Ribonucleotide reductase

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Ribonucleotide diphosphate reductase, large subunit

Existing structural data : 2WGH , 3HNC , 3HND , 3HNE , 3HNF

Properties of human protein
Mass / length primary structure 792 amino acids
Secondary to quaternary structure Heterodimer
Identifier
Gene names RRM1 R1; RIR1; RR1
External IDs
Enzyme classification
EC, category 1.17.4.1 ,  oxidoreductase
Response type Reduction of a hydroxyl group
Substrate Deoxyribonucleotide Diphosphate + Thioredoxin Disulfide + H 2 O
Products Ribonucleotide Diphosphate + Thioredoxin
Occurrence
Parent taxon Creature
Exceptions Archaea
Orthologue
human House mouse
Entrez 6240 20133
Ensemble ENSG00000167325 ENSMUSG00000030978
UniProt P23921 P07742
Refseq (mRNA) NM_001033 NM_009103
Refseq (protein) NP_001024 NP_033129
Gene locus Chr 11: 4.09 - 4.14 Mb Chr 7: 102.44 - 102.47 Mb
PubMed search 6240 20133

Ribonucleotide diphosphate reductase, small subunit
Ribonucleotide diphosphate reductase, small subunit
Ribbon model of the dimer of the R2 subunit of the Class I RNR of Escherichia coli , according to PDB  1AV8

Existing structural data : 2UW2 , 3OLJ , 3VPM , 3VPN , 3VPO

Properties of human protein
Mass / length primary structure 389 amino acids
Secondary to quaternary structure Heterodimer
Cofactor 2 Fe 2+
Identifier
Gene names RRM2 R2; RR2; RR2M
External IDs
Enzyme classification
EC, category 1.17.4.1 ,  oxidoreductase
Response type Reduction of a hydroxyl group
Substrate Deoxyribonucleotide Diphosphate + Thioredoxin Disulfide + H 2 O
Products Ribonucleotide Diphosphate + Thioredoxin
Occurrence
Homology family RNR subunit M2
Parent taxon Euteleostomi
Orthologue
human House mouse
Entrez 6241 20135
Ensemble ENSG00000171848 ENSMUSG00000020649
UniProt P31350 P11157
Refseq (mRNA) NM_001034 NM_009104
Refseq (protein) NP_001025 NP_033130
Gene locus Chr 2: 10.12 - 10.13 Mb Chr 12: 24.71 - 24.71 Mb
PubMed search 6241 20135

The ribonucleotide reductase (often called RNR is abbreviated) an enzyme which is the last link in the chain of synthesis of the DNA forming building blocks. It reduces the 2'- hydroxy group of nucleotides .

Meaning and occurrence

Ribonucleotide reductase is an indispensable enzyme in the organism to produce DNA building blocks.

Since the enzyme reduces the 2'-hydroxy group of the nucleotides, it can also be seen as a link between the DNA and RNA world. In this context, there is also speculation as to whether RNR was the enzyme that paved the way from a primitive RNA to today's DNA world. (See also: chemical evolution and ribozyme )
Like many enzymes, the ribonucleotide reductase also catalyzes the corresponding reverse reaction ( oxidation of deoxynucleotide to nucleotide). However, this reaction does not play a role in biological processes.

Biological function

The catalyzed reaction of the RNA

The ribonucleotide reductase reduces the nucleotides into their respective deoxynucleotides. The enzyme does not differentiate which nucleotide it is ( adenosine , guanosine , cytidine or thymidine phosphates), both di- and the respective triphosphates are reduced. Monophosphates and (phosphate-free) nucleosides are not converted.

There are several classes of ribonucleotide reductase (Class I to Class III). Although all classes catalyze the same reaction , they are structurally very different. The classes are divided according to the way the system generates the radical. Each class is divided into further subclasses; but for the sake of simplicity this should not be carried out.

Class I.

Class I ( EC  1.17.4.1 ) is the type of enzyme that occurs in humans and has been best studied. The enzymes are aerobic .
Class I-RNR are made up of two different sub-units: R1 and R2.

Molecular structure of the tyrosyl radical (left) with the neighboring iron-oxygen-iron complex (right) which stabilizes the radical.

R1 contains several binding sites for effectors, as well as the binding pocket ( active site ) in which the nucleotide is reduced. In R2, a radical is stored on a tyrosine side chain. This radical has an astonishingly long half-life of around four days. R1 and R2 have a very low affinity , so that the enzyme is rarely present as an overall complex. This is also the reason why it has never been possible to crystallize the ribonucleotide reductase as a whole .

For the catalytic step, the radical has to be transported from the tyrosyl radical in R2 to a cysteine in R1. The distance is estimated to be 35  angstroms . Presumably, the electron skips several amino acids in order to cover the enormous distance (by molecular standards).

Class II

Class II-RNR ( EC  1.17.4.2 ) occur in the organism Lactobacillus lehmannii . Here the radical is generated in situ by breaking the cobalt - carbon bond in coenzyme B12 . Enzymes in this class are facultatively aerobic . You can work in the presence or in the absence of oxygen.

