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Annotation rule MF_04140
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General rule information [?]

Accession MF_04140
Dates 23-MAY-2019 (Created)
20-NOV-2019 (Last updated, Version 5)
Name FEN_T5
Scope
Viruses
Template P06229 (FEN_BPT5)
Triggered by

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 [?]

Function Catalyzes 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 Mg(2+)
K(+)
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 Mg(2+)
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
Domain Three 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;
PF02739; 5_3_exonuc_N; 1;

Computed features [?]

General Coiled_coil; -; 0-unlimited; trigger=yes;

Features [?]

From: FEN_BPT5 (P06229)
Key     From     To       Description   Tag   Condition   FTGroup
CHAIN     Nter     Cter       Flap endonuclease        
DOMAIN     190     263       5'-3' exonuclease        
REGION     82     116       Helical arch     Y-K-x*  
REGION     188     224       DNA-binding; H3TH     x(2)-[ED]-x*-G-D-x-x-D-x*  
METAL     130     130       Magnesium 1; catalytic     D  
METAL     130     130       Magnesium 2; catalytic     D   2
METAL     153     153       Magnesium 2; catalytic     D   2
METAL     155     155       Magnesium 2; catalytic     D   2
METAL     155     155       Magnesium 3     D  
METAL     201     201       Magnesium 3     D  
METAL     209     209       Potassium; via carbonyl oxygen     V   1
METAL     212     212       Potassium; via carbonyl oxygen     I   1
BINDING     83     83       DNA     K  

Additional information [?]

Size range 200-350 amino acids
Related rules None
Fusion None


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