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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1b5d
Original Entry
Title:
Transferase
Compound:
Deoxycytidylate hydroxymethylase
Mutant:
No
UniProt/Swiss-Prot:
P08773-DCHM_BPT4
EC Class:
2.1.2.8
Other CSA Entries:
Overview of all sites for 1b5d
Homologues of 1b5d
Entries for UniProt/Swiss-Prot: P08773
Entries for EC: 2.1.2.8
Other Databases:
PDB entry: 1b5d
PDBsum entry: 1b5d
UniProt/Swiss-Prot: P08773
IntEnz entry: 2.1.2.8
Literature Report:
Introduction:
Deoxycytidylate (dCMP) 5-hydroxymethylase (CH) of bacteriophage T4 catalyses the addition of a protective hydroxymethyl group to cytosine monophosphate as a method of avoiding digestion by the host restriction systems. It requires the presence of methylenetetrahydrofolate (CH2THF)
Mechanism:
Glu60 acts through a water molecule to donate a proton to N10 of CH2THF allowing the formation of an imminium ion at the N5 position. This later permits the donation of a methyl group to dCMP.
The sulphur atom of Cys148 undergoes nucleophilic attack on the cytosine ring with the aid of Asp179 which donates a proton to the ring. Asp179 subsequently accepts the proton back, initiating attack on the carbon of the imminium ion by C5 of cytosine forming a bridging methyl group between the C5 of cytosine and N5 of THF. Cytosine loses a proton from the C5 position to reform the double bond and at the same time accepts a proton from Asp179. Loss of this proton to Asp179 causes a double bond to be formed at the new bridging methyl with concomitant lysis of the C-THF bond.
The pi system is then attacked by water at the new carbon which causes the lysis of the bond to cystine. A loss of a proton from the water results in formation of the product .
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 60 60Sidechain
Acid/baseWater
Promotes the formation of the imminium ion form of C2THF through a water.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7599133 Current protein Conservation of residue
PubMed ID 7599133 Current protein Mutagenesis of residue
PubMed ID 7599133 Current protein Kinetic studies
PubMed ID 10064578 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 148 148Sidechain
NucleophileSubstrate
Holds dCMP in position during the reaction and activates the C5 position. Allows the final addition of water.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7599133 Current protein Kinetic studies
PubMed ID 8068692 Current protein Kinetic studies
PubMed ID 8068692 Current protein Mutagenesis of residue
PubMed ID 10064578 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 179 179Sidechain
Acid/baseSubstrate
Acts as a proton acceptor and donor to dCMP
Evidence from paper Evidence concerns Evidence type
PubMed ID 8068692 Current protein Kinetic studies
PubMed ID 10064578 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 8068692 Current protein Mutagenesis of residue
Notes:
The cofactor C2THF was not crystalised with the enzyme.
References:
Which EBI biological databases are available and how do I access them? EBI Site Map