EC Number   |
Reaction |
Reference |
|---|
   3.1.11.7 | adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA] |
a two-step mechanism for hydrolysis of 5'-AMP from RNA-DNA and DNA, APTX catalytic mechanism, overview. In the first step, the active site nucleophile (His260 of the HIT loop in APTX) attacks the 5'-adenylate phosphoanhydride forming a transient enzyme-AMP intermediate and releasing a DNA vphosphate product. Several hydrogen bonds with active-site residues and peptide backbone amides stabilize the negative charge on the transitin-state of step 1. The nucleophile (His260) is activated by a hydrogen bond to the carbonyl of His258, while His251 is proposed to protonate the 5'-phosphate leaving group. The second step involves hydrolysis of the His260-AMP-RNA/DNA intermediate, using chemistry that is essentially the reverse of the first step with water replacing the 5'-phosphate, and with His251 proposed to act as a general base to deprotonate a water nucleophile |
752086 |
| 3.1.11.7 | adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA] |
the catalytic reaction proceeds in three steps: substrate protonation, DNA deadenylation and histidine-AMP intermediate hydrolysis. The calculated activation energies for the second and third reactions are 19.0 and 10.5 kcal/mol, which can be attributed to a penta-coordinated AMP-phosphoryl formation and closing of a water molecule, respectively. A histidine-AMP intermediate is hydrolyzed easily in the third step when a water molecule closes within 3 A to the phosphorus nucleus |
750307 |
| 3.1.11.7 | adenosine-5'-diphospho-5'-[DNA] + H2O = AMP + phospho-5'-[DNA] |
a two-step mechanism for hydrolysis of 5'-AMP from RNA-DNA and DNA, APTX catalytic mechanism, overview. In the first step, the active site nucleophile (His260 of the HIT loop in APTX) attacks the 5'-adenylate phosphoanhydride forming a transient enzyme-AMP intermediate and releasing a DNA 5'-phosphate product. Several hydrogen bonds with active-site residues and peptide backbone amides stabilize the negative charge on the transition-state of step 1. The nucleophile (His260) is activated by a hydrogen bond to the carbonyl of His258, while His251 is proposed to protonate the 5'-phosphate leaving group. The second step involves hydrolysis of the His260-AMP-RNA/DNA intermediate, using chemistry that is essentially the reverse of the first step with water replacing the 5'-phosphate, and with His251 proposed to act as a general base to deprotonate a water nucleophile |
752086 |
| 3.1.11.7 | adenosine-5'-diphospho-5'-[DNA] + H2O = AMP + phospho-5'-[DNA] |
the catalytic reaction proceeds in three steps: substrate protonation, DNA deadenylation and histidine-AMP intermediate hydrolysis. The calculated activation energies for the second and third reactions are 19.0 and 10.5 kcal/mol, which can be attributed to a penta-coordinated AMP-phosphoryl formation and closing of a water molecule, respectively. A histidine-AMP intermediate is hydrolyzed easily in the third step when a water molecule closes within 3 A to the phosphorus nucleus |
750307 |
