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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1ra0
Original Entry
Title:
Hydrolase
Compound:
Cytosine deaminase
Mutant:
Yes
UniProt/Swiss-Prot:
P25524-CODA_ECOLI
EC Class:
3.5.4.1
Other CSA Entries:
Overview of all sites for 1ra0
Homologues of 1ra0
Entries for UniProt/Swiss-Prot: P25524
Entries for EC: 3.5.4.1
Other Databases:
PDB entry: 1ra0
PDBsum entry: 1ra0
UniProt/Swiss-Prot: P25524
IntEnz entry: 3.5.4.1
Literature Report:
Introduction:
Cytosine deaminase (CD) catalyses the deamination of cytosine to uracil and ammonia. It is an enzyme produced by bacteria and yeast, but not mammalian cells, and is a potential gene therapy agent. CD deaminates 5-fluorocytosine to potent antimetabolite 5-fluorouracil, which can block DNA replication in cells.

Bacterial CD (bCD) is capable of deaminating a wide range of cytosine derivatives with varying efficiency. It is dependent of Fe2+ for maximal catalytic activity.
Mechanism:
The reaction mechanism proceeds through the stereo-specific addition of a metal-bound hydroxyl group, acting as a nucleophile, to the cytosine substrate at the C4 position. A tetrahedral transition state is formed that decomposes through the elimination of ammonia to form the product uracil.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLNA 156 157Sidechain
ElectrostaticSubstrate
Gln156 forms hydrogen bonds with the N1 nitrogen and O2 oxygen of the pyrimidine ring, helping to orientate the substrate, and polarise the aromatic structure of the pyrimidine ring, also making the C4 carbon more reactive towards an addition by the activated water molecule.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11812140 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 217 218Sidechain
Acid/baseSubstrate
Glu217 acts as a catalytic acid/base residue. It donates a proton to the N3 nitrogen, increasing the susceptibility of the C4 carbon to nucleophilic attack by weakening the N3 to C4 double bond character.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11812140 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15381761 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
FEA 500 0
ElectrophileWater
The Fe2+ ion acts as an electrophile to help activate the water molecule, resulting in the formation of the attacking hydroxyl group.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8226944 Current protein Ligand is essential for catalysis
PubMed ID 8226944 Current protein Kinetic studies
PubMed ID 11812140 Current protein Residue is positioned appropriately (ligand position known)
Notes:
Evidence seems a bit weak. The mechanisms in different articles correspond, but the only solid evidence for the involvement of the Glu and Gln residues is crystallography.
References:
Which EBI biological databases are available and how do I access them? EBI Site Map