Ligand single-stranded DNA

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Basic Ligand Information

Molecular Structure
Picture of single-stranded DNA (click for magnification)
Molecular Formula
BRENDA Name
InChIKey
C15H25O17P4R5
single-stranded DNA
RGHHSNMVTDWUBI-UHFFFAOYSA-N
Synonyms:
(deoxyribonucleotide)n, 3'-phosphate DNA-termini, DNA with 3'-phosphate ends, DNA with 5'-phosphate ends, single stranded DNA, ss-DNA, ssDNA

Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (21 results)

EC NUMBER
PROVEN IN VIVO REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
ssDNA + ferrocene-labeled dideoxy-UTP = ssDNA-ddUFc + diphosphate
show the reaction diagram
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ssDNA + H2O = ?
show the reaction diagram
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single-stranded DNA + H2O = 5'-phosphomononucleotides
show the reaction diagram
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single-stranded DNA + H2O = ?
show the reaction diagram
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single stranded DNA + H2O = 5'-phosphomonoester oligonucleotides
show the reaction diagram
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single-stranded DNA + H2O = hydrolyzed single-stranded DNA
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ssDNA + H2O = 5'-phosphodinucleotide + 5'-phosphooligonucleotide
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single-stranded DNA + H2O = 5'-phosphooligonucleotides
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ssDNA + H2O = fragments of ssDNA
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ssDNA + H2O = ?
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In Vivo Product in Enzyme-catalyzed Reactions (3 results)

EC NUMBER
PROVEN IN VIVO REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
double-stranded DNA + H2O = single-stranded DNA + 5'-phospho-2'-deoxynucleotides
show the reaction diagram
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double-stranded DNA = single-stranded DNA
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DNA-RNA hybrid + H2O = ssDNA + 5'-phosphomonoester oligonucleotides
show the reaction diagram
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Substrate in Enzyme-catalyzed Reactions (56 results)

EC NUMBER
REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate
show the reaction diagram
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ssDNA + ferrocene-labeled dideoxy-UTP = ssDNA-ddUFc + diphosphate
show the reaction diagram
-
single-stranded DNA + H2O = 5'-phosphomononucleotides
show the reaction diagram
-
single stranded DNA + H2O = 5'-phosphomonoester oligonucleotides
show the reaction diagram
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ssDNA + H2O = nucleoside 3'-phosphate + ?
show the reaction diagram
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single-stranded DNA + H2O = ?
show the reaction diagram
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ssDNA + H2O = oligonucleotides + ?
show the reaction diagram
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DNA with 3'-phosphate ends + H2O = DNA + phosphate
show the reaction diagram
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ssDNA + H2O = ?
show the reaction diagram
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single-stranded DNA + H2O = ?
show the reaction diagram
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ssDNA + H2O = ?
show the reaction diagram
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Product in Enzyme-catalyzed Reactions (5 results)

EC NUMBER
REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
double-stranded DNA + H2O = single-stranded DNA + 5'-phospho-2'-deoxynucleotides
show the reaction diagram
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double-stranded DNA = single-stranded DNA
show the reaction diagram
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49-mer oligonucleotide + H2O = 3-alpha,beta-unsaturated aldehyde + 3'-phosphate DNA-termini
show the reaction diagram
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DNA-RNA hybrid + H2O = ssDNA + 5'-phosphomonoester oligonucleotides
show the reaction diagram
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DNA with 5'-hydroxyl ends + ATP = DNA with 5'-phosphate ends + ADP
show the reaction diagram
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Activator in Enzyme-catalyzed Reactions (27 results)

EC NUMBER
COMMENTARY
LITERATURE
ENZYME 3D STRUCTURE
ATP and protein hydrolysis
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RecA protein and single-stranded DNA are required for activity being attributed to a Ser/Lys dyad. The LexA protein represses the SOS regulon, which regulates the genes involved in DNA repair. In the presence of single-stranded DNA, the RecA interacts with repressor LexA, causing it to undergo an autocatalytic cleavage which disrupts the DNA-binding part of the repressor, and inactivates it. The consequent derepression of the SOS regulon leads to DNA repair
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the presence of single-stranded DNA stimulates the rate of dTTP hydrolysis about 100fold in the case of wild type enzyme
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the MacRFC complex (a protein complex of Mac-RFCS1, MacRFCS2, and MacRFCL) possesses very low intrinsic ATPase activity. This activity is stimulated about 33fold by ssDNA
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Inhibitor in Enzyme-catalyzed Reactions (14 results)

EC NUMBER
COMMENTARY
LITERATURE
ENZYME 3D STRUCTURE
strong inhibition of relaxation
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inhibits the reaction catalyzed by carboxyltransferase in a competitive manner with respect to both malonyl-CoA and biocytin. DNA and heparin can also bind to the enzyme simultaneously, but the binding of either molecule has a strong synergistic effect on binding of the other, binding structure and inhibition mechanism, overview
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Enzyme Kinetic Parameters

kcat Value (Turnover Number) (7 results)

EC NUMBER
TURNOVER NUMBER [1/S]
TURNOVER NUMBER MAXIMUM [1/S]
COMMENTARY
LITERATURE
115.5
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at 37°C, in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 3 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 10% (v/v) glycerol, 5% (v/v) dimethyl sulfoxide

KM Value (1 result)

EC NUMBER
KM VALUE [MM]
KM VALUE MAXIMUM [MM]
COMMENTARY
LITERATURE
0.016
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at 37°C, in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 3 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 10% (v/v) glycerol, 5% (v/v) dimethyl sulfoxide

Ki Value (2 results)

EC NUMBER
KI VALUE [MM]
KI VALUE MAXIMUM [MM]
COMMENTARY
LITERATURE

References & Links

Links to other databases for single-stranded DNA

ChEBI
PubChem
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PubChem