Flap endonuclease 1-A - Xenopus laevis (African clawed frog)

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P70040 (FEN1A_XENLA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 67. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Flap endonuclease 1-A
Short name=FEN-1-A
EC=3.1.-.-

Alternative name(s):
Flap structure-specific endonuclease 1-A
Short name=xFEN-1a

Gene names

Name:

fen1-a

Organism

Xenopus laevis (African clawed frog)

Taxonomic identifier

8355 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

Protein attributes

Sequence length	382 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA. Ref.1 Ref.2
Cofactor	Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding By similarity. Ref.2
Subunit structure	Interacts with PCNA. Three molecules of fen1 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity By similarity. Ref.1 Ref.2
Subcellular location	Nucleus › nucleolus By similarity. Nucleus › nucleoplasm By similarity. Mitochondrion By similarity. Note: Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage By similarity. Ref.2
Developmental stage	First expressed at a low level in stage II oocytes. Expression increases dramatically from oocyte stages III to V (at protein level). Also expressed in embryos. Ref.2
Post-translational modification	Phosphorylated. Phosphorylation upon DNA damage induces relocalization to the nuclear plasma By similarity. HAMAP-Rule MF_03140
Sequence similarities	Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.

Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Cellular component	Mitochondrion Nucleus
Coding sequence diversity	Polymorphism
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Exonuclease Hydrolase Nuclease
PTM	Phosphoprotein
Gene Ontology (GO)
Biological_process	DNA replication Inferred from physical interaction Ref.2. Source: UniProtKB DNA replication, removal of RNA primer Inferred from electronic annotation. Source: HAMAP base-excision repair Inferred from direct assay Ref.1. Source: UniProtKB
Cellular_component	mitochondrion Inferred from electronic annotation. Source: UniProtKB-SubCell nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay Ref.2. Source: UniProtKB
Molecular_function	5'-3' exonuclease activity Inferred from electronic annotation. Source: HAMAP 5'-flap endonuclease activity Inferred from direct assay Ref.2. Source: UniProtKB DNA binding Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 382

382

Flap endonuclease 1-A HAMAP-Rule MF_03140

PRO_0000244491

Regions

Region

1 – 104

104

N-domain HAMAP-Rule MF_03140

Region

122 – 253

132

I-domain HAMAP-Rule MF_03140

Region

336 – 344

Interaction with PCNA By similarity

Sites

Metal binding

Magnesium 1 By similarity

Metal binding

Magnesium 1 By similarity

Metal binding

158

Magnesium 1 By similarity

Metal binding

160

Magnesium 1 By similarity

Metal binding

179

Magnesium 2 By similarity

Metal binding

181

Magnesium 2 By similarity

Metal binding

233

Magnesium 2 By similarity

Binding site

DNA substrate By similarity

Binding site

DNA substrate By similarity

Binding site

158

DNA substrate By similarity

Binding site

231

DNA substrate By similarity

Binding site

233

DNA substrate By similarity

Natural variations

Natural variant

V → I in allele fen-1a'. Ref.1 Ref.2 Ref.4

Sequences

Sequence

Length

Mass (Da)

Tools

P70040 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: 9B1DB0EDAD158D57
Show »

FASTA

382

42,668

        10         20         30         40         50         60 
MGIHGLAKLI ADVAPAAIKE HDIKSYFGRK VAVDASMCIY QFLIAVRQDG NTLQNEEGET 

        70         80         90        100        110        120 
TSHLMGMFYR TIRMVEHGIK PVYVFDGKPP QMKSGELAKR SERRAEAEKL LEAAEEAGEV 

       130        140        150        160        170        180 
ENIEKFTKRL VKVTKQHNEE CKKLLTLMGI PYVDAPCEAE ATCAALVKAG KVYAAATEDM 

       190        200        210        220        230        240 
DALTFGTPVL LRHLTASEAK KLPIQEFHLN RVIQDIGITH EQFVDLCILL GSDYCETIRG 

       250        260        270        280        290        300 
IGPKRAIDLI RQHKTIDEII DNIDLKKYPV PENWLHKEAK HLFLEPEVVD TDITELKWIE 

       310        320        330        340        350        360 
PDEEGLVAFM CGEKQFSEDR IRNGAKKLAK NRQGSTQGRL DDFFKVTGSV SSTKRKEAES 

       370        380 
KGSAKKKAKT GGTPAGKFKR GK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Involvement of flap endonuclease 1 in base excision DNA repair." Kim K., Biade S., Matsumoto Y. J. Biol. Chem. 273:8842-8848(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, IDENTIFICATION IN A COMPLEX WITH PCNA, VARIANT ILE-33. Tissue: Oocyte.
[2]	"Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism." Bibikova M., Wu B., Chi E., Kim K.-H., Trautman J.K., Carroll D. J. Biol. Chem. 273:34222-34229(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, COFACTOR, IDENTIFICATION IN A COMPLEX WITH PCNA, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, VARIANT ILE-33. Tissue: Tadpole head.
[3]	"Cloning and investigation of Xenopus Fen1: developmental expression and function in DNA replication." Li J.-L., Cox L.S. Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	NIH - Xenopus Gene Collection (XGC) project Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ILE-33. Tissue: Oocyte and Ovary.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF036327 mRNA. Translation: AAB88707.1. U64563 mRNA. Translation: AAB06176.1. AF065397 mRNA. Translation: AAD02814.1. BC169761 mRNA. Translation: AAI69761.1. BC169765 mRNA. Translation: AAI69765.1. BC124977 mRNA. Translation: AAI24978.1.
RefSeq	NP_001080960.1. NM_001087491.1.
UniGene	Xl.440.
3D structure databases
ProteinModelPortal	P70040.
SMR	P70040. Positions 2-356.
ModBase	Search...
Protein-protein interaction databases
IntAct	P70040. 1 interaction.
Proteomic databases
PRIDE	P70040.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	394303.
KEGG	xla:394303.
Organism-specific databases
CTD	394303.
Xenbase	XB-GENE-955523. fen1.
Phylogenomic databases
HOVERGEN	HBG000844.
KO	K04799.
Family and domain databases
HAMAP	MF_00614. Fen.
InterPro	IPR020045. 5-3_exonuclease_C. IPR023426. Flap_endonuc. IPR008918. HhH2. IPR006086. XPG-I_dom. IPR006084. XPG/Rad2. IPR019974. XPG_CS. IPR006085. XPG_DNA_repair_N. [Graphical view]
PANTHER	PTHR11081. PTHR11081. 1 hit.
Pfam	PF00867. XPG_I. 1 hit. PF00752. XPG_N. 1 hit. [Graphical view]
PRINTS	PR00853. XPGRADSUPER.
SMART	SM00279. HhH2. 1 hit. SM00484. XPGI. 1 hit. SM00485. XPGN. 1 hit. [Graphical view]
SUPFAM	SSF47807. 5_3_exo_C. 1 hit.
PROSITE	PS00841. XPG_1. 1 hit. PS00842. XPG_2. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

FEN1A_XENLA

Accession

Primary (citable) accession number: P70040
Secondary accession number(s): B7ZQC8, O57351, Q08AW7

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2006
Last sequence update:	February 1, 1997
Last modified:	April 3, 2013
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents