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Catalytic Site Atlas

CSA LITERATURE entry for 1l1l

E.C. nameribonucleoside-triphosphate reductase
SpeciesLactobacillus leichmannii (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1l1l
CSA Entries With UniProtID Q59490
CSA Entries With EC Number
PDBe Entry 1l1l
PDBSum Entry 1l1l
MACiE Entry M0140

Literature Report

IntroductionRibonucleotide 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.
MechansimThe 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.
Note the crystal structure is only of the apoenzyme. Not Cys731 and 736 are missing from this PDB file but are catalyitc residues.

Catalytic Sites for 1l1l

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysA408408macie:sideChainForms thiyl radical via hydrogen exchange with 5′-deoxyadenosyl radical, which exchanges a hydrogen to form a radical at the ribonucleoside triphosphate substrate. Later on return step occurs to regenerate original resting state.
GluA410410macie:sideChainDeprotonates riboside radical hydroxyl group to form a ketone and transfer radical to next carbon atom, with concomitant deprotonation of Cys119 and elimination of water. Later acts as a general acid to oxidise ketone to secondary alcohol. Forms part of redox chain with Asn406 to form radical on riboside again.
CysA119119macie:sideChainActs as a general acid to eliminate water from the riboside radical. Then nucleophilically attacks Cys419 to form a disulphide bridge. Later bridge is transferred to Cys419 and Cys731 with concomitant proton transfer to Cys119. Also the radical on Cys419 is transferred to the riboside via a redox chain, from Cys119 to Asn406.
CysA419419macie:sideChainActs as an electrophile to form disulphide bridge with Cys119, in concert with forming a radical via hydrogen exchange with the riboside radical. Later forms disulphide bridge with Cys731, then abstracts proton from Cys736 to return to original resting state.

Literature References

Notes:Note pdb missing Cys731 and Cys736 important catalytic residues also in MACiE.
Kolberg M
Structure, function, and mechanism of ribonucleotide reductases.
Biochim Biophys Acta 2004 1699 1-34
PubMed: 15158709
Wilkerson DP
Effect of work rate on the functional 'gain' of Phase II pulmonary O2 uptake response to exercise.
Respir Physiol Neurobiol 2004 142 211-223
PubMed: 15450481
Nordlund P
Ribonucleotide reductases.
Annu Rev Biochem 2006 75 681-706
PubMed: 16756507
Sampson HA
Safety of an amino acid-derived infant formula in children allergic to cow milk.
Pediatrics 1992 90 463-465
PubMed: 1518709