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Protein

Flap endonuclease 1

Gene

fen

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA.

Cofactori

Mg2+UniRule annotationNote: 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.UniRule annotation

pH dependencei

Optimum pH is 6-7.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi27 – 271Magnesium 1UniRule annotation
Metal bindingi80 – 801Magnesium 1UniRule annotation
Metal bindingi152 – 1521Magnesium 1
Metal bindingi154 – 1541Magnesium 1
Metal bindingi173 – 1731Magnesium 2UniRule annotation
Metal bindingi175 – 1751Magnesium 2UniRule annotation
Metal bindingi224 – 2241Magnesium 2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.99.B1. 3260.

Names & Taxonomyi

Protein namesi
Recommended name:
Flap endonuclease 1UniRule annotation (EC:3.1.-.-UniRule annotation)
Short name:
FEN-1UniRule annotation
Alternative name(s):
Flap structure-specific endonuclease 1UniRule annotation
Gene namesi
Name:fenUniRule annotation
Ordered Locus Names:MJ1444
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 326326Flap endonuclease 1PRO_0000154053Add
BLAST

Interactioni

Subunit structurei

Interacts with PCNA. PCNA stimulates the nuclease activity without altering cleavage specificity.

Protein-protein interaction databases

STRINGi243232.MJ_1444.

Structurei

Secondary structure

1
326
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 83Combined sources
Helixi17 – 193Combined sources
Beta strandi23 – 275Combined sources
Helixi28 – 3811Combined sources
Helixi56 – 7015Combined sources
Beta strandi74 – 796Combined sources
Beta strandi96 – 983Combined sources
Helixi111 – 1155Combined sources
Helixi121 – 1244Combined sources
Helixi129 – 14214Combined sources
Beta strandi146 – 1483Combined sources
Helixi153 – 16210Combined sources
Beta strandi165 – 1706Combined sources
Beta strandi172 – 1743Combined sources
Helixi175 – 1795Combined sources
Beta strandi182 – 1909Combined sources
Beta strandi196 – 1994Combined sources
Helixi200 – 2078Combined sources
Helixi211 – 22111Combined sources
Turni227 – 2326Combined sources
Helixi235 – 2439Combined sources
Helixi247 – 2548Combined sources
Helixi258 – 2669Combined sources
Helixi283 – 2908Combined sources
Turni291 – 2944Combined sources
Helixi298 – 31518Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A76X-ray2.00A1-326[»]
1A77X-ray2.00A1-326[»]
ProteinModelPortaliQ58839.
SMRiQ58839. Positions 2-316.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ58839.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 9898N-domainAdd
BLAST
Regioni116 – 245130I-domainAdd
BLAST
Regioni317 – 3259Interaction with PCNAUniRule annotation

Sequence similaritiesi

Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04050. Archaea.
COG0258. LUCA.
InParanoidiQ58839.
KOiK04799.
OMAiGSQDYDS.
PhylomeDBiQ58839.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR023426. Flap_endonuc.
IPR019973. Flap_structure-sp_endonuc_arc.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PANTHERiPTHR11081. PTHR11081. 1 hit.
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsiTIGR03674. fen_arch. 1 hit.

Sequencei

Sequence statusi: Complete.

Q58839-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGVQFGDFIP KNIISFEDLK GKKVAIDGMN ALYQFLTSIR LRDGSPLRNR
60 70 80 90 100
KGEITSAYNG VFYKTIHLLE NDITPIWVFD GEPPKLKEKT RKVRREMKEK
110 120 130 140 150
AELKMKEAIK KEDFEEAAKY AKRVSYLTPK MVENCKYLLS LMGIPYVEAP
160 170 180 190 200
SEGEAQASYM AKKGDVWAVV SQDYDALLYG APRVVRNLTT TKEMPELIEL
210 220 230 240 250
NEVLEDLRIS LDDLIDIAIF MGTDYNPGGV KGIGFKRAYE LVRSGVAKDV
260 270 280 290 300
LKKEVEYYDE IKRIFKEPKV TDNYSLSLKL PDKEGIIKFL VDENDFNYDR
310 320
VKKHVDKLYN LIANKTKQKT LDAWFK
Length:326
Mass (Da):37,527
Last modified:November 1, 1996 - v1
Checksum:i311427F2B4B67580
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99454.1.
PIRiC64480.

Genome annotation databases

EnsemblBacteriaiAAB99454; AAB99454; MJ_1444.
KEGGimja:MJ_1444.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99454.1.
PIRiC64480.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A76X-ray2.00A1-326[»]
1A77X-ray2.00A1-326[»]
ProteinModelPortaliQ58839.
SMRiQ58839. Positions 2-316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_1444.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB99454; AAB99454; MJ_1444.
KEGGimja:MJ_1444.

Phylogenomic databases

eggNOGiarCOG04050. Archaea.
COG0258. LUCA.
InParanoidiQ58839.
KOiK04799.
OMAiGSQDYDS.
PhylomeDBiQ58839.

Enzyme and pathway databases

BRENDAi3.1.99.B1. 3260.

Miscellaneous databases

EvolutionaryTraceiQ58839.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR023426. Flap_endonuc.
IPR019973. Flap_structure-sp_endonuc_arc.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PANTHERiPTHR11081. PTHR11081. 1 hit.
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsiTIGR03674. fen_arch. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  2. "Methanococcus jannaschii flap endonuclease: expression, purification, and substrate requirements."
    Rao H.G., Rosenfeld A., Wetmur J.G.
    J. Bacteriol. 180:5406-5412(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  3. "Expression, purification, characterization and crystallization of flap endonuclease-1 from Methanococcus jannaschii."
    Bae K.W., Baek K.W., Cho C.S., Hwang K.Y., Kim H.-R., Sung H.-C., Cho Y.
    Mol. Cells 9:45-48(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
  4. "The crystal structure of flap endonuclease-1 from Methanococcus jannaschii."
    Hwang K.Y., Baek K., Kim H.-Y., Cho Y.
    Nat. Struct. Biol. 5:707-713(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Entry informationi

Entry nameiFEN_METJA
AccessioniPrimary (citable) accession number: Q58839
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: November 1, 1996
Last modified: November 11, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.