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Q9D842

- APLF_MOUSE

UniProt

Q9D842 - APLF_MOUSE

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Protein

Aprataxin and PNK-like factor

Gene

Aplf

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli

Functioni

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.By similarity

Catalytic activityi

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei371 – 3711Poly-ADP-riboseBy similarity
Binding sitei376 – 3761Poly-ADP-riboseBy similarity
Binding sitei381 – 3811Poly-ADP-riboseBy similarity
Binding sitei382 – 3821Poly-ADP-riboseBy similarity
Binding sitei418 – 4181Poly-ADP-riboseBy similarity
Binding sitei423 – 4231Poly-ADP-riboseBy similarity
Binding sitei424 – 4241Poly-ADP-riboseBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri372 – 39322PBZ-type 1Add
BLAST
Zinc fingeri414 – 43522PBZ-type 2Add
BLAST

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: UniProtKB
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB
  3. endodeoxyribonuclease activity Source: UniProtKB
  4. metal ion binding Source: UniProtKB-KW
  5. nucleotide binding Source: UniProtKB

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: UniProtKB
  2. DNA catabolic process, endonucleolytic Source: GOC
  3. double-strand break repair Source: UniProtKB
  4. positive regulation of DNA ligation Source: Ensembl
  5. regulation of isotype switching Source: MGI
  6. single strand break repair Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Aprataxin and PNK-like factor (EC:4.2.99.18)
Alternative name(s):
Apurinic-apyrimidinic endonuclease APLF
Gene namesi
Name:Aplf
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 6

Organism-specific databases

MGIiMGI:1919353. Aplf.

Subcellular locationi

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.By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. nucleus Source: UniProtKB
  3. site of double-strand break Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 499499Aprataxin and PNK-like factorPRO_0000089343Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei116 – 1161Phosphoserine; by ATMBy similarity

Post-translational modificationi

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

Keywords - PTMi

ADP-ribosylation, Phosphoprotein

Proteomic databases

MaxQBiQ9D842.
PRIDEiQ9D842.

PTM databases

PhosphoSiteiQ9D842.

Expressioni

Gene expression databases

BgeeiQ9D842.
GenevestigatoriQ9D842.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi215153. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ9D842.
SMRiQ9D842. Positions 354-441.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 108108FHA-likeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni401 – 41111Flexible linkerBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi274 – 2774Poly-Ser
Compositional biasi445 – 48541Asp-richAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the APLF family.Curated
Contains 1 FHA-like domain.Curated
Contains 2 PBZ-type zinc fingers.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri372 – 39322PBZ-type 1Add
BLAST
Zinc fingeri414 – 43522PBZ-type 2Add
BLAST

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG85452.
GeneTreeiENSGT00390000010591.
HOGENOMiHOG000033995.
HOVERGENiHBG095728.
InParanoidiQ9D842.
KOiK13295.
OMAiKRILPAW.
OrthoDBiEOG73805W.
PhylomeDBiQ9D842.
TreeFamiTF326160.

Family and domain databases

Gene3Di2.60.200.20. 1 hit.
InterProiIPR000253. FHA_dom.
IPR008984. SMAD_FHA_domain.
IPR019406. Znf_C2H2_APLF-like.
[Graphical view]
PfamiPF10283. zf-CCHH. 2 hits.
[Graphical view]
SUPFAMiSSF49879. SSF49879. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9D842-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MPSDFFLQPL DGGPRVPVGP GQTVIGRGPL LGITDKRVSR RHAILEVVDS
60 70 80 90 100
QLRIKPIHRN PCFYQSSEKS QHSPMETQVW SQLHPGDSFS LLLDKYAFRV
110 120 130 140 150
FSAESEVEME CTLRNSQMLD EDDILSEMQK SPVVNLPDKT TGASQLQGSP
160 170 180 190 200
EITKTKCPTI DPMSSSGECR AFSEHQPRPT QRKRILPAWM LAESLSDQSL
210 220 230 240 250
STPAEGGDKD VIQRSGKAGT CEDRTPGNTS WHGKKRLSPS GNSKSVSAEQ
260 270 280 290 300
DPGKKCRKAD QEGPGVSSEN VPESSSSNIV KDPDVDIVKT NKQKDGILIE
310 320 330 340 350
ELGEVSKHKA ATKPTTNEEG ESCARVQSKS PPEKSQGCHP ESSSAPSSPD
360 370 380 390 400
ALHTDTADPV LGCSEESKVR RTACMYGANC YRRNPLHFQH FSHPGDSDYG
410 420 430 440 450
EVHGTDEGVI GDRPECPYGA SCYRKNPQHK MEYRHSALPA RVALDEDDDD
460 470 480 490
VGQPSDDEDE EDYEPTDEDS DWHPGKDDEE QEDVDELLKE AKSSLHLKH
Length:499
Mass (Da):54,968
Last modified:August 16, 2005 - v2
Checksum:i4B41A9C0C8937963
GO
Isoform 2 (identifier: Q9D842-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-108: Missing.
     493-499: SSLHLKH → RFMRRKK

Note: No experimental confirmation available.

