P06229 · FEN_BPT5
- ProteinFlap endonuclease
- GeneD15
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids291 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
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 (PubMed:10364212, PubMed:15077103, PubMed:9874768).
Active on flap (branched duplex DNA containing a free single-stranded 5'-end), 5'overhangs and pseudo-Y structures (PubMed:10364212, PubMed:15077103, PubMed:9874768).
The substrates require a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA (PubMed:9874768).
This function may be used for example to trim such branched molecules generated by Okazaki fragments synthesis during replication
Active on flap (branched duplex DNA containing a free single-stranded 5'-end), 5'overhangs and pseudo-Y structures (PubMed:10364212, PubMed:15077103, PubMed:9874768).
The substrates require a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA (PubMed:9874768).
This function may be used for example to trim such branched molecules generated by Okazaki fragments synthesis during replication
Catalytic activity
Cofactor
K+ (UniProtKB | Rhea| CHEBI:29103 )
Note: Binds divalent metal cations, probably Mg2+. 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 exonuclease activity whereas low pH favors the endonuclease activity. Metal ions enhance substrate binding.
Activity regulation
Inhibited by p-hydroxymercuribenzoate (PHMB).
pH Dependence
Optimum pH is 9.3 for the exonuclease activity, 5.5 for endonuclease activity. High pH favors the exonuclease activity whereas low pH favors the endonuclease activity.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 83 | DNA (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 130 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 130 | Mg2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 153 | Mg2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 155 | Mg2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 155 | Mg2+ 3 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 201 | Mg2+ 3 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 209 | K+ (UniProtKB | ChEBI) | ||||
Sequence: V | ||||||
Binding site | 212 | K+ (UniProtKB | ChEBI) | ||||
Sequence: I |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | viral replication complex | |
Molecular Function | 5'-3' DNA exonuclease activity | |
Molecular Function | 5'-3' exonuclease activity | |
Molecular Function | 5'-flap endonuclease activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA exonuclease activity | |
Molecular Function | double-stranded DNA 5'-3' DNA exonuclease activity | |
Molecular Function | double-stranded DNA endonuclease activity | |
Molecular Function | metal ion binding | |
Biological Process | DNA replication, Okazaki fragment processing | |
Biological Process | late viral transcription | |
Biological Process | viral DNA genome replication |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameFlap endonuclease
- EC number
- Short namesFEN
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageViruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Demerecviridae > Markadamsvirinae > Tequintavirus > Tequintavirus T5
- Virus hosts
Accessions
- Primary accessionP06229
- Secondary accessions
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
Phenotypes & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 33 | 10 fold increase in the dissociation constant for pseudo-Y binding. 3 fold increase in the dissociation constant for 5'overhangs binding. | ||||
Sequence: R → A | ||||||
Mutagenesis | 82 | 3.5-fold decrease in binding affinity for DNA. No effect on endonuclease and exonuclease activities. | ||||
Sequence: Y → F | ||||||
Mutagenesis | 83 | No exonuclease activity, retains full endonuclease activity on a flap structure. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. | ||||
Sequence: K → A | ||||||
Mutagenesis | 115 | Complete loss of inhibition by PHMB; when associated with S-266. | ||||
Sequence: C → S | ||||||
Mutagenesis | 128-130 | Loss of both exo- and endonuclease activity, still binds DNA. | ||||
Sequence: EAD → QAN | ||||||
Mutagenesis | 153 | Complete loss of enzymatic activity. | ||||
Sequence: D → K | ||||||
Mutagenesis | 155 | Complete loss of enzymatic activity. | ||||
Sequence: D → K | ||||||
Mutagenesis | 172 | 10 fold increase in the dissociation constant for pseudo-Y binding. No effect on 5'overhangs binding. | ||||
Sequence: R → A | ||||||
Mutagenesis | 196 | 10% exonuclease activity, little change in endonuclease activity. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. | ||||
Sequence: K → A | ||||||
Mutagenesis | 201-204 | Retains most endo- but very little exonuclease activity; binds pseudo-Y substrate more tightly than wt. | ||||
Sequence: DLGD → ILGS | ||||||
Mutagenesis | 201-204 | Retains most endonuclease but complete loss of exonuclease activity; binds pseudo-Y substrate more tightly than wt. | ||||
Sequence: DLGD → RLGP or RLGR | ||||||
Mutagenesis | 215 | Wild-type exo- and endonuclease activities. 10 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. | ||||
Sequence: K → A | ||||||
Mutagenesis | 216 | 100 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. | ||||
Sequence: R → A | ||||||
Mutagenesis | 241 | 10 fold increase in the dissociation constant for pseudo-Y binding. 10 fold increase in the dissociation constant for 5'overhangs binding. | ||||
Sequence: K → A | ||||||
Mutagenesis | 266 | Complete loss of inhibition by PHMB; when associated with S-115. | ||||
Sequence: C → S |
PTM/Processing
Features
Showing features for initiator methionine, chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed; by host | ||||
Sequence: M | ||||||
Chain | PRO_0000165217 | 2-291 | Flap endonuclease | |||
Sequence: SKSWGKFIEEEEAEMASRRNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ |
Expression
Induction
Expressed in the early phase of the viral replicative cycle.
Keywords
- Developmental stage
Structure
Family & Domains
Features
Showing features for region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 82-116 | Helical arch | ||||
Sequence: YKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCK | ||||||
Region | 188-224 | DNA-binding; H3TH | ||||
Sequence: DVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREF | ||||||
Domain | 190-263 | 5'-3' exonuclease | ||||
Sequence: EQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLP |
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.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length291
- Mass (Da)33,448
- Last updated2007-01-23 v3
- Checksum234C9564E491B4E9
Sequence caution
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AY543070 EMBL· GenBank· DDBJ | AAS77176.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AY587007 EMBL· GenBank· DDBJ | AAX12058.1 EMBL· GenBank· DDBJ | Genomic DNA | Different initiation | |
AY692264 EMBL· GenBank· DDBJ | AAU05267.1 EMBL· GenBank· DDBJ | Genomic DNA |