Cofactors

Adenosylcob(III)alamin.

Reaction Mechanisms

ribonucleoside-triphosphate reductase (class II) By Reference

Ribonucleotide reductase (RNR) is the enzyme responsible for the conversion of the four standard ribonucleotides, 5V -di(or tri)-phospho -adenosine, -cytidine, -guanosine, and -uridine, to their 2V -deoxyribonucleotide counterparts and thereby provides the precursors needed for both synthesis and repair of DNA. Class II enzymes are found in bacteria that can live under both aerobic and anaerobic conditions, and also in some of their phages. The prototype from this class is the monomeric enzyme from Lactobacillus leichmannii , but as more and more members of this class have been found that are predominately homodimers, the Lactobacillus enzyme seems to be rather an extreme of the class. They all, however, utilize a cobaltous cofactor, adenosylcobalamin, a vitamin B12 derivative, that interacts directly with an active site cysteine to form the reactive cysteine radical needed for ribonucleotide reduction.




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Step 6
• Step 7
• Step 8
• Step 9
• Step 10
• Step 11
• Step 12
• Step 13
• Products

The cofactor adenosylcobalamin generates a 5-deoxyadenosyl radical by homolytic cleavage of its carbon-cobalt bond generate a protein thiyl radical on the side chain of Cys408 via a hydrogen transfer reaction. The radical on the sulfur of Cys408 is transferred to the ribonucleoside triphosphate substrate via a hydrogen transfer reaction. Glu410 deprotonates the ribonucleoside radical, reducing the secondary alcohol group to a ketone group and transfers the radical to the next carbon along, resulting in the elimination of water and concomitant deprotonation of Cys119. The deoxyibonucleoside intermediate acquires a hydrogen from Cys419, transferring the radical to this residue. Cys419 then undergoes attack from Cys119, forming a disulfide bond. The radical on the Cys419-Cys119 species is transferred through a chain of hydrogen bonded active site residues, Asn406 and Glu410, to the substrate 2'-position. The ketone group is then re-oxidised to a secondary alcohol with concomitant deprotonation of Glu410. The 2'-deoxyribonucleoside triphosphate product is formed by hydrogen transfer from Cys408, generating a thiyl radical. The thiyl radical of Cys408 is transferred back to the deoxyadenosine via a hydrogen transfer. The cofactor is regenerated via a colligation reaction between the cobalamine portion and the deoxyadenosyl portion. The disulfide bond between Cys119 and Cys419 is transferred to Cys419 and Cys731 with concomitant proton transfer to Cys119. The disulfide bond between Cys419 and Cys731 is transferred to Cys731 and Cys736 with concomitant proton transfer to Cys419. The disulfide bond between Cys731 and Cys736 is transferred to Cys736 and the thioredoxin acceptor with concomitant proton transfer to Cys731. The disulfide bond between Cys736 and thioredoxin is transferred to the second free thiol of thioredoxin with concomitant proton transfer to Cys736, regenerating the enzyme and producing the fully oxidised thioredoxin.The exact order of events is unclear in the latter stages.


Catalytic Residues

AA	Uniprot	Uniprot Resid	PDB	PDB Resid
Cys	Q59490	119	1l1l	119
Cys	Q59490	408	1l1l	408
Cys	Q59490	736	1l1l	736
Cys	Q59490	731	1l1l	731
Glu	Q59490	410	1l1l	410
Cys	Q59490	419	1l1l	419
Asn	Q59490	406	1l1l	406

Step Components

overall product formed, proton transfer, enzyme-substrate complex formation, native state of cofactor regenerated, dehydration, intermediate formation, decoordination from a metal ion, colligation, electron relay, cofactor used, radical propagation, elimination (not covered by the Ingold mechanisms), enzyme-substrate complex cleavage, radical termination, coordination to a metal ion, hydrogen transfer, homolysis, bimolecular nucleophilic substitution, intermediate terminated, native state of enzyme regenerated, electron transfer, intermediate collapse, radical formation, overall reactant used, cyclisation, decyclisation, coordination, intramolecular nucleophilic substitution



Step 1.

The cofactor (a deoxy derivative of vitamin B12) decomposes via a homolysis reaction to produce B12 (the cobalamine, cobalt containing, portion) and deoxyadenosyl portion.



Step 2.

The deoxyadenosyl radical is transferred to Cys408 via a hydrogen transfer reaction



Step 3.

The radical on the sulfur of Cys408 is transferred to the ribonucleoside triphosphate substrate via a hydrogen transfer reaction.



Step 4.

Glu410 deprotonates the ribonucleoside radical, reducing the secondary alcohol group to a ketone group and transfers the radical to the next carbon along, resulting in the elimination of water and concomitant deprotonation of Cys119.



Step 5.

The deoxyibonucleoside intermediate acquires a hydrogen from Cys419, transferring the radical to this residue. Cys419 then undergoes attack from Cys119, forming a disulfide bond



Step 6.

The radical on the Cys419-Cys119 species is transferred through a chain of hydrogen bonded active site residues, Asn406 and Glu410, to the substrate 2'-position. The ketone group is then re-oxidised to a secondary alcohol with concomitant deprotonation of Glu410



Step 7.

The 2'-deoxyribonucleoside triphosphate product is formed by hydrogen transfer from Cys408, generating a thiyl radical



Step 8.

The thiyl radical of Cys408 is transferred back to the deoxyadenosine via a hydrogen transfer.



Step 9.

The cofactor is regenerated via a colligation reaction between the cobalamine portion and the deoxyadenosyl portion



Step 10.

The disulfide bond between Cys119 and Cys419 is transferred to Cys419 and Cys731 with concomitant proton transfer to Cys119. The exact order of events is unclear



Step 11.

The disulfide bond between Cys419 and Cys731 is transferred to Cys731 and Cys736 with concomitant proton transfer to Cys419. The exact order of events is unclear



Step 12.

The disulfide bond between Cys731 and Cys736 is transferred to Cys736 and the thioredoxin acceptor with concomitant proton transfer to Cys731. The exact order of events is unclear



Step 13.

The disulfide bond between Cys736 and thioredoxin is transferred to the second free thiol of thioredoxin with concomitant proton transfer to Cys736, regenerating the enzyme and producing the fully oxidised thioredoxin. The exact order of events is unclear



Products.

The products of the reaction.

View All 2 Reaction Mechanisms in M-CSA

Reaction Parameters

There are no kinetic parameters information for this Enzyme

Associated Proteins

Citations

• Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15.
• Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera.
• Early-Phase Drive to the Precursor Pool: Chloroviruses Dive into the Deep End of Nucleotide Metabolism.
• Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus.
• Prognostic and Immunological Potential of Ribonucleotide Reductase Subunits in Liver Cancer.
• Direct-Acting Antiviral Drug Modulates the Mitochondrial Biogenesis in Different Tissues of Young Female Rats.
• Adaptation of Lacticaseibacillus rhamnosus CM MSU 529 to Aerobic Growth: A Proteomic Approach.
• Anoxia Rapidly Induces Changes in Expression of a Large and Diverse Set of Genes in Endothelial Cells.
• Antioxidant Mechanism of Lactiplantibacillus plantarum KM1 Under H₂O₂ Stress by Proteomics Analysis.
• Low salinity activates a virulence program in the generalist marine pathogen Photobacterium damselae subsp. damselae.
• Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin.