TDRKH_BOMMO
ID TDRKH_BOMMO Reviewed; 629 AA.
AC H9JD76;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2017, sequence version 2.
DT 25-MAY-2022, entry version 39.
DE RecName: Full=Tudor and KH domain-containing protein homolog {ECO:0000305};
DE AltName: Full=Partner of PIWIs protein {ECO:0000303|PubMed:23970546};
DE Short=BmPAPI {ECO:0000303|PubMed:23970546, ECO:0000303|PubMed:26919431};
GN Name=PAPI {ECO:0000303|PubMed:23970546};
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 FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH SIWI AND AGO3, AND DOMAIN.
RX PubMed=23970546; DOI=10.1261/rna.040428.113;
RA Honda S., Kirino Y., Maragkakis M., Alexiou P., Ohtaki A., Murali R.,
RA Mourelatos Z., Kirino Y.;
RT "Mitochondrial protein BmPAPI modulates the length of mature piRNAs.";
RL RNA 19:1405-1418(2013).
RN [3]
RP FUNCTION, INTERACTION WITH SIWI AND PNLDC1, DOMAIN, AND MUTAGENESIS OF
RP ILE-69 AND VAL-142.
RX PubMed=26919431; DOI=10.1016/j.cell.2016.01.008;
RA Izumi N., Shoji K., Sakaguchi Y., Honda S., Kirino Y., Suzuki T.,
RA Katsuma S., Tomari Y.;
RT "Identification and functional analysis of the pre-piRNA 3' trimmer in
RT silkworms.";
RL Cell 164:962-973(2016).
CC -!- FUNCTION: Participates in the primary piRNA biogenesis pathway and is
CC required during spermatogenesis to repress transposable elements and
CC prevent their mobilization, which is essential for the germline
CC integrity (PubMed:23970546, PubMed:26919431). The piRNA metabolic
CC process mediates the repression of transposable elements during meiosis
CC by forming complexes composed of piRNAs and Piwi proteins (Siwi or
CC Ago3) and govern the methylation and subsequent repression of
CC transposons (PubMed:23970546, PubMed:26919431). Required for the final
CC steps of primary piRNA biogenesis by participating in the processing of
CC 31-37 nt intermediates into mature piRNAs: acts by recruiting the
CC exonuclease PNLDC1/trimmer to Siwi-bound pre-piRNAs (PubMed:26919431).
CC {ECO:0000269|PubMed:23970546, ECO:0000269|PubMed:26919431}.
CC -!- SUBUNIT: Interacts with (symmetrically methylated) Siwi
CC (PubMed:23970546, PubMed:26919431). Interacts with (symmetrically
CC methylated) Ago3 (PubMed:23970546). Interacts with PNLDC1/trimmer;
CC interaction takes place on the mitochondrial surface and recruits
CC PNLDC1/trimmer to Siwi-bound pre-piRNAs (PubMed:26919431).
CC {ECO:0000269|PubMed:23970546, ECO:0000269|PubMed:26919431}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion outer membrane
CC {ECO:0000269|PubMed:23970546}; Single-pass membrane protein
CC {ECO:0000255}. Note=Localizes to the outer surface of mitochondria.
CC {ECO:0000269|PubMed:23970546}.
CC -!- DOMAIN: The Tudor domain specifically recognizes and binds
CC symmetrically methylated Siwi and Ago3. {ECO:0000269|PubMed:23970546,
CC ECO:0000305|PubMed:26919431}.
CC -!- SIMILARITY: Belongs to the Tdrkh family. {ECO:0000305}.
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DR EMBL; BABH01036235; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BABH01036236; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BABH01036237; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BABH01036238; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PDB; 5VQG; X-ray; 2.60 A; A=245-462.
DR PDB; 5VQH; X-ray; 2.40 A; A/B=245-462.
DR PDB; 5VY1; X-ray; 3.05 A; A/B=245-462.
DR PDBsum; 5VQG; -.
DR PDBsum; 5VQH; -.
DR PDBsum; 5VY1; -.
DR AlphaFoldDB; H9JD76; -.
