hm5CSN – 5'-hydroxymethylcytosine

Name
WID	hm5CSN
Name	5'-hydroxymethylcytosine
Traditional name	4-amino-5-(hydroxymethyl)-1H-pyrimidin-2-one
IUPAC name	4-amino-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one
Cross references	PubChem: 8194137

Classification
Type	modified_nucleobase

Structure
Empirical formula (pH 7.5)	H₇C₅N₃O₂
SMILES (pH 7.5)	C(C1=CNC(=O)N=C1N)O
Charge (pH 7.5)	0
Is hydrophobic	False
Molecular weight (Da)	141.13
van der Waals volume (pH 7.5; Å³ molecule^‑1)	117.56
pI	12.09
logP	-2.12
logD (pH 7.5)	-2.12

Function
Reaction participant	DNA base glucosyl transfer (5'-hydroxymethylcytosine ==> beta-D-glucosylhydroxymethylcytosine; glucose) [c]: GLC + hm5CSN ⇒ glchm5CSN + H2O DNA radiation (gamma-ray) induced base oxidation (5-methylcytosine ==> 5'-hydroxymethylcytosine; hydroxyl radical) gamma_radiation[e] + hydroxyl_radical[c] + m5CSN[c] ⇒ H[c] + hm5CSN[c]

Comments
Comments	occurs in bacteriophage DNA [PUB_0477]; majority of m5dC in bacteria is due to action of restriction-modification systems [PUB_0478]; 100% replacement cytidine in E. coli phages T2, T4, T6 [PUB_0478]; hypermodification renders bacteriophage DNA resistant to several restriction endonucleases [PUB_078]
References	Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. FASEB J 9, 1034-42 (1995). WholeCell: PUB_0478, PubMed: 7649402 Warren RA. Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34, 137-58 (1980). WholeCell: PUB_0477, PubMed: 7002022

Metadata
Created	2012-10-01 15:07:00
Last updated	2012-10-01 15:12:15