Show »
Length:391
Mass (Da):43,042
Checksum:iD666D7635D0AFF78
GO
Isoform 3 (identifier: Q9D842-3) [UniParc]FASTAAdd to Basket

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.

Show »
Length:478
Mass (Da):53,015
Checksum:i44710524EAB5EFA4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti178 – 1781R → H in AAH02179. (PubMed:15489334)Curated
Sequence conflicti470 – 4701S → F in BAB25711. (PubMed:16141072)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 108108Missing in isoform 2. 1 PublicationVSP_014983Add
BLAST
Alternative sequencei1 – 3232MPSDF…GPLLG → MPSVPEGGGYE in isoform 3. 1 PublicationVSP_014982Add
BLAST
Alternative sequencei493 – 4997SSLHLKH → RFMRRKK in isoform 2 and isoform 3. 2 PublicationsVSP_014984

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK008513 mRNA. Translation: BAB25711.1.
AK034191 mRNA. Translation: BAC28625.1.
BC002179 mRNA. Translation: AAH02179.1.
CCDSiCCDS20324.1. [Q9D842-3]
CCDS51839.1. [Q9D842-1]
RefSeqiNP_001163960.1. NM_001170489.1. [Q9D842-1]
NP_077213.2. NM_024251.4. [Q9D842-3]
UniGeneiMm.31770.

Genome annotation databases

EnsembliENSMUST00000032130; ENSMUSP00000032130; ENSMUSG00000030051. [Q9D842-1]
ENSMUST00000065997; ENSMUSP00000066232; ENSMUSG00000030051. [Q9D842-3]
GeneIDi72103.
KEGGimmu:72103.
UCSCiuc009ctq.2. mouse. [Q9D842-3]
uc009ctr.2. mouse. [Q9D842-1]
uc012eon.1. mouse. [Q9D842-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK008513 mRNA. Translation: BAB25711.1 .
AK034191 mRNA. Translation: BAC28625.1 .
BC002179 mRNA. Translation: AAH02179.1 .
CCDSi CCDS20324.1. [Q9D842-3 ]
CCDS51839.1. [Q9D842-1 ]
RefSeqi NP_001163960.1. NM_001170489.1. [Q9D842-1 ]
NP_077213.2. NM_024251.4. [Q9D842-3 ]
UniGenei Mm.31770.

3D structure databases

ProteinModelPortali Q9D842.
SMRi Q9D842. Positions 354-441.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 215153. 1 interaction.

PTM databases

PhosphoSitei Q9D842.

Proteomic databases

MaxQBi Q9D842.
PRIDEi Q9D842.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000032130 ; ENSMUSP00000032130 ; ENSMUSG00000030051 . [Q9D842-1 ]
ENSMUST00000065997 ; ENSMUSP00000066232 ; ENSMUSG00000030051 . [Q9D842-3 ]
GeneIDi 72103.
KEGGi mmu:72103.
UCSCi uc009ctq.2. mouse. [Q9D842-3 ]
uc009ctr.2. mouse. [Q9D842-1 ]
uc012eon.1. mouse. [Q9D842-2 ]

Organism-specific databases

CTDi 200558.
MGIi MGI:1919353. Aplf.

Phylogenomic databases

eggNOGi NOG85452.
GeneTreei ENSGT00390000010591.
HOGENOMi HOG000033995.
HOVERGENi HBG095728.
InParanoidi Q9D842.
KOi K13295.
OMAi KRILPAW.
OrthoDBi EOG73805W.
PhylomeDBi Q9D842.
TreeFami TF326160.

Miscellaneous databases

NextBioi 335444.
PROi Q9D842.
SOURCEi Search...

Gene expression databases

Bgeei Q9D842.
Genevestigatori Q9D842.

Family and domain databases

Gene3Di 2.60.200.20. 1 hit.
InterProi IPR000253. FHA_dom.
IPR008984. SMAD_FHA_domain.
IPR019406. Znf_C2H2_APLF-like.
[Graphical view ]
Pfami PF10283. zf-CCHH. 2 hits.
[Graphical view ]
SUPFAMi SSF49879. SSF49879. 1 hit.
ProtoNeti Search...

Publicationsi

  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.
    , 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.

Entry informationi

Entry nameiAPLF_MOUSE
AccessioniPrimary (citable) accession number: Q9D842
Secondary accession number(s): Q8BZL5, Q99LX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2005
Last sequence update: August 16, 2005
Last modified: October 29, 2014
This is version 100 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3