Page last updated: 2024-10-24

DNA-directed DNA polymerase activity

Definition

Target type: molecularfunction

Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group. [EC:2.7.7.7, GOC:vw, ISBN:0198547684]

DNA-directed DNA polymerase activity is a fundamental enzymatic process that underlies DNA replication and repair. DNA polymerases catalyze the synthesis of new DNA strands by adding nucleotides to a pre-existing DNA template strand. The process involves the following steps:

1. **Template Binding:** The DNA polymerase binds to the template DNA strand, which serves as a guide for the synthesis of the new strand.
2. **Primer Recognition:** The polymerase recognizes and binds to a short primer strand of RNA or DNA that has already been synthesized and annealed to the template. This primer provides a free 3'-hydroxyl group to which the polymerase can add nucleotides.
3. **Nucleotide Selection and Incorporation:** The polymerase selects and incorporates the correct nucleotide based on the complementary base pairing rules. Each incoming nucleotide must pair with its complementary base on the template strand (adenine with thymine, guanine with cytosine).
4. **Phosphate Transfer:** The polymerase catalyzes the formation of a phosphodiester bond between the 3'-hydroxyl group of the primer and the 5'-phosphate group of the incoming nucleotide, adding the new nucleotide to the growing DNA chain.
5. **Translocation:** After each nucleotide is added, the polymerase moves along the template strand in a process called translocation, preparing for the addition of the next nucleotide.

DNA polymerases are essential for maintaining genetic integrity and ensuring the faithful transmission of genetic information during cell division. They play critical roles in various cellular processes, including:

* **DNA Replication:** DNA polymerases synthesize new DNA strands during replication, ensuring the duplication of the entire genome before cell division.
* **DNA Repair:** DNA polymerases are involved in repairing damaged DNA, correcting errors that may occur during replication or due to environmental damage.
* **Recombination:** DNA polymerases participate in genetic recombination, a process that shuffles genetic information and contributes to genetic diversity.

Mutations in DNA polymerases can lead to various genetic disorders, including cancer, immune deficiencies, and developmental abnormalities. Understanding the molecular function of DNA-directed DNA polymerase activity is crucial for unraveling the mechanisms of DNA replication and repair, and for developing therapeutic strategies for treating diseases related to DNA polymerase dysfunction.'
"

Proteins (17)

ProteinDefinitionTaxonomy
DNA nucleotidylexotransferaseA DNA nucleotidylexotransferase that is encoded in the genome of cow. [OMA:P06526, PRO:DNx]Bos taurus (cattle)
DNA polymerase etaA DNA polymerase eta that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y253]Homo sapiens (human)
DNA polymerase iotaA DNA polymerase iota that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UNA4]Homo sapiens (human)
DNA polymerase lambdaA DNA polymerase lambda that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGP5]Homo sapiens (human)
DNA-directed DNA/RNA polymerase muA DNA-directed DNA/RNA polymerase mu that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NP87]Homo sapiens (human)
DNA polymerase nuA DNA polymerase nu that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q7Z5Q5]Homo sapiens (human)
DNA polymerase betaA DNA polymerase beta that is encoded in the genome of human. [PRO:CNA]Homo sapiens (human)
DNA polymerase kappaA DNA polymerase kappa that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UBT6]Homo sapiens (human)
DNA polymerase etaA DNA polymerase eta that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y253]Homo sapiens (human)
DNA polymerase iotaA DNA polymerase iota that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UNA4]Homo sapiens (human)
DNA polymerase lambdaA DNA polymerase lambda that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGP5]Homo sapiens (human)
DNA-directed DNA/RNA polymerase muA DNA-directed DNA/RNA polymerase mu that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NP87]Homo sapiens (human)
DNA polymerase nuA DNA polymerase nu that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q7Z5Q5]Homo sapiens (human)
DNA polymerase subunit gamma-1A DNA polymerase subunit gamma-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P54098]Homo sapiens (human)
DNA polymerase delta catalytic subunitA DNA polymerase delta catalytic subunit that is encoded in the genome of human. [PRO:DNx, UniProtKB:P28340]Homo sapiens (human)
DNA polymerase alpha catalytic subunitA DNA polymerase alpha catalytic subunit that is encoded in the genome of human. [PRO:DNx]Homo sapiens (human)
DNA polymerase betaA DNA polymerase beta that is encoded in the genome of human. [PRO:CNA]Homo sapiens (human)

Compounds (39)

CompoundDefinitionClassesRoles
digallic aciddigallic acid: structure given in first sourcebenzoate ester;
gallate ester
aurintricarboxylic acidaurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'.

Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues.
monohydroxybenzoic acid;
quinomethanes;
tricarboxylic acid
fluorochrome;
histological dye;
insulin-like growth factor receptor 1 antagonist
candesartan cilexetilcandesartan cilexetil: a prodrug which is metabolized to an active form candesartan to exert its biological effectsbiphenyls
foscarnetFoscarnet: An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV.

phosphonoformic acid : Phosphoric acid in which one of the hydroxy groups is replaced by a carboxylic acid group. It is used as the trisodium salt as an antiviral agent in the treatment of cytomegalovirus retinitis (CMV retinitis, an inflamation of the retina that can lead to blindness) and as an alternative to ganciclovir for AIDS patients who require concurrent antiretroviral therapy but are unable to tolerate ganciclovir due to haematological toxicity.
carboxylic acid;
one-carbon compound;
phosphonic acids
antiviral drug;
geroprotector;
HIV-1 reverse transcriptase inhibitor;
sodium-dependent Pi-transporter inhibitor
pamoic acidpamoic acid: RN given refers to parent cpd; structuredicarboxylic acid
Dillapiole5-allyl 6,7-dimethoxy 1,3-benzodioxole: a plant based insecticide; structure in first sourcebenzodioxolesmetabolite
oleanolic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
plant metabolite
ochracinochracin: produced by Aspergillus alutaceus; structure in first sourceisochromanes
zidovudinezidovudine : A pyrimidine 2',3'-dideoxyribonucleoside compound having a 3'-azido substituent and thymine as the nucleobase.

Zidovudine: A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia.
azide;
pyrimidine 2',3'-dideoxyribonucleoside
antimetabolite;
antiviral drug;
HIV-1 reverse transcriptase inhibitor
ursolic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
geroprotector;
plant metabolite
thymidine 5'-triphosphatedTTP : A thymidine phosphate having a triphosphate group at the 5'-position.

thymidine 5'-triphosphate: RN given refers to parent cpd
pyrimidine 2'-deoxyribonucleoside 5'-triphosphate;
thymidine phosphate
Escherichia coli metabolite;
mouse metabolite
betulinic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
anti-HIV agent;
anti-inflammatory agent;
antimalarial;
antineoplastic agent;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
plant metabolite
calanolide a(+)-calanolide A : An organic heterotetracyclic compound that is 11,12-dihydro-2H,6H,10H-dipyrano[2,3-f:2',3'-h]chromen-2-one substituted by a hydroxy group at position 12, methyl groups at positions 6, 6, 10 and 11 and a propyl group at position 4 (the 10R,11S,12S stereoisomer). Isolated from Calophyllum lanigerum var austrocoriaceum and Calophyllum brasiliense, it exhibits potent activity against HIV-1 reverse transcriptase.

calanolide A: NSC 661122 and costatolide are isomers; a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum (Clusiaceae); structure in first source
cyclic ether;
delta-lactone;
organic heterotetracyclic compound;
secondary alcohol
HIV-1 reverse transcriptase inhibitor;
plant metabolite
2',3'-dideoxythymidine triphosphateddTTP : A pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate having thymine as the nucleobase.pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate;
thymidine phosphate
2',3'-dideoxyadenosine triphosphatepurine deoxyribonucleoside triphosphate
zidovudine triphosphate
illimaquinoneillimaquinone: structure given in first source; isolated from the Red Sea sponge Smenospongia; inhibits the RNase H. activity of HIV-1 reverse transcriptasemonohydroxy-1,4-benzoquinones;
prenylquinone
metabolite
sitosterol, (3beta)-isomersitosterol : A member of the class of phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3.

Sobatum: tradename; active fraction of Solanum trilobatum; reduces side-effects of radiation-induced toxicity
3beta-hydroxy-Delta(5)-steroid;
3beta-sterol;
C29-steroid;
phytosterols;
stigmastane sterol
anticholesteremic drug;
antioxidant;
mouse metabolite;
plant metabolite;
sterol methyltransferase inhibitor
resveratroltrans-resveratrol : A resveratrol in which the double bond has E configuration.resveratrolantioxidant;
phytoalexin;
plant metabolite;
quorum sensing inhibitor;
radical scavenger
TTPpyrimidine ribonucleoside 5'-triphosphate
aphidicolinaphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication.

Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells.
tetracyclic diterpenoidantimicrobial agent;
antimitotic;
antineoplastic agent;
antiviral drug;
apoptosis inducer;
Aspergillus metabolite;
DNA synthesis inhibitor;
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor;
fungal metabolite
pnu183792PNU183792: structure in first source
stigmasterolstigmasta-5,22-dien-3-ol: isolated from freeze-dried powder of Blackberries (Rubus ursinus L.) which showed an activity on inhibition of chemocarcinogen

stigmasterol : A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions.
3beta-hydroxy-Delta(5)-steroid;
3beta-sterol;
phytosterols;
stigmastane sterol
plant metabolite
ellagic acidcatechols;
cyclic ketone;
lactone;
organic heterotetracyclic compound;
polyphenol
antioxidant;
EC 1.14.18.1 (tyrosinase) inhibitor;
EC 2.3.1.5 (arylamine N-acetyltransferase) inhibitor;
EC 2.4.1.1 (glycogen phosphorylase) inhibitor;
EC 2.5.1.18 (glutathione transferase) inhibitor;
EC 2.7.1.127 (inositol-trisphosphate 3-kinase) inhibitor;
EC 2.7.1.151 (inositol-polyphosphate multikinase) inhibitor;
EC 2.7.4.6 (nucleoside-diphosphate kinase) inhibitor;
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor;
EC 5.99.1.2 (DNA topoisomerase) inhibitor;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
food additive;
fungal metabolite;
geroprotector;
plant metabolite;
skin lightening agent
pecilocinpecilocin: fungicidal antibiotic produced by Paecilomyces varioti Bainier var. antibioticus; structureN-acylpyrrolidine
lyonisidedaucosterol : A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa.beta-D-glucoside;
monosaccharide derivative;
steroid saponin
plant metabolite
manoalidemanoalide : A sesterterpenoid isolated from the marine sponge Luffariella variabilis and which has been shown to exhibit inhibitory activity towards phospholipase A2.

manoalide: phospholipase A2 inhibitor; sesterterpene from marine sponge L. variabilis; structure given in first source
butenolide;
lactol;
sesterterpenoid
EC 3.1.1.4 (phospholipase A2) inhibitor;
EC 5.99.1.2 (DNA topoisomerase) inhibitor;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
metabolite
corosolic acidtriterpenoidmetabolite
oblongifolin coblongifolin C: has antineoplastic activity; isolated from Garcinia yunnanensis; structure in first source
3-o-methylfunicone3-O-methylfunicone: derived from Penicillium pinophilum; structure in first source
edgeworinedgeworin: from Dirca occidentalis Gray; structure given in first source
sch 725680Sch 725680: an aazaphilone from Aspergillus sp.; structure in first source
guttiferone kguttiferone K: antiproliferative compound of Rheedia calcicola from the Madagascar rain forest; structure in first source
raltegravir1,2,4-oxadiazole;
dicarboxylic acid amide;
hydroxypyrimidine;
monofluorobenzenes;
pyrimidone;
secondary carboxamide
antiviral drug;
HIV-1 integrase inhibitor
GS-443902GS-441524 triphosphate: intracellular active metabolite of remdesivir

GS-443902 : An organic triphosphate that is GS-441524 in which the 5'-hydroxy group has been replaced by a triphosphate group. It is the active metabolite of remdesivir.
aromatic amine;
C-nucleoside;
nitrile;
organic triphosphate;
pyrrolotriazine
anticoronaviral agent;
antiviral drug;
drug metabolite
pinophilin bpinophilin B: from cultures of a fungus (Penicillium pinophilum Hedgcok) derived from a seaweed; structure in first source
deoxyguanosine triphosphatedeoxyguanosine phosphate;
guanyl deoxyribonucleotide;
purine 2'-deoxyribonucleoside 5'-triphosphate
Arabidopsis thaliana metabolite;
Escherichia coli metabolite;
human metabolite;
mouse metabolite;
plant metabolite;
Saccharomyces cerevisiae metabolite
acyclovir triphosphate
n(2)-(4-n-butylphenyl) 2'-deoxyguanosineN(2)-(4-n-butylphenyl) 2'-deoxyguanosine: RN & structure given in first source