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Q9D842 (APLF_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Aprataxin and PNK-like factor

EC=4.2.99.18
Alternative name(s):
Apurinic-apyrimidinic endonuclease APLF
Gene names
Name:Aplf
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length499 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage By similarity.

Catalytic activity

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

Subunit structure

Interacts with LIG4, PARP1, XRCC1, XRCC4 and XRCC5 By similarity.

Subcellular location

Nucleus. Cytoplasmcytosol. Note: Localizes to DNA damage sites. Accumulates at single-strand breaks and double-strand breaks via the PBZ-type zinc fingers By similarity.

Domain

The PBZ-type zinc fingers (also named CYR) mediate non-covalent poly(ADP-ribose)-binding. Poly(ADP-ribose)-binding is dependent on the presence of zinc and promotes its recruitment to DNA damage sites By similarity.

The FHA-like domain mediates interaction with XRCC1 and XRCC4 By similarity.

Post-translational modification

Poly-ADP-ribosylated. In addition to binding non covalently poly(ADP-ribose) via its PBZ-type zinc fingers, the protein is also covalently poly-ADP-ribosylated by PARP1 By similarity.

Phosphorylated in an ATM-dependent manner upon double-strand DNA break By similarity.

Sequence similarities

Belongs to the APLF family.

Contains 1 FHA-like domain.

Contains 2 PBZ-type zinc fingers.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   DomainCoiled coil
Repeat
Zinc-finger
   LigandMetal-binding
Nucleotide-binding
Zinc
   Molecular functionLyase
   PTMADP-ribosylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA catabolic process, endonucleolytic

Inferred from sequence or structural similarity. Source: GOC

cellular response to DNA damage stimulus

Inferred from sequence or structural similarity. Source: UniProtKB

double-strand break repair

Inferred from sequence or structural similarity. Source: UniProtKB

nucleic acid phosphodiester bond hydrolysis

Inferred from sequence or structural similarity. Source: GOC

regulation of isotype switching

Inferred from mutant phenotype PubMed 21211721. Source: MGI

single strand break repair

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentcytosol

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_function3'-5' exonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

DNA-(apurinic or apyrimidinic site) lyase activity

Inferred from sequence or structural similarity. Source: UniProtKB

endodeoxyribonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9D842-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9D842-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-108: Missing.
     493-499: SSLHLKH → RFMRRKK
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9D842-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-32: MPSDFFLQPLDGGPRVPVGPGQTVIGRGPLLG → MPSVPEGGGYE
     493-499: SSLHLKH → RFMRRKK
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 499499Aprataxin and PNK-like factor
PRO_0000089343

Regions

Domain1 – 108108FHA-like
Zinc finger372 – 39322PBZ-type 1
Zinc finger414 – 43522PBZ-type 2
Region401 – 41111Flexible linker By similarity
Compositional bias274 – 2774Poly-Ser
Compositional bias445 – 48541Asp-rich

Sites

Binding site3711Poly-ADP-ribose By similarity
Binding site3761Poly-ADP-ribose By similarity
Binding site3811Poly-ADP-ribose By similarity
Binding site3821Poly-ADP-ribose By similarity
Binding site4181Poly-ADP-ribose By similarity
Binding site4231Poly-ADP-ribose By similarity
Binding site4241Poly-ADP-ribose By similarity

Amino acid modifications

Modified residue1161Phosphoserine; by ATM By similarity

Natural variations

Alternative sequence1 – 108108Missing in isoform 2.
VSP_014983
Alternative sequence1 – 3232MPSDF…GPLLG → MPSVPEGGGYE in isoform 3.
VSP_014982
Alternative sequence493 – 4997SSLHLKH → RFMRRKK in isoform 2 and isoform 3.
VSP_014984

Experimental info

Sequence conflict1781R → H in AAH02179. Ref.2
Sequence conflict4701S → F in BAB25711. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified August 16, 2005. Version 2.
Checksum: 4B41A9C0C8937963

FASTA49954,968
        10         20         30         40         50         60 
MPSDFFLQPL DGGPRVPVGP GQTVIGRGPL LGITDKRVSR RHAILEVVDS QLRIKPIHRN 

