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HAMAP rule MF_04100

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General rule information [?]

Accession MF_04100
Dates 28-JUN-2016 (Created)
19-NOV-2022 (Last updated, Version 9)
Name DPOL_T4
Scope
Viruses; Caudoviricetes
Templates P04415 (DPOL_BPT4); Q38087 (DPOL_BPR69): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
DPOL
Protein name
RecName: Full=DNA-directed DNA polymerase;
EC 2.7.7.7;
EC 3.1.11.-;

Comments [?]

Function Replicates the viral genomic DNA. This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction for proofreading purpose.
Catalytic activity RHEA:22508: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
EC 2.7.7.7
Cofactor Mg(2+)
Subunit Part of the replicase complex that includes the DNA polymerase, the polymerase clamp, the clamp loader complex, the single-stranded DNA binding protein, and the primase/helicase. Interacts with the polymerase clamp; this interaction constitutes the polymerase holoenzyme.
Domain The N-terminus contains the 3'-5' exonuclease activity. The C-terminus contains the polymerase activity and is involved in binding to the polymerase clamp protein. A beta hairpin structure is necessary for the proofreading function of the polymerase.
Similarity Belongs to the DNA polymerase type-B family.

Keywords [?]

DNA replication
DNA-binding
DNA-directed DNA polymerase
Exonuclease
Hydrolase
Magnesium
Metal-binding
Multifunctional enzyme
Nuclease
Nucleotidyltransferase
Transferase
Viral DNA replication

Gene Ontology [?]

GO:0008408; Molecular function: 3'-5' exonuclease activity.
GO:0003677; Molecular function: DNA binding.
GO:0003887; Molecular function: DNA-directed DNA polymerase activity.
GO:0000166; Molecular function: nucleotide binding.
GO:0039686; Biological process: bidirectional double-stranded viral DNA replication.

Cross-references [?]

PROSITE PS00116; DNA_POLYMERASE_B; 1;
Pfam PF00136; DNA_pol_B; 1;
PF03104; DNA_pol_B_exo1; 1;

Features [?]

From: DPOL_BPT4 (P04415)
Key     From     To       Description   Tag   Condition   FTGroup
REGION     101     337       3'-5'exonuclease        
REGION     245     261       Beta hairpin        
REGION     377     Cter       Polymerase        
REGION     893     Cter       Interaction with the polymerase clamp        
BINDING     112     112       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic; for 3'-5' exonuclease activity     D  
BINDING     114     114       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic; for 3'-5' exonuclease activity     E  
BINDING     219     219       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" /ligand_note="catalytic; for 3'-5' exonuclease activity     D  
BINDING     324     324       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic; for 3'-5' exonuclease activity     D  
BINDING     324     324       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" /ligand_note="catalytic; for 3'-5' exonuclease activity     D  
From: DPOL_BPR69 (Q38087)
BINDING     414     416       /ligand="substrate     S-L-Y  
BINDING     482     482       /ligand="substrate     R  
BINDING     560     560       /ligand="substrate     K  
REGION     705     708       Binding of DNA in B-conformation     K-K-R-Y  
BINDING     411     411       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="3" /ligand_note="catalytic; for polymerase activity     D  
BINDING     411     411       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="4" /ligand_note="catalytic; for polymerase activity     D  
BINDING     412     412       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="4" /ligand_note="catalytic; for polymerase activity     L  
BINDING     623     623       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="3" /ligand_note="catalytic; for polymerase activity     D  
BINDING     623     623       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="4" /ligand_note="catalytic; for polymerase activity     D  
SITE     621     621       Optimization of metal coordination by the polymerase active site     D  
SITE     706     706       Optimization of metal coordination by the polymerase active site     K  
SITE     714     714       Essential for viral replication     D  

Additional information [?]

Size range 828-998 amino acids
Related rules None
Fusion None


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