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Allosteric Regulation and Radical Transfer in Ribonucleotide Reductase
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The stability of biological life over time requires that the integrity of the genetic material of an organism, the genome, be maintained as it is passed on from one generation to the next. All known cellular life has DNA-based genomes, which are duplicated before each cell division in a process called replication. During and after DNA replication, the integrity of the genetic information is maintained by various proofreading and DNA repair mechanisms. The accuracy of DNA replication and repair is affected by DNA precursor pool imbalances. Feedback regulation of the enzymes involved in DNA precursor biosynthesis has evolved in parallel with the DNA replication and repair system in order to ensure stable precursor pools.

Ribonucleotide reductase (RNR), an enzyme that irreversibly reduces ribonucleotides into deoxyribonucleotides, is a key component in the regulation of the DNA precursor pools. It has sophisticated allosteric regulatory mechanisms that govern both overall activity and substrate specificity, responding to the cellular concentrations of ATP and of the triphosphate forms of the product deoxyribonucleotides, the final DNA precursors.

Using X-ray crystallography we have solved several structures of two ribonucleotide reductases, an anaerobic (class III) enzyme from Bacteriophage T4 and a coenzyme B12-dependent (class II) enzyme from Thermotoga maritima, in complex with various nucleotides and cofactors. The structural information reveals a complete molecular mechanism for the allosteric substrate specificity regulation of class II RNRs which, due to structural homology, is likely also to be valid for the aerobic class I RNRs. The work on the class III RNRs has produced a partial mechanism for the specificity regulation of this class. Both mechanisms utilize Loop 2, a conserved structural element, in the transmission of the allosteric signal.

The discovery of a metal binding domain in the anaerobic RNRs and details of coenzyme B12 binding shed more light on generation and transfer of the protein based radicals used in the reduction reaction.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik , 2004. , 57 p.
Keyword [en]
allosteric regulation, substrate specificity, ribonucleotide reductase, radical
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:su:diva-251ISBN: 91-7265-931-9 (print)OAI: oai:DiVA.org:su-251DiVA: diva2:191545
Public defence
2004-10-13, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 14:00 (English)
Opponent
Supervisors
Available from: 2004-09-22 Created: 2004-09-22 Last updated: 2009-04-06Bibliographically approved
List of papers
1. Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase
Open this publication in new window or tab >>Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase
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2004 (English)In: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 11, no 11, 1142-1149 p.Article in journal (Refereed) Published
Abstract [en]

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.

Keyword
NUCLEOTIDES, NUCLEIC acids, DNA -- Synthesis, GENES, DNA, HEREDITY
National Category
Biochemistry and Molecular Biology Physical Sciences
Identifiers
urn:nbn:se:su:diva-23368 (URN)10.1038/nsmb838 (DOI)
Available from: 2004-09-22 Created: 2004-09-22 Last updated: 2017-12-13Bibliographically approved
2. Structural Basis for Allosteric Substrate Specificity Regulation in Anaerobic Ribonucleotide Reductase
Open this publication in new window or tab >>Structural Basis for Allosteric Substrate Specificity Regulation in Anaerobic Ribonucleotide Reductase
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2001 In: Structure, ISSN 0969-2126, Vol. 9, no 8, 739-750 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23369 (URN)
Note
Part of urn:nbn:se:su:diva-251Available from: 2004-09-22 Created: 2004-09-22Bibliographically approved
3. Poised for radical transfer: crystal structure of a class II ribonucleotide reductase in complex with cobalamin and adenosine
Open this publication in new window or tab >>Poised for radical transfer: crystal structure of a class II ribonucleotide reductase in complex with cobalamin and adenosine
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-23370 (URN)
Note
Part of urn:nbn:se:su:diva-251Available from: 2004-09-22 Created: 2004-09-22 Last updated: 2010-01-13Bibliographically approved
4. A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase
Open this publication in new window or tab >>A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase
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2003 In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, Vol. 100, no 7, 3826-3831 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23371 (URN)
Note
Part of urn:nbn:se:su:diva-251Available from: 2004-09-22 Created: 2004-09-22Bibliographically approved

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