Cofactors

Zn(2+).

Reaction Mechanism

cytidine deaminase By Reference

Cytosine deaminase (CD) catalyses the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The enzyme is of widespread interest both for antimicrobial drug design and for gene therapy applications against tumours.




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Products

The full catalytic cycle is composed of three major steps, including the substrate (cytosine) binding, the release of ammonia and the departure of the product (uracil) from the active site.

The catalytic zinc ion is bound to His102, Cys129, Cys132, and a catalytic water. The positive charge of the metal ion polarises the O-H bond in water, increasing its acidity towards the close proximity Glu104. Thus, the first step involved the proton transfer from the zinc-bound water to Glu104, the rotation of the carboxyl group of Glu104 and the proton transfer from the protonated Glu104 to cytosine. The subsequent nucleophilic attack at the C2 of the substrate by the resulting hydroxide anion leads to a tetrahedral intermediate. The second step concerns the formation of both ammonia and uracil. Once again this steps involves the proton transfers from the zinc-bound hydroxide anion to Glu104 and from Glu104 to the amine group which are stepwise rather than synchronous as in the first step. This step forms ammonia and uracil. Uracil remains strongly bound to the zinc metal. The final step consists of several proton transfers shuttled by Glu104 and one nucleophilic attack. One water molecule, which replaces the ammonia from the second step, heterolytically splits with its proton going to Glu104 and the hydroxide anion synchronously attacking C2 of uracil.

Catalytic Residues

AA	Uniprot	Uniprot Resid	PDB	PDB Resid
Cys	P0ABF6	132	1ctt	132
His	P0ABF6	102	1ctt	102
Glu	P0ABF6	104	1ctt	104
Cys	P0ABF6	129	1ctt	129

Step Components

proton transfer, unimolecular elimination by the conjugate base, bimolecular nucleophilic addition, native state of enzyme regenerated, deamination



Step 1.

Glu104 deprotonates water.



Step 2.

This step may well occur in a concerted manner with step 1. Glu104 rotates in the active site and donates its proton to the cytidine substrate.



Step 3.

Activated water initiates a nucleophilic attack on the substrate in an addition reaction.



Step 4.

Glu104 deprotonates the added hydroxyl group.



Step 5.

The oxyanion collapses, eliminating ammonia with concomitant deprotonation of Glu104. Water displaces the product(s) from the active site.



Products.

The products of the reaction.

View Reaction Mechanisms in M-CSA

Reaction Parameters

There are no kinetic parameters information for this Enzyme

Associated Proteins

Citations

• A new technique for the analysis of metabolic pathways of cytidine analogues and cytidine deaminase activities in cells.
• Cytidine deaminase status as a marker of response to azacytidine treatment in MDS and AML patients.
• Cytidine deaminase enzyme activity is a predictive biomarker in gemcitabine-treated cancer patients.
• Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.
• Enhanced single-base mutation diversity by the combination of cytidine deaminase with DNA-repairing enzymes in yeast.
• Mutagenesis system by fusing cytidine deaminase with T7 promoter in yeast
• Necessity of HuR/ELAVL1 for the activation-induced cytidine deaminase-dependent decrease in topoisomerase 1 in antibody diversification.
• The APOBEC3B cytidine deaminase is an adenovirus restriction factor.
• Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system.
• The cytidine deaminase APOBEC3A is required for large ribosomal subunit biogenesis
• [Activation-induced cytidine deaminase (AID) involved in the regulation of B cell immune senescence].