DR SMR; H9JD76; -.
DR HOGENOM; CLU_023629_0_1_1; -.
DR InParanoid; H9JD76; -.
DR Proteomes; UP000005204; Unassembled WGS sequence.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005741; C:mitochondrial outer membrane; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:1990511; P:piRNA biosynthetic process; IDA:UniProtKB.
DR GO; GO:0007283; P:spermatogenesis; IEA:UniProtKB-KW.
DR CDD; cd04508; TUDOR; 1.
DR Gene3D; 2.40.50.90; -; 1.
DR Gene3D; 3.30.1370.10; -; 2.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR035437; SNase_OB-fold_sf.
DR InterPro; IPR002999; Tudor.
DR Pfam; PF00013; KH_1; 2.
DR Pfam; PF00567; TUDOR; 1.
DR SMART; SM00322; KH; 2.
DR SMART; SM00333; TUDOR; 1.
DR SUPFAM; SSF54791; SSF54791; 2.
DR PROSITE; PS50084; KH_TYPE_1; 2.
DR PROSITE; PS50304; TUDOR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Differentiation; Membrane; Mitochondrion;
KW Mitochondrion outer membrane; Reference proteome; Repeat; RNA-binding;
KW RNA-mediated gene silencing; Spermatogenesis; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..629
FT /note="Tudor and KH domain-containing protein homolog"
FT /id="PRO_0000439350"
FT TRANSMEM 9..29
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 46..109
FT /note="KH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 119..185
FT /note="KH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 297..362
FT /note="Tudor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT REGION 198..240
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 464..526
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 223..240
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 500..526
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 69
FT /note="I->N: Loss of activity; when associated with N-142."
FT /evidence="ECO:0000269|PubMed:26919431"
FT MUTAGEN 142
FT /note="V->N: Loss of activity; when associated with N-69."
FT /evidence="ECO:0000269|PubMed:26919431"
FT STRAND 248..257
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 260..267
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 268..284
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 287..291
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:5VQH"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 314..323
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 333..338
FT /evidence="ECO:0007829|PDB:5VQH"
FT TURN 339..341
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 344..348
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 357..360
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 367..371
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 395..404
FT /evidence="ECO:0007829|PDB:5VQH"
FT TURN 405..408
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 412..423
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 432..442
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:5VQH"
FT HELIX 450..456
FT /evidence="ECO:0007829|PDB:5VQH"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:5VQH"
SQ SEQUENCE 629 AA; 69543 MW; 0FEBB159F1FE76C8 CRC64;
MSLNTKLALP IALGLSLVTV TAFVAYYVLK RDEEENDNKT VKITKINTIE IHVPKSIVPA
LIGRNGSNIK DLQKKSGAQI HFKKFTDQDY DVCVVRGRAD TTQLAETLIH DFIKQQPTIM
SESITVPSWS CGRIIGSGGE NVNDISHRSG ARVKVESPKS TDKVAEHLVT FRGTKEQIEV
AKKLVENCVS LERCRREIEQ SKRPPRHSSS PPSPCPSPGD RDADADAQGD VDHTRVKYKR
PETTGPSIEV YVSAVSSPSR FWVQFVGPQV AQLDDLVAHM TEYYSKKENR EAHTLRHVSV
GQVVAAVFRH DGRWYRARVH DIRPNEFDSS QQVADVFYLD YGDSEYVATH ELCELRADLL
RLRFQAMECF LAGVRPASGE EAVSPSGQTW DKWHPQAVER FEELTQVARW KALVSRTCTY
KKTATAEGEK DKEIPGIKLF DVTDEGELDV GAVLVAEGWA VAGPAPSPRP SPPRGHTTPF
GDLSKSKVLS MTGGGGRSSS VPKDHKDDGS NVLTVEGDDS KDKDGITASK SLASGLEKSD
RHPLSISNFD LSYPDPSRNK QLNGSDDFLH GERQNIDNEI TIDTLVPPSP LSNAPILSKT
LQDEFKANMN RIDSHHSNLE NLGKSAFEK
