Download Mechanism of ribonuclease

Mechanism of ribonuclease
RNA structure
Structure Of RNase protein
• The size of RNase A is small:
• Has 124 amino acid
residues
• Contains 19 of the 20
natural amino acids,
lacking only tryptophan
• Has similar shape to a
kidney with active site
residues lying in the cleft
Structure Of RNase protein
• Long four-stranded
antiparallel β-sheet and
three short α-helixes
• Cross-linked by four
disulfide bonds
involving all eight of
its cysteine residues
Example of acid-base catalysis:
• Ribonucleases are enzymes that
hydrolyze RNA by cutting the P-O ester
bond attached to ribose 5’ carbon.
• It represents a typical example of acid
base catalysis.
Ribonuclease A
NH2
N
N
O
O
P
Adenosine
N
N
O CH2
O
O
O
Ribonuclease A
O
O
OH
N
P O
Uridine
O
O
CH2
O
O
P
O
N
O
OH
O
RNA Binding
SUBSTRATE SPECIFICITY:
• RNase A catalyzes the cleavage of the PO bond of an RNA strand and the
hydrolysis of the P-O bond of a nucleoside
2’,3’-cyclic phosphodiester on the 3’-side
of a pyrimidine residue.
• Pancreatic RNase is specific for a
pyrimidine base (uracil or cytosine) on the
3’ side of phosphate bond that is cleaved.
• The hydrolysis of RNA catalyzed by
RNase A occurs in two steps with a 2’,3’
cyclic phosphate diester intermediate.
Mechanism of RNase A
Figure 11-10 part 1
Mechanism of RNase A
Figure 11-10 part 2
In the formation of 2’,3’ cyclic phosphate diester
intermediate.
• His 12 acts as general base and remove the
proton from 2‘-hydroxy group of ribose.
• This will increase the nucleophilic character of
the oxygen atom.
• His 119 will act as general acid and protonate
one oxygen of the phosphate
–ve charge.
• The side chain of Lys41 and the main chain of
Phe120 enhance catalysis by stabilizing this
transition state