3.1.11.7: adenosine-5'-diphospho-5'-[DNA] diphosphatase
This is an abbreviated version!
For detailed information about adenosine-5'-diphospho-5'-[DNA] diphosphatase, go to the full flat file.
Word Map on EC 3.1.11.7
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3.1.11.7
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apraxia
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oculomotor
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single-strand
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ocular
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cerebellar
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early-onset
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hypoalbuminemia
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polynucleotide
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5'-adenylated
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xrcc4
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friedreich
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ataxia-oculomotor
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fen1
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forkhead-associated
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deadenylation
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medicine
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cross-complementing
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3'-phosphoglycolate
- 3.1.11.7
- apraxia
-
oculomotor
-
single-strand
-
ocular
- cerebellar
-
early-onset
- hypoalbuminemia
- polynucleotide
-
5'-adenylated
- xrcc4
- friedreich
-
ataxia-oculomotor
- fen1
-
forkhead-associated
-
deadenylation
- medicine
-
cross-complementing
-
3'-phosphoglycolate
transferred to EC 3.6.1.71
Synonyms
Synonyms
aprataxin, APTX, DNA-adenylate hydrolase, HNT3, RNA-DNA deadenylase
ECTree
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Reaction
Reaction on EC 3.1.11.7 - adenosine-5'-diphospho-5'-[DNA] diphosphatase
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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
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
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA]
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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
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