactor assembly in class Ib RNRs. |
| Author | Stubbe, JoAnne Cotruvo, Joseph A Rosenzweig, Amy C Boal, Amie K |
| AuthorAffiliation | Department of Chemistry Northwestern University Massachusetts Institute of Technology Department of Biology |
| AuthorAffiliation_xml | – name: Department of Chemistry – name: Northwestern University – name: Department of Biology – name: Massachusetts Institute of Technology – name: Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston IL 60208 – name: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 – name: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 |
| Author_xml | – sequence: 1 givenname: Amie K surname: Boal fullname: Boal, Amie K – sequence: 2 givenname: Joseph A surname: Cotruvo fullname: Cotruvo, Joseph A – sequence: 3 givenname: JoAnne surname: Stubbe fullname: Stubbe, JoAnne email: amyr@northwestern.edu, stubbe@mit.edu – sequence: 4 givenname: Amy C surname: Rosenzweig fullname: Rosenzweig, Amy C email: amyr@northwestern.edu, stubbe@mit.edu |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22443445$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1047906$$D View this record in Osti.gov |
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| GrantInformation | This work was supported by National Institutes of Health Grants GM58518 (A.C.R.) and GM81393 (J.S.), a National Research Service Award fellowship to A.K.B., and a National Defense Science and Engineering Graduate fellowship to J.A.C. |
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| Snippet | Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, MnIII 2-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction... Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn(III)(2)-Y(•), in their homodimeric NrdF (β2) subunit to initiate... Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mnᴵᴵᴵ₂-Y•, in their homodimeric NrdF (β2) subunit to initiate reduction... Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn{sub 2}{sup III}-Y{sm_bullet}, in their homodimeric NrdF ({beta}2)... Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn III 2 -Y•, in their homodimeric NrdF (β2) subunit to initiate... |
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| SubjectTerms | 60 APPLIED LIFE SCIENCES BACILLUS BACILLUS SUBTILIS Bacillus subtilis - enzymology BASIC BIOLOGICAL SCIENCES Catalytic Domain CRYSTAL STRUCTURE Crystallography, X-Ray DIMERS ENZYMES ESCHERICHIA COLI Manganese - chemistry OXIDOREDUCTASES phylogeny PROTEINS RADICALS RESIDUES RESOLUTION ribonucleotide reductase Ribonucleotide Reductases - chemistry ribonucleotides sequence alignment SOLVENTS STAPHYLOCOCCUS |
| Title | The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase |
| URI | http://dx.doi.org/10.1021/bi201925t https://www.ncbi.nlm.nih.gov/pubmed/22443445 https://www.proquest.com/docview/1011850020 https://www.proquest.com/docview/1836652982 https://www.osti.gov/biblio/1047906 https://pubmed.ncbi.nlm.nih.gov/PMC3348363 |
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