Class III

Here the radical is stored on a glycyl side chain. Bacteriophage T4, for example, works with this class of enzyme. Class III RNRs are anaerobic , meaning they only work in an oxygen-free environment.

Mechanism of reduction

The exact process of nucleotide reduction has not yet been fully clarified. There is clear evidence of a radical mechanism, the central step being the formation of a thiyl radical, a sulfur-centered radical. To do this, the enzyme stores a stable radical that has to be transported into the binding pocket with every turn-over . After the chemical reaction, the radical is recovered and transported back to the 'storage location'. It is assumed that the electron hops over several amino acids, all of which are connected by hydrogen bonds .

The following diagram shows the process with the assumed intermediate steps as it is currently being discussed in science.

Biochemical mechanism of the reduction of a nucleotide
  • First, a radical is transferred to the 3 'position of the ribose (step from 1st to 2nd picture).
  • After splitting off water at the 2 'position (Fig. 2 → 3), the radical is transferred to two cysteine ​​chains of the enzyme (Fig. 3 → 4).
  • The radical is then transferred back to the original cysteine ​​via ribose (Fig. 4 → 6).

Overall, with oxidation of two cysteine ​​side chains, the ribose is reduced to deoxyribose. A DNA building block was produced from an RNA component. This building block is now ready to be built into the DNA double helix by the DNA polymerase .

regulation

Since the RNA only needs to be active in specific phases of cell division, there are mechanisms, as with most enzymes, to switch the RNA on and off. In addition, in a complicated system it is precisely regulated which of the four nucleotides is to be reduced. The activators and effectors are only briefly listed here, without going into the details:

Activators:

  • ATP activates the enzyme
  • dATP disables it

Effectors:

  • ATP and dATP → CDP / CTP and UDP / UTP are reduced
  • dGTP → ADP / ATP
  • dTTP → GDP / GTP

Discovery of ribonucleotide reductase

Since the structure of DNA was elucidated by James Watson and Francis Crick in 1953, the question arose of how the cell produces the individual building blocks for the DNA polymer. Eight years later, an enzyme mixture was isolated from different cells for the first time, with a high level of activity in reducing nucleotides into their corresponding deoxynucleotides.

In the 1990s, the three-dimensional structures of the two subunits were determined separately by means of crystal structure studies . Questions about the mechanism of the docking of the two subunits R1 and R2 to one another, the transport of radicals by the enzyme over a relatively large distance and the generation of the radical during the production of the enzyme are examined.

The RNR in Cancer Research and Cancer Therapy

Ribonucleotide reductase is also the focus of cancer research . Because the enzyme is needed whenever the cell divides or has to repair DNA damage, the cell depends on the RNA for growth. The enzyme is comparatively slow with a turnover rate of approx. 10  s −1 . This is not a problem due to the slow rate of division of normal cells, but cancer cells are inhibited from rapid growth. However, there are cancer cells that increase the turnover rate of the RNA through modifications. An active ingredient that blocks precisely these modified enzymes would slow down or even stop cancer growth.

In the treatment of myeloid leukemia (especially when there are signs of leukostasis ) and other myeloproliferative diseases such as essential thrombocythemia and polycythemia vera (rubra), hydroxycarbamide (e.g. Syrea®, Litalir®), an inhibitor of ribonucleotide reductase, is used as a chemotherapeutic agent used.

Sources and further information

Individual evidence

  1. ↑ Homologues at OMA
  2. ↑ a b Ulla Uhlin, Hans Eklund: Structure of ribonucleotide reductase protein R1. In: Nature , Volume 370, 1994, pp. 533-539.
  3. ↑ Britt-Marie Sjöberg et al .: Two conserved tyrosine residues in R1 participate in an intermolecular electron transfer in ribonucleotide reductase. In: J. Biol. Chem. , Vol. 271, No. 34, 1996, pp. 20655-20659.
  4. ↑ Stubbe et al. In: Chem. Rev. , Volume 98, 1998, pp. 705-762.
  5. ↑ JoAnne Stubbe, Daniel G. Nocera et al .: Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer? In: Chemical Reviews , Volume 103, 2003, pp. 2167-2201.
  6. ↑ Peter Reichard, Astor Baldesten, Lars Rutberg: Formation of deoxycytidine phosphates from cytidine phosphates in extracts from Escherichia coli. In: J Biol Chem . , Vol. 236, No. 4, 1961, pp. 1150-1157.
  7. ↑ P. Nordlund, B.-M. Sjöberg, H. Eklund: Three-dimensional structure of the free radical protein of ribonucleotide reductase. In: Nature , Vol. 345, 1990, pp. 593-598.
  8. ↑ Yun Yen: Ribonucleotide reductase subunit one as gene therapy target. In: Clinical Cancer Research , Volume 9, 2003, pp. 4304-4308.

literature

Web links

This version was added to the list of articles worth reading on November 22, 2006 .