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Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) (Exonuclease 3'-5' domain-like-containing protein 2)

 EXD2_HUMAN              Reviewed;         621 AA.
Q9NVH0; B4DIH6; G5E947; Q6AWB6; Q8N3D3;
24-OCT-2003, integrated into UniProtKB/Swiss-Prot.
31-OCT-2012, sequence version 2.
12-SEP-2018, entry version 141.
RecName: Full=Exonuclease 3'-5' domain-containing protein 2 {ECO:0000312|HGNC:HGNC:20217};
EC=3.1.11.1 {ECO:0000269|PubMed:26807646};
AltName: Full=Exonuclease 3'-5' domain-like-containing protein 2;
Name=EXD2 {ECO:0000312|HGNC:HGNC:20217};
Synonyms=C14orf114 {ECO:0000312|HGNC:HGNC:20217},
EXDL2 {ECO:0000303|PubMed:26807646};
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANT
HIS-518.
TISSUE=Hippocampus, and Teratocarcinoma;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANT
HIS-518.
TISSUE=Endometrium, and Melanoma;
PubMed=17974005; DOI=10.1186/1471-2164-8-399;
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=12508121; DOI=10.1038/nature01348;
Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C.,
Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A.,
Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S.,
Sun H., Du H., Pepin K., Artiguenave F., Robert C., Cruaud C.,
Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P.,
Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N.,
Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C.,
Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S.,
Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B.,
Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M.,
Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S.,
Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D.,
Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A.,
Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M.,
Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V.,
Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L.,
Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J.,
Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W.,
Quetier F., Waterston R., Hood L., Weissenbach J.;
"The DNA sequence and analysis of human chromosome 14.";
Nature 421:601-607(2003).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
TISSUE=Lung;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
FUNCTION.
PubMed=20603073; DOI=10.1016/j.molcel.2010.06.023;
Smogorzewska A., Desetty R., Saito T.T., Schlabach M., Lach F.P.,
Sowa M.E., Clark A.B., Kunkel T.A., Harper J.W., Colaiacovo M.P.,
Elledge S.J.;
"A genetic screen identifies FAN1, a Fanconi anemia-associated
nuclease necessary for DNA interstrand crosslink repair.";
Mol. Cell 39:36-47(2010).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[8]
FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, MUTAGENESIS OF
108-ASP--GLU-110, AND INTERACTION WITH BRCA1; MRE11 AND RBBP8.
PubMed=26807646; DOI=10.1038/ncb3303;
Broderick R., Nieminuszczy J., Baddock H.T., Deshpande R.A.,
Gileadi O., Paull T.T., McHugh P.J., Niedzwiedz W.;
"EXD2 promotes homologous recombination by facilitating DNA end
resection.";
Nat. Cell Biol. 18:271-280(2016).
-!- FUNCTION: Exonuclease required for double-strand breaks resection
and efficient homologous recombination. Plays a key role in
controlling the initial steps of chromosomal break repair, it is
recruited to chromatin in a damage-dependent manner and
functionally interacts with the MRN complex to accelerate
resection through its 3'-5' exonuclease activity, which
efficiently processes double-stranded DNA substrates containing
nicks. {ECO:0000269|PubMed:20603073, ECO:0000269|PubMed:26807646}.
-!- CATALYTIC ACTIVITY: Exonucleolytic cleavage in the 3'- to 5'-
direction to yield nucleoside 5'-phosphates.
{ECO:0000269|PubMed:26807646}.
-!- SUBUNIT: Interacts with RBBP8, MRE11 and BRCA1.
{ECO:0000269|PubMed:26807646}.
-!- INTERACTION:
Q99708:RBBP8; NbExp=3; IntAct=EBI-11324738, EBI-745715;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:26807646}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9NVH0-1; Sequence=Displayed;
Name=2;
IsoId=Q9NVH0-2; Sequence=VSP_044367;
-!- SIMILARITY: Belongs to the EXD2 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAH10568.1; Type=Frameshift; Positions=269; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AK001600; BAA91781.1; -; mRNA.
