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HAMAP rule MF_04140

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General rule information [?]

Accession MF_04140
Dates 23-MAY-2019 (Created)
19-NOV-2022 (Last updated, Version 7)
Name FEN_T5
Scope(s) Viruses
Template(s) P06229 (FEN_BPT5); [ Recover all ]
Triggered by HAMAP; MF_04140 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier FEN
Protein name RecName: Full=Flap endonuclease;
                 Short=FEN;
                 EC=3.1.11.-;
AltName: Full=5'-3' exonuclease;
AltName: Full=Exodeoxyribonuclease;
                 EC=3.1.11.3;

Comments [?]

FUNCTIONCatalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules and probably plays a role in viral genome replication. Active on flap (branched duplex DNA containing a free single-stranded 5'-end), 5'overhangs and pseudo-Y structures. The substrates require a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA. This function may be used for example to trim such branched molecules generated by Okazaki fragments synthesis during replication.
CATALYTIC ACTIVITY Reaction=Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.; EC=3.1.11.3;
case <FTGroup:2> and <FTGroup:1>
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=K(+); Xref=ChEBI:CHEBI:29103; Note=Binds divalent metal cations, probably Mg(2+). In vitro low metal concentrations selectively stimulate the endonuclease reaction. Endonuclease activity is suggested to require only the first cation, whereas exonuclease activity is suggested to require binding of both. High pH favors the exonuclase activity whereas low pH favors the endonuclease activity. Metal ions enhance substrate binding. K(+) is bound to the H3TH region;
else
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Note=Binds divalent metal cations, probably Mg(2+). In vitro low metal concentrations selectively stimulate the endonuclease reaction. Endonuclease activity is suggested to require only the first cation, whereas exonuclease activity is suggested to require binding of both. High pH favors the exonuclase activity whereas low pH favors the endonuclease activity. Metal ions enhance substrate binding
end case
DOMAINThree alpha-helices form a helical arch which forms a hole in the protein and through which the 5' flap of the scissile ssDNA is threaded.

Keywords [?]

DNA replication
DNA-binding
Early protein
Endonuclease
Exonuclease
Hydrolase
Metal-binding
Magnesium
Nuclease
case <FTGroup:1>
Potassium
end case
Viral DNA replication

Gene Ontology [?]

GO:0008409; Molecular function:5'-3' exonuclease activity
GO:0017108; Molecular function:5'-flap endonuclease activity
GO:0003677; Molecular function:DNA binding
GO:0046872; Molecular function:metal ion binding
GO:0033567; Biological process:DNA replication, Okazaki fragment processing
GO:0039693; Biological process:viral DNA genome replication

Cross-references [?]

Pfam PF01367; 5_3_exonuc; 1;
Pfam PF02739; 5_3_exonuc_N; 1;
General Coiled_coil; -; 0-unlimited;

Features [?]

From: FEN_BPT5 (P06229)
Key From To Description Tag Condition FTGroup
CHAIN Nter Cter /note="Flap endonuclease"
DOMAIN 190 263 /note="5'-3' exonuclease"
REGION 82 116 /note="Helical arch" Y-K-x*
REGION 188 224 /note="DNA-binding; H3TH" x(2)-[ED]-x*-G-D-x-x-D-x*
BINDING 130 130 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"
/ligand_note="catalytic"		 D
BINDING 130 130 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"
/ligand_note="catalytic"		 D 2
BINDING 153 153 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"
/ligand_note="catalytic"		 D 2
BINDING 155 155 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"
/ligand_note="catalytic"		 D 2
BINDING 155 155 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 D
BINDING 201 201 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 D
BINDING 209 209 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"		 V 1
BINDING 212 212 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"		 I 1
BINDING 83 83 /ligand="DNA"
/ligand_id="ChEBI:CHEBI:16991"		 K

Additional information [?]

Size range 200-350 amino acids
Related rules None
Fusion Nter: None Cter: None



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