DNA-dependent DNA polymerase

DNA-dependent DNA polymerase (DdDp) plays a role in DNA replication. It catalyzes the synthesis of the DNA strand complementary to a given DNA template. Viruses encode polymerases A-family (virus, bacteria), B-Family (virus, eukaryotes and archaea) and C-family (virus and bacteria).

Naming: By convention viral polymerases are called RNA/DNA-dependent whereas cellular polymerases are called RNA/DNA-directed.

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Enzymatic reaction:

  • DNA nucleotidyltransferase (DNA-dependent) EC 2.7.7.7 RHEA:22508
Mechanism Viral DdDp are characterized by a conserved motif in which two conserved aspartic acid residues are bound to two magnesium ions. The reaction begins with the deprotonation of primer's 3' OH, in a manner that doesn't require a base . Subsequently, the 3'-oxygen acts as a nucleophile to attack the phosphate bond and eventually releases a pyrophosphate.

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Viral molecular biology Virus entry
Transcription and replication
Virus exit
Replication cycles
Virion
Enzymes
Viral replication
ProteinDB Proteins sequences: NCBI, UniProt
Structure: PDB entries
Escherichia phage T7 (Family A)

Herpes simplex virus (Family B)

Human Adenovirus C (Family pB)
model-44328
FamilyPrimerDomainVirusesCellsNotes
DNA_ARNAIPR002298dsDNA bacteria viruses:
(Caudoviricetes)
Bacteria
DNA_BRNAIPR006172dsDNA bacteria and archaea viruses:
(Caudoviricetes, Preplasmiviricota)
dsDNA eukaryotic viruses:
(Nucleocytoviricota, Preplasmiviricota, Herpeviricetes, Naldaviricetes)		Eukaryotes and archaea
pDNA_BProtein-primingdsDNA viruses: TectiliviricetesNoneNo helicases, but unique SSB
DNA_CRNAdsDNA viruses: (Caudoviricetes)Bacteria

Data adapted from: The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes Darius Kazlauskas, Mart Krupovic, Ceslovas Venclovas; Nucleic Acids Res. 2016 Jun 2;44(10):4551-64.