Tuesday, January 19, 2016

Bio (8): Nucleases, methylatransferases..........

Enzymes can be of six types i.e. hydrolases, transferases, lyases, oxidoreductases, isomerases and ligases. Examples of each category are hydrolases (peptidase, lipase, esterase, phosphatase, dehalogenase, deacylase, ), transferases (methyl, acyl, amino (transaminase), adenocyl, rhamnosyl, sufuryl (sulfurase); kinasepolymerase); lyases (dehydratase, decarboxylase, cyclase), oxidoreductases (peroxidases, hydroxylases, oxidase, reductase, dehydrogenase, dioxygenase), isomerases (racemase, epimerase, mutse) and ligases (synthase). 
#Enzymes often have domains belonging to multiple classes, making things complicated.
#As enzymes are pH and temperature-sensitive, they often undergo changes and become hypothetical. It misleads our understanding of pathogen biology.
#Chymotrypsin fold has His490, Asp552 and Ser646
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A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids
Nuclease might be endonucleases or exonucleases; also might be deoxyribonuclease (cleaving DNA) and ribonuclease (cleaving RNA).
Nuclease is a subgroup of the hydrolases.
Restriction nuclease cuts nucleic acid at specific restriction sites and produce restriction fragments (used as atool in recombinant DNA technology). It can be Type I and II (recognize 4 to 8 bp sequence).
Homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them.Homing endonucleases bind very long (12 to 40 bp), even asymmetric recognition sequences.
HNH domain in ndonuclease create zinc finger.
S1 P1 nuclease (a 36kb glycoprotein): cleave RNA and single stranded DNA
S1 nuclaese needs Zn2+ cofactor for catalysis (So, starving bacteria of Zn might help to kill it. In host Zn is anundant; does in vitro medium has Zn?)
PIN (N-terminus of the PilT protein) domain cleaves single stranded RNA in a sequence dependent manner
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Methyltransferases are enzymes that methylate their substrates
class I: have Rossman fold for binding S-Adenosyl methionine (SAM).
class II methyltransferases: contain a SET domain
class III methyltransferases: membrane associated
They can be classified as protein methyltransferases, DNA methyltransferases, Natural product methyltransferases, and Non-SAM dependent methyltransferases.

SAM is the classical methyl donor for methyltrasferases
Methionine sulfur serves as the nucleophile that transfers the methyl group of SAM to the enzyme substrate.
Dam methylase (Deoxyadenosine methylase) adds a methyl group to the adenine of the sequence 5'-GATC-3' in DNA

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