        70         80         90        100        110        120 
PCFYQSSEKS QHSPMETQVW SQLHPGDSFS LLLDKYAFRV FSAESEVEME CTLRNSQMLD 

       130        140        150        160        170        180 
EDDILSEMQK SPVVNLPDKT TGASQLQGSP EITKTKCPTI DPMSSSGECR AFSEHQPRPT 

       190        200        210        220        230        240 
QRKRILPAWM LAESLSDQSL STPAEGGDKD VIQRSGKAGT CEDRTPGNTS WHGKKRLSPS 

       250        260        270        280        290        300 
GNSKSVSAEQ DPGKKCRKAD QEGPGVSSEN VPESSSSNIV KDPDVDIVKT NKQKDGILIE 

       310        320        330        340        350        360 
ELGEVSKHKA ATKPTTNEEG ESCARVQSKS PPEKSQGCHP ESSSAPSSPD ALHTDTADPV 

       370        380        390        400        410        420 
LGCSEESKVR RTACMYGANC YRRNPLHFQH FSHPGDSDYG EVHGTDEGVI GDRPECPYGA 

       430        440        450        460        470        480 
SCYRKNPQHK MEYRHSALPA RVALDEDDDD VGQPSDDEDE EDYEPTDEDS DWHPGKDDEE 

       490 
QEDVDELLKE AKSSLHLKH 

« Hide

Isoform 2 [UniParc].

Checksum: D666D7635D0AFF78
Show »

FASTA39143,042
Isoform 3 [UniParc].

Checksum: 44710524EAB5EFA4
Show »

FASTA47853,015

References

[1]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
Strain: C57BL/6J.
Tissue: Diencephalon and Small intestine.
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Strain: FVB/N.
Tissue: Mammary gland.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK008513 mRNA. Translation: BAB25711.1.
AK034191 mRNA. Translation: BAC28625.1.
BC002179 mRNA. Translation: AAH02179.1.
CCDSCCDS20324.1. [Q9D842-3]
CCDS51839.1. [Q9D842-1]
RefSeqNP_001163960.1. NM_001170489.1. [Q9D842-1]
NP_077213.2. NM_024251.4. [Q9D842-3]
UniGeneMm.31770.

3D structure databases

ProteinModelPortalQ9D842.
SMRQ9D842. Positions 354-441.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid215153. 1 interaction.

PTM databases

PhosphoSiteQ9D842.

Proteomic databases

PRIDEQ9D842.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000032130; ENSMUSP00000032130; ENSMUSG00000030051. [Q9D842-1]
ENSMUST00000065997; ENSMUSP00000066232; ENSMUSG00000030051. [Q9D842-3]
GeneID72103.
KEGGmmu:72103.
UCSCuc009ctq.2. mouse. [Q9D842-3]
uc009ctr.2. mouse. [Q9D842-1]
uc012eon.1. mouse. [Q9D842-2]

Organism-specific databases

CTD200558.
MGIMGI:1919353. Aplf.

Phylogenomic databases

eggNOGNOG85452.
GeneTreeENSGT00390000010591.
HOGENOMHOG000033995.
HOVERGENHBG095728.
InParanoidQ9D842.
KOK13295.
OMAKRILPAW.
OrthoDBEOG73805W.
PhylomeDBQ9D842.
TreeFamTF326160.

Gene expression databases

BgeeQ9D842.
GenevestigatorQ9D842.

Family and domain databases

Gene3D2.60.200.20. 1 hit.
InterProIPR000253. FHA_dom.
IPR008984. SMAD_FHA_domain.
IPR019406. Znf_C2H2_APLF-like.
[Graphical view]
PfamPF10283. zf-CCHH. 2 hits.
[Graphical view]
SUPFAMSSF49879. SSF49879. 1 hit.
ProtoNetSearch...

Other

NextBio335444.
PROQ9D842.
SOURCESearch...

Entry information

Entry nameAPLF_MOUSE
AccessionPrimary (citable) accession number: Q9D842
Secondary accession number(s): Q8BZL5, Q99LX6
Entry history
Integrated into UniProtKB/Swiss-Prot: August 16, 2005
Last sequence update: August 16, 2005
Last modified: July 9, 2014
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot