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InterPro: IPR000358 Ribonucleotide reductase
Protein matches
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UniProtKB Matches: 2412 proteins |
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Accession
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IPR000358 Ribonucl_redctse |
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Type
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Family |
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Signatures
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InterPro Relationships
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Contains
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IPR012348 Ribonucleotide reductase-related
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GO Term annotation
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Process
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GO:0009186 deoxyribonucleoside diphosphate metabolic process
GO:0055114 oxidation reduction
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Function
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GO:0004748 ribonucleoside-diphosphate reductase activity
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InterPro annotation
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 Entry Details in BioMart
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Abstract
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Ribonucleotide reductase (EC:1.17.4.1) [1, 2] catalyzes the reductive synthesis
of deoxyribonucleotides from their corresponding ribonucleotides:
2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O = ribonucleoside diphosphate + reduced thioredoxin
It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a
diiron-tyrosyl radical, Class II RNRs, found in bacteria,
bacteriophage, algae and archaea, use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs, found in
anaerobic bacteria and bacteriophage, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Many
organisms have more than one class of RNR present in their
genomes.
Ribonucleotide reductase is an
oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a
small subunit (300 to 400 residues) - class II RNRs are less complex,
using the small molecule B12 in place of the small chain [3].
The small chain binds two iron atoms [4] (three Glu, one Asp, and two His are
involved in metal binding) and contains an active site tyrosine radical. The
regions of the sequence that contain the metal-binding residues and the active
site tyrosine are conserved in ribonucleotide reductase small chain from
prokaryotes, eukaryotes and viruses.
We have selected one of these regions as a signature pattern. It contains the
active site residue as well as a glutamate and a histidine involved in the
binding of iron.
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Structural links
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Database links
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Pfam Clan: CL0044.10
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Publications
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1.
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Nilsson O, Lundqvist T, Hahne S, Sjoberg BM.
Structure-function studies of the large subunit of ribonucleotide reductase from Escherichia coli.
Biochem. Soc. Trans. 16 91-4 1988
[PubMed: 3286319]
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2.
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Reichard P.
From RNA to DNA, why so many ribonucleotide reductases?
Science 260 1773-7 1993
[PubMed: 8511586]
http://www.sciencemag.org/cgi/content/abstract/260/5115/1773
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3.
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Sintchak MD, Arjara G, Kellogg BA, Stubbe J, Drennan CL.
The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer.
Nat. Struct. Biol. 9 293-300 2002
[PubMed: 11875520]
http://dx.doi.org/10.1038/nsb774
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4.
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Nordlund P, Sjoberg BM, Eklund H.
Three-dimensional structure of the free radical protein of ribonucleotide reductase.
Nature 345 593-8 1990
[PubMed: 2190093]
http://dx.doi.org/10.1038/345593a0
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Additional Reading
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Uppsten M, Davis J, Rubin H, Uhlin U.
Crystal structure of the biologically active form of class Ib ribonucleotide reductase small subunit from Mycobacterium tuberculosis.
FEBS Lett. 569 2004 117-22
[PubMed: 15225619]
http://dx.doi.org/10.1016/j.febslet.2004.05.059
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Sommerhalter M, Saleh L, Bollinger JM Jr, Rosenzweig AC.
Structure of Escherichia coli ribonucleotide reductase R2 in space group P6122.
Acta Crystallogr. D Biol. Crystallogr. 61 2005 1649-54
[PubMed: 16301799]
http://dx.doi.org/10.1107/S0907444905034062
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Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F.
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies.
J. Biol. Chem. 280 2005 11233-46
[PubMed: 15634667]
http://dx.doi.org/10.1074/jbc.M414634200
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Uppsten M, Farnegardh M, Domkin V, Uhlin U.
The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action.
J. Mol. Biol. 359 2006 365-77
[PubMed: 16631785]
http://dx.doi.org/10.1016/j.jmb.2006.03.035
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Hogbom M, Nordlund P.
A protein carboxylate coordinated oxo-centered tri-nuclear iron complex with possible implications for ferritin mineralization.
FEBS Lett. 567 2004 179-82
[PubMed: 15178319]
http://dx.doi.org/10.1016/j.febslet.2004.04.068
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Nordlund P, Eklund H.
Structure and function of the Escherichia coli ribonucleotide reductase protein R2.
J. Mol. Biol. 232 1993 123-64
[PubMed: 8331655]
http://dx.doi.org/10.1006/jmbi.1993.1374
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InterPro 23.1
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