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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(s) Viruses
Caudoviricetes
Template(s) P04415 (DPOL_BPT4); Q38087 (DPOL_BPR69); [ Recover all ]
Triggered by HAMAP; MF_04100 (Get profile general information and statistics)

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 [?]

FUNCTIONReplicates 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 Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:173112; EC=2.7.7.7;
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
SUBUNITPart 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.
DOMAINThe 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.
SIMILARITYBelongs 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;
Pfam PF03104; DNA_pol_B_exo1; 1;

Features [?]

From: DPOL_BPT4 (P04415)
Key From To Description Tag Condition FTGroup
REGION 101 337 /note="3'-5'exonuclease"
REGION 245 261 /note="Beta hairpin"
REGION 377 Cter /note="Polymerase"
REGION 893 Cter /note="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)
Key From To Description Tag Condition FTGroup
BINDING 414 416 /ligand="substrate" S-L-Y
BINDING 482 482 /ligand="substrate" R
BINDING 560 560 /ligand="substrate" K
REGION 705 708 /note="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 /note="Optimization of metal coordination by the polymerase active site" D
SITE 706 706 /note="Optimization of metal coordination by the polymerase active site" K
SITE 714 714 /note="Essential for viral replication" D

Additional information [?]

Size range 828-998 amino acids
Related rules None
Fusion Nter: None Cter: None



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