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piRNA biogenesis protein EXD1 (Exonuclease 3'-5' domain-containing protein 1) (Exonuclease 3'-5' domain-like-containing protein 1) (Inactive exonuclease EXD1) (BmExd1)

 EXD1_BOMMO              Reviewed;         315 AA.
H9IUR0;
16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
16-MAR-2016, sequence version 2.
12-SEP-2018, entry version 28.
RecName: Full=piRNA biogenesis protein EXD1 {ECO:0000305};
AltName: Full=Exonuclease 3'-5' domain-containing protein 1 {ECO:0000250|UniProtKB:Q8NHP7};
AltName: Full=Exonuclease 3'-5' domain-like-containing protein 1 {ECO:0000250|UniProtKB:Q8NHP7};
AltName: Full=Inactive exonuclease EXD1 {ECO:0000305};
Short=BmExd1 {ECO:0000303|PubMed:26669262};
Name=EXD1 {ECO:0000303|PubMed:26669262};
Bombyx mori (Silk moth).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia;
Bombycoidea; Bombycidae; Bombycinae; Bombyx.
NCBI_TaxID=7091;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=p50T;
PubMed=19121390; DOI=10.1016/j.ibmb.2008.11.004;
International Silkworm Genome Consortium;
"The genome of a lepidopteran model insect, the silkworm Bombyx
mori.";
Insect Biochem. Mol. Biol. 38:1036-1045(2008).
[2]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 73-315, FUNCTION, SUBCELLULAR
LOCATION, SUBUNIT, IDENTIFICATION IN THE PET COMPLEX, AND DOMAIN.
PubMed=26669262; DOI=10.1016/j.molcel.2015.11.009;
Yang Z., Chen K.M., Pandey R.R., Homolka D., Reuter M., Janeiro B.K.,
Sachidanandam R., Fauvarque M.O., McCarthy A.A., Pillai R.S.;
"PIWI slicing and EXD1 drive biogenesis of nuclear piRNAs from
cytosolic targets of the mouse piRNA pathway.";
Mol. Cell 61:138-152(2016).
-!- FUNCTION: RNA-binding component of the PET complex, a multiprotein
complex required for the processing of piRNAs during
spermatogenesis. The piRNA metabolic process mediates the
repression of transposable elements during meiosis by forming
complexes composed of piRNAs and Piwi proteins and governs the
methylation and subsequent repression of transposable elements,
preventing their mobilization, which is essential for the germline
integrity. The PET complex is required during the secondary piRNAs
metabolic process for the PIWIL2 slicing-triggered loading of
PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA
adapter. EXD1 is an inactive exonuclease.
{ECO:0000269|PubMed:26669262}.
-!- SUBUNIT: Homodimer (PubMed:26669262). Component of the PET
complex, at least composed of EXD1, SIWI, TDRD12 and piRNAs
(PubMed:26669262). {ECO:0000269|PubMed:26669262}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:26669262}.
Note=Component of the meiotic nuage, also named P granule, a germ-
cell-specific organelle required to repress transposon activity
during meiosis. {ECO:0000269|PubMed:26669262}.
-!- DOMAIN: The 3'-5' exonuclease domain lacks the conserved Asp-Glu-
Asp-Asp (DEDD) residues that coordinates divalent ions essential
for exonuclease activity. {ECO:0000305|PubMed:26669262}.
-!- SIMILARITY: Belongs to the EXD1 family. {ECO:0000305}.
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EMBL; BABH01000658; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PDB; 5FIQ; X-ray; 2.40 A; A/C/E/G/I=73-315.
PDB; 5FIS; X-ray; 1.60 A; A/B=73-315.
PDBsum; 5FIQ; -.
PDBsum; 5FIS; -.
SMR; H9IUR0; -.
STRING; 7091.BGIBMGA000990-TA; -.
PRIDE; H9IUR0; -.
eggNOG; KOG2405; Eukaryota.
eggNOG; ENOG4111GM1; LUCA.
InParanoid; H9IUR0; -.
Proteomes; UP000005204; Unassembled WGS sequence.
GO; GO:0043186; C:P granule; IDA:UniProtKB.
GO; GO:1990923; C:PET complex; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
GO; GO:0031047; P:gene silencing by RNA; IMP:UniProtKB.
GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IEA:GOC.
GO; GO:0034587; P:piRNA metabolic process; IMP: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.
SUPFAM; SSF53098; SSF53098; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Meiosis;
Reference proteome; RNA-binding; RNA-mediated gene silencing.
CHAIN 1 315 piRNA biogenesis protein EXD1.
/FTId=PRO_0000435800.
DOMAIN 141 228 3'-5' exonuclease. {ECO:0000255}.
HELIX 79 90 {ECO:0000244|PDB:5FIS}.
STRAND 93 95 {ECO:0000244|PDB:5FIS}.
STRAND 97 99 {ECO:0000244|PDB:5FIS}.
HELIX 100 110 {ECO:0000244|PDB:5FIS}.
STRAND 113 117 {ECO:0000244|PDB:5FIS}.
HELIX 125 127 {ECO:0000244|PDB:5FIS}.
STRAND 133 136 {ECO:0000244|PDB:5FIS}.
STRAND 141 144 {ECO:0000244|PDB:5FIS}.
HELIX 146 149 {ECO:0000244|PDB:5FIS}.
HELIX 151 155 {ECO:0000244|PDB:5FIS}.
HELIX 158 163 {ECO:0000244|PDB:5FIS}.
STRAND 164 173 {ECO:0000244|PDB:5FIS}.
HELIX 175 185 {ECO:0000244|PDB:5FIS}.
STRAND 191 194 {ECO:0000244|PDB:5FIS}.
HELIX 195 207 {ECO:0000244|PDB:5FIS}.
HELIX 217 225 {ECO:0000244|PDB:5FIS}.
HELIX 238 242 {ECO:0000244|PDB:5FIS}.
STRAND 243 245 {ECO:0000244|PDB:5FIS}.
HELIX 248 259 {ECO:0000244|PDB:5FIS}.
HELIX 261 271 {ECO:0000244|PDB:5FIS}.
HELIX 274 288 {ECO:0000244|PDB:5FIS}.
HELIX 292 299 {ECO:0000244|PDB:5FIS}.
TURN 300 303 {ECO:0000244|PDB:5FIS}.
HELIX 309 313 {ECO:0000244|PDB:5FIS}.
SEQUENCE 315 AA; 36486 MW; 00ADA77D0EC7EC5C CRC64;
MDNLYTKGEL LQVHTKNYDV FEGRFYSMAQ DKTKISLYDV KEIPHGDAND GVLHYYDSEI
REVVKLQEST EKKVLKISQT KYEEILKISK KYIFINQVDK SFHEAVDDLN QQDFIAVSGD
GANMGRKCKM PFLVLSTDHQ IYIFDIQVMQ YHAFESGLKK ILEGDSPKKI AHDCRKLSDC
LYHKHNVKLK SVFDTQVGDL IITKNKKVTL PNKVKSLGEC LTNYLGLQQN TIDEKLDIVQ
STERPLSVKI KDSLARNIAF LHHLSEVINE EMQLPFYRGV ECYIENIRSS DDFKAWELCG
KLNQIPKEFR NAIDY


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