EMBL; AK295601; BAG58488.1; -; mRNA.
EMBL; AL834434; CAD39094.2; -; mRNA.
EMBL; BX647767; CAH10568.1; ALT_FRAME; mRNA.
EMBL; AL359317; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471061; EAW80985.1; -; Genomic_DNA.
EMBL; BC001962; AAH01962.1; -; mRNA.
CCDS; CCDS53902.1; -. [Q9NVH0-1]
CCDS; CCDS9793.1; -. [Q9NVH0-2]
RefSeq; NP_001180289.1; NM_001193360.1. [Q9NVH0-1]
RefSeq; NP_001180290.1; NM_001193361.1. [Q9NVH0-1]
RefSeq; NP_001180291.1; NM_001193362.1. [Q9NVH0-1]
RefSeq; NP_001180292.1; NM_001193363.1. [Q9NVH0-1]
RefSeq; NP_060669.1; NM_018199.3. [Q9NVH0-2]
RefSeq; XP_005267874.1; XM_005267817.3. [Q9NVH0-2]
RefSeq; XP_011535210.1; XM_011536908.2. [Q9NVH0-2]
RefSeq; XP_016876910.1; XM_017021421.1. [Q9NVH0-2]
UniGene; Hs.533878; -.
ProteinModelPortal; Q9NVH0; -.
SMR; Q9NVH0; -.
BioGrid; 120514; 13.
DIP; DIP-61996N; -.
IntAct; Q9NVH0; 10.
MINT; Q9NVH0; -.
STRING; 9606.ENSP00000313140; -.
iPTMnet; Q9NVH0; -.
PhosphoSitePlus; Q9NVH0; -.
BioMuta; EXD2; -.
DMDM; 410516875; -.
EPD; Q9NVH0; -.
MaxQB; Q9NVH0; -.
PaxDb; Q9NVH0; -.
PeptideAtlas; Q9NVH0; -.
PRIDE; Q9NVH0; -.
ProteomicsDB; 82795; -.
TopDownProteomics; Q9NVH0-2; -. [Q9NVH0-2]
DNASU; 55218; -.
Ensembl; ENST00000312994; ENSP00000313140; ENSG00000081177. [Q9NVH0-1]
Ensembl; ENST00000409014; ENSP00000386915; ENSG00000081177. [Q9NVH0-2]
Ensembl; ENST00000409018; ENSP00000387331; ENSG00000081177. [Q9NVH0-1]
Ensembl; ENST00000409242; ENSP00000386839; ENSG00000081177. [Q9NVH0-2]
Ensembl; ENST00000409675; ENSP00000386762; ENSG00000081177. [Q9NVH0-2]
Ensembl; ENST00000409949; ENSP00000386632; ENSG00000081177. [Q9NVH0-2]
GeneID; 55218; -.
KEGG; hsa:55218; -.
UCSC; uc001xkt.4; human. [Q9NVH0-1]
CTD; 55218; -.
EuPathDB; HostDB:ENSG00000081177.18; -.
GeneCards; EXD2; -.
HGNC; HGNC:20217; EXD2.
HPA; HPA002906; -.
HPA; HPA005848; -.
MIM; 616940; gene.
neXtProt; NX_Q9NVH0; -.
OpenTargets; ENSG00000081177; -.
PharmGKB; PA164719421; -.
eggNOG; KOG4373; Eukaryota.
eggNOG; ENOG410XS63; LUCA.
GeneTree; ENSGT00390000014318; -.
HOGENOM; HOG000046597; -.
KO; K20777; -.
OMA; DIPFRSK; -.
OrthoDB; EOG091G08I1; -.
PhylomeDB; Q9NVH0; -.
TreeFam; TF324246; -.
ChiTaRS; EXD2; human.
GenomeRNAi; 55218; -.
