Nucleoside deoxyribosyltransferase

 

Nucleoside 2'-deoxyribosyltransferase catalyses cleavage of the 2'-deoxyribosyl-nucleoside glycosidic bond through the formation of a covalent deoxyribosyl-enzyme intermediate. The enzyme is found in various Lactobacilli species where it participates in nucleoside recycling. There is considerable interest for nucleoside 2'-deoxyribosyltransferase to be used as an industrial biocatalyst in creating natural and non-natural nucleosides.

 

Reference Protein and Structure

Sequence
Q9R5V5 UniProt (2.4.2.6) IPR007710 (Sequence Homologues) (PDB Homologues)
Biological species
Lactobacillus leichmannii (Bacteria) Uniprot
PDB
1f8x - CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE (2.5 Å) PDBe PDBsum 1f8x
Catalytic CATH Domains
3.40.50.450 CATHdb (see all for 1f8x)
Click To Show Structure

Enzyme Reaction (EC:2.4.2.6)

2'-deoxyadenosine
CHEBI:17256ChEBI
+
cytosine
CHEBI:16040ChEBI
→
2'-deoxycytidine
CHEBI:15698ChEBI
+
adenine
CHEBI:16708ChEBI
Alternative enzyme names: Trans-N-deoxyribosylase, Trans-N-glycosidase, Trans-deoxyribosylase, Deoxyribose transferase, Nucleoside trans-N-deoxyribosylase, Nucleoside deoxyribosyltransferase I (purine nucleoside:purine deoxyribosyltransferase: strictly specific for transfer between purine bases), Nucleoside deoxyribosyltransferase II (purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyltransferase), Purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyl transferase,

Enzyme Mechanism

Introduction

The mechanism is thought the proceed via double displacement, resulting in retention of stereochemical configuration in the product, much like the retaining glycosidases. The catalytic nucleophile Glu98 attacks at the scissile glycosidic bond of 2'-deoxyribose-nucleoside, forming an enzyme-substrate intermediate which then collapses on attack by the second base, forming a new deoxyribosyl nucleoside. Asp92 is thought to act as a general acid to the departing glycosidic oxygen while Asp72 stabilises the oxo-carbenium character transition state. It is then proposed for the incoming nucleobase act as a nucleophile to form a new 2'-deoxyribonucleoside. What is still unclear is whether the mechanism is Sn1, with oxocarbenium ion intermediates or Sn2 through a oxocarbenium ion like transition state. More research is needed to identify this and also the exact nature attack of the nucleobase in the latter part of the mechanism.

Catalytic Residues Roles

UniProt PDB* (1f8x)
Tyr7 Tyr7A The phenolic oxygen of the residue hydrogen bonds to the nucleophilic Glu98, orientating it towards the substrate in catalysis. electrostatic stabiliser
Glu98 Glu98A The residue acts as a nucleophile towards the substrate glycosidic link in an overall double inversion attack. It is positioned for catalysis by hydrogen bonding to the close proximity Tyr7. covalently attached, electrostatic stabiliser
Asp72 Asp72A The reside acts to stabilise the oxo-carbenium ion transition state. electrostatic stabiliser
Asp92 Asp92A The residue is thought to act as a general acid to the glycosidic oxygen of the cleaved bond. proton shuttle (general acid/base), proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Short SA et al. (1996), J Biol Chem, 271, 4978-4987. Active Site Amino Acids That Participate in the Catalytic Mechanism of Nucleoside 2`-Deoxyribosyltransferase. DOI:10.1074/jbc.271.9.4978. PMID:8617773.
  2. Fresco-Taboada A et al. (2013), Appl Microbiol Biotechnol, 97, 3773-3785. New insights on nucleoside 2'-deoxyribosyltransferases: a versatile biocatalyst for one-pot one-step synthesis of nucleoside analogs. DOI:10.1007/s00253-013-4816-y. PMID:23529679.
  3. Armstrong SR et al. (1996), Structure, 4, 97-107. Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. DOI:10.1016/s0969-2126(96)00013-5. PMID:8805514.
  4. Porter DJ et al. (1995), J Biol Chem, 270, 15551-15556. Identification of the Active Site Nucleophile in Nucleoside 2-Deoxyribosyltransferase as Glutamic Acid 98. DOI:10.1074/jbc.270.26.15551. PMID:7797550.
  5. McCarter JD et al. (1994), Curr Opin Struct Biol, 4, 885-892. Mechanisms of enzymatic glycoside hydrolysis. DOI:10.1016/0959-440X(94)90271-2.

Step 1.

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Catalytic Residues Roles

Residue Roles
Glu98A electrostatic stabiliser, covalently attached
Asp72A electrostatic stabiliser
Asp92A proton donor, proton shuttle (general acid/base)
Tyr7A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday, Morwenna Hall