EXD1_BOMMO
ID EXD1_BOMMO Reviewed; 315 AA.
AC H9IUR0;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 16-MAR-2016, sequence version 2.
DT 25-MAY-2022, entry version 36.
DE RecName: Full=piRNA biogenesis protein EXD1 {ECO:0000305};
DE AltName: Full=Exonuclease 3'-5' domain-containing protein 1 {ECO:0000250|UniProtKB:Q8NHP7};
DE AltName: Full=Exonuclease 3'-5' domain-like-containing protein 1 {ECO:0000250|UniProtKB:Q8NHP7};
DE AltName: Full=Inactive exonuclease EXD1 {ECO:0000305};
DE Short=BmExd1 {ECO:0000303|PubMed:26669262};
GN Name=EXD1 {ECO:0000303|PubMed:26669262};
OS Bombyx mori (Silk moth).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea;
OC Bombycidae; Bombycinae; Bombyx.
OX NCBI_TaxID=7091;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=p50T;
RX PubMed=19121390; DOI=10.1016/j.ibmb.2008.11.004;
RG International Silkworm Genome Consortium;
RT "The genome of a lepidopteran model insect, the silkworm Bombyx mori.";
RL Insect Biochem. Mol. Biol. 38:1036-1045(2008).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 73-315, FUNCTION, SUBCELLULAR
RP LOCATION, SUBUNIT, IDENTIFICATION IN THE PET COMPLEX, AND DOMAIN.
RX PubMed=26669262; DOI=10.1016/j.molcel.2015.11.009;
RA Yang Z., Chen K.M., Pandey R.R., Homolka D., Reuter M., Janeiro B.K.,
RA Sachidanandam R., Fauvarque M.O., McCarthy A.A., Pillai R.S.;
RT "PIWI slicing and EXD1 drive biogenesis of nuclear piRNAs from cytosolic
RT targets of the mouse piRNA pathway.";
RL Mol. Cell 61:138-152(2016).
CC -!- FUNCTION: RNA-binding component of the PET complex, a multiprotein
CC complex required for the processing of piRNAs during spermatogenesis.
CC The piRNA metabolic process mediates the repression of transposable
CC elements during meiosis by forming complexes composed of piRNAs and
CC Piwi proteins and governs the methylation and subsequent repression of
CC transposable elements, preventing their mobilization, which is
CC essential for the germline integrity. The PET complex is required
CC during the secondary piRNAs metabolic process for the PIWIL2 slicing-
CC triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably
CC acts as an RNA adapter. EXD1 is an inactive exonuclease.
CC {ECO:0000269|PubMed:26669262}.
CC -!- SUBUNIT: Homodimer (PubMed:26669262). Component of the PET complex, at
CC least composed of EXD1, SIWI, TDRD12 and piRNAs (PubMed:26669262).
CC {ECO:0000269|PubMed:26669262}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:26669262}.
CC Note=Component of the meiotic nuage, also named P granule, a germ-cell-
CC specific organelle required to repress transposon activity during
CC meiosis. {ECO:0000269|PubMed:26669262}.
CC -!- DOMAIN: The 3'-5' exonuclease domain lacks the conserved Asp-Glu-Asp-
CC Asp (DEDD) residues that coordinates divalent ions essential for
CC exonuclease activity. {ECO:0000305|PubMed:26669262}.
CC -!- SIMILARITY: Belongs to the EXD1 family. {ECO:0000305}.
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DR EMBL; BABH01000658; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PDB; 5FIQ; X-ray; 2.40 A; A/C/E/G/I=73-315.
DR PDB; 5FIS; X-ray; 1.60 A; A/B=73-315.
DR PDBsum; 5FIQ; -.
DR PDBsum; 5FIS; -.
DR AlphaFoldDB; H9IUR0; -.
DR SMR; H9IUR0; -.
DR STRING; 7091.BGIBMGA000990-TA; -.
DR eggNOG; KOG2405; Eukaryota.
DR HOGENOM; CLU_960502_0_0_1; -.
DR InParanoid; H9IUR0; -.
DR Proteomes; UP000005204; Unassembled WGS sequence.
DR GO; GO:0043186; C:P granule; IDA:UniProtKB.
DR GO; GO:1990923; C:PET complex; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0031047; P:gene silencing by RNA; IMP:UniProtKB.
DR GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0034587; P:piRNA metabolic process; IMP:UniProtKB.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF01612; DNA_pol_A_exo1; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Meiosis; Reference proteome; RNA-binding;
KW RNA-mediated gene silencing.
FT CHAIN 1..315
FT /note="piRNA biogenesis protein EXD1"
FT /id="PRO_0000435800"
FT DOMAIN 141..228
FT /note="3'-5' exonuclease"
FT /evidence="ECO:0000255"
FT HELIX 79..90
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 100..110
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 133..136
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 146..149
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 151..155
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 158..163
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 164..173
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 175..185
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 195..207
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 217..225
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 238..242
FT /evidence="ECO:0007829|PDB:5FIS"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 248..259
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 261..271
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 274..288
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 292..299
FT /evidence="ECO:0007829|PDB:5FIS"
FT TURN 300..303
FT /evidence="ECO:0007829|PDB:5FIS"
FT HELIX 309..313
FT /evidence="ECO:0007829|PDB:5FIS"
SQ 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