PRO; PR:Q9NVH0; -.
Proteomes; UP000005640; Chromosome 14.
Bgee; ENSG00000081177; Expressed in 217 organ(s), highest expression level in C1 segment of cervical spinal cord.
CleanEx; HS_EXDL2; -.
ExpressionAtlas; Q9NVH0; baseline and differential.
Genevisible; Q9NVH0; HS.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0008408; F:3'-5' exonuclease activity; IDA:UniProtKB.
GO; GO:0008852; F:exodeoxyribonuclease I activity; IEA:UniProtKB-EC.
GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:UniProtKB.
GO; GO:0000729; P:DNA double-strand break processing; IDA:UniProtKB.
GO; GO:0006302; P:double-strand break repair; IDA:UniProtKB.
GO; GO:0000724; P:double-strand break repair via homologous recombination; IDA:UniProtKB.
GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IDA:UniProtKB.
Gene3D; 3.30.420.10; -; 1.
InterPro; IPR002562; 3'-5'_exonuclease_dom.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
Pfam; PF01612; DNA_pol_A_exo1; 1.
SMART; SM00474; 35EXOc; 1.
SUPFAM; SSF53098; SSF53098; 1.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Exonuclease; Hydrolase;
Nuclease; Nucleus; Polymorphism; Reference proteome.
CHAIN 1 621 Exonuclease 3'-5' domain-containing
protein 2.
/FTId=PRO_0000089924.
DOMAIN 155 247 3'-5' exonuclease.
VAR_SEQ 1 125 Missing (in isoform 2).
{ECO:0000303|PubMed:14702039,
ECO:0000303|PubMed:15489334,
ECO:0000303|PubMed:17974005}.
/FTId=VSP_044367.
VARIANT 231 231 D -> N (in dbSNP:rs35010854).
/FTId=VAR_050980.
VARIANT 518 518 Q -> H (in dbSNP:rs8007859).
{ECO:0000269|PubMed:14702039,
ECO:0000269|PubMed:17974005}.
/FTId=VAR_050981.
MUTAGEN 108 110 DCE->ACA: Loss of 3'-5' exonuclease
activity. {ECO:0000269|PubMed:26807646}.
CONFLICT 287 287 V -> G (in Ref. 2; CAD39094).
{ECO:0000305}.
SEQUENCE 621 AA; 70353 MW; CD66A3E68A40C7FF CRC64;
MSRQNLVALT VTTLLGVAVG GFVLWKGIQR RRRSKTSPVT QQPQQKVLGS RELPPPEDDQ
LHSSAPRSSW KERILKAKVV TVSQEAEWDQ IEPLLRSELE DFPVLGIDCE WVNLEGKASP
LSLLQMASPS GLCVLVRLPK LICGGKTLPR TLLDILADGT ILKVGVGCSE DASKLLQDYG
LVVRGCLDLR YLAMRQRNNL LCNGLSLKSL AETVLNFPLD KSLLLRCSNW DAETLTEDQV
IYAARDAQIS VALFLHLLGY PFSRNSPGEK NDDHSSWRKV LEKCQGVVDI PFRSKGMSRL
GEEVNGEATE SQQKPRNKKS KMDGMVPGNH QGRDPRKHKR KPLGVGYSAR KSPLYDNCFL
HAPDGQPLCT CDRRKAQWYL DKGIGELVSE EPFVVKLRFE PAGRPESPGD YYLMVKENLC
VVCGKRDSYI RKNVIPHEYR KHFPIEMKDH NSHDVLLLCT SCHAISNYYD NHLKQQLAKE
FQAPIGSEEG LRLLEDPERR QVRSGARALL NAESLPTQRK EELLQALREF YNTDVVTEEM
LQEAASLETR ISNENYVPHG LKVVQCHSQG GLRSLMQLES RWRQHFLDSM QPKHLPQQWS
VDHNHQKLLR KFGEDLPIQL S


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