YTDC2_PONAB
ID YTDC2_PONAB Reviewed; 1430 AA.
AC Q5R746; A0A2J8XEL0;
DT 05-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 20-JUN-2018, sequence version 2.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=3'-5' RNA helicase YTHDC2 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:B2RR83};
DE AltName: Full=YTH domain-containing protein C2 {ECO:0000250|UniProtKB:B2RR83};
GN Name=YTHDC2 {ECO:0000250|UniProtKB:B2RR83};
OS Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Pongo.
OX NCBI_TaxID=9601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Pollen A., Hastie A., Hormozdiari F., Dougherty M., Liu R., Chaisson M.,
RA Hoppe E., Hill C., Pang A., Hillier L., Baker C., Armstrong J.,
RA Shendure J., Paten B., Wilson R., Chao H., Schneider V., Ventura M.,
RA Kronenberg Z., Murali S., Gordon D., Cantsilieris S., Munson K., Nelson B.,
RA Raja A., Underwood J., Diekhans M., Fiddes I., Haussler D., Eichler E.;
RT "High-resolution comparative analysis of great ape genomes.";
RL Submitted (DEC-2017) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 726-1430.
RC TISSUE=Brain cortex;
RG The German cDNA consortium;
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: 3'-5' RNA helicase that plays a key role in the male and
CC female germline by promoting transition from mitotic to meiotic
CC divisions in stem cells. Specifically recognizes and binds N6-
CC methyladenosine (m6A)-containing RNAs, a modification present at
CC internal sites of mRNAs and some non-coding RNAs that plays a role in
CC the efficiency of RNA processing and stability. Essential for ensuring
CC a successful progression of the meiotic program in the germline by
CC regulating the level of m6A-containing RNAs. Acts by binding and
CC promoting degradation of m6A-containing mRNAs: the 3'-5' RNA helicase
CC activity is required for this process and RNA degradation may be
CC mediated by XRN1 exoribonuclease. Required for both spermatogenesis and
CC oogenesis. {ECO:0000250|UniProtKB:B2RR83}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:B2RR83};
CC -!- SUBUNIT: Interacts with MEIOC; binds transcripts that regulate the
CC mitotic cell cycle inhibiting progression into metaphase, thereby
CC allowing meiotic prophase to proceed normally (By similarity).
CC Interacts (via ANK repeats) with XRN1. Interacts with ZCCHC4.
CC Associates with the small ribosomal subunit (By similarity).
CC {ECO:0000250|UniProtKB:B2RR83, ECO:0000250|UniProtKB:Q9H6S0}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:B2RR83}.
CC Cytoplasm, perinuclear region {ECO:0000250|UniProtKB:Q9H6S0}.
CC -!- DOMAIN: The YTH domain mediates RNA-binding. It recognizes and binds
CC N6-methyladenosine (m6A)-containing RNAs.
CC {ECO:0000250|UniProtKB:Q9H6S0}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAH92414.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; NDHI03003367; PNJ80467.1; -; Genomic_DNA.
DR EMBL; CR860272; CAH92414.1; ALT_INIT; mRNA.
DR RefSeq; NP_001126423.1; NM_001132951.1.
DR AlphaFoldDB; Q5R746; -.
DR SMR; Q5R746; -.
DR STRING; 9601.ENSPPYP00000017549; -.
DR Ensembl; ENSPPYT00000018258; ENSPPYP00000017549; ENSPPYG00000015691.
DR GeneID; 100173406; -.
DR KEGG; pon:100173406; -.
DR CTD; 64848; -.
DR eggNOG; KOG0920; Eukaryota.
DR eggNOG; KOG0922; Eukaryota.
DR eggNOG; KOG1902; Eukaryota.
DR GeneTree; ENSGT00940000155826; -.
DR InParanoid; Q5R746; -.
DR OrthoDB; 278674at2759; -.
DR Proteomes; UP000001595; Chromosome 5.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0035770; C:ribonucleoprotein granule; ISS:UniProtKB.
DR GO; GO:0034458; F:3'-5' RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:1990247; F:N6-methyladenosine-containing RNA binding; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0051729; P:germline cell cycle switching, mitotic to meiotic cell cycle; ISS:UniProtKB.
DR GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0048599; P:oocyte development; ISS:UniProtKB.
DR GO; GO:0007286; P:spermatid development; ISS:UniProtKB.
DR CDD; cd06007; R3H_DEXH_helicase; 1.
DR Gene3D; 1.25.40.20; -; 1.
DR Gene3D; 3.30.1370.50; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR002110; Ankyrin_rpt.
DR InterPro; IPR036770; Ankyrin_rpt-contain_sf.
DR InterPro; IPR011709; DEAD-box_helicase_OB_fold.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR007502; Helicase-assoc_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR034083; R3H_DEXH_helicase.
DR InterPro; IPR001374; R3H_dom.
DR InterPro; IPR036867; R3H_dom_sf.
DR InterPro; IPR007275; YTH_domain.
DR InterPro; IPR031083; YTHDC2-like.
DR PANTHER; PTHR18934:SF100; PTHR18934:SF100; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF07717; OB_NTP_bind; 1.
DR Pfam; PF01424; R3H; 1.
DR Pfam; PF04146; YTH; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00847; HA2; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00393; R3H; 1.
DR SUPFAM; SSF48403; SSF48403; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF82708; SSF82708; 1.
DR PROSITE; PS50297; ANK_REP_REGION; 1.
DR PROSITE; PS50088; ANK_REPEAT; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51061; R3H; 1.
DR PROSITE; PS50882; YTH; 1.
PE 2: Evidence at transcript level;
KW ANK repeat; ATP-binding; Cytoplasm; Differentiation; Helicase; Hydrolase;
KW Meiosis; Nucleotide-binding; Oogenesis; Phosphoprotein; Reference proteome;
KW Repeat; RNA-binding; Spermatogenesis.
FT CHAIN 1..1430
FT /note="3'-5' RNA helicase YTHDC2"
FT /id="PRO_0000249341"
FT DOMAIN 38..106
FT /note="R3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00382"
FT DOMAIN 203..369
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT REPEAT 506..538
FT /note="ANK 1"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT REPEAT 539..571
FT /note="ANK 2"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT DOMAIN 612..784
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 1288..1418
FT /note="YTH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00225"
FT REGION 1..37
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1164..1288
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 316..319
FT /note="DEAH box"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT COMPBIAS 1164..1178
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1188..1202
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1232..1252
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 216..223
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1294..1296
FT /ligand="RNA"
FT /ligand_id="ChEBI:CHEBI:33697"
FT /ligand_part="N(6)-methyladenosine 5'-phosphate residue"
FT /ligand_part_id="ChEBI:CHEBI:74449"
FT /evidence="ECO:0000250|UniProtKB:Q9Y5A9"
FT BINDING 1310
FT /ligand="RNA"
FT /ligand_id="ChEBI:CHEBI:33697"
FT /ligand_part="N(6)-methyladenosine 5'-phosphate residue"
FT /ligand_part_id="ChEBI:CHEBI:74449"
FT /evidence="ECO:0000250|UniProtKB:Q96MU7"
FT BINDING 1360
FT /ligand="RNA"
FT /ligand_id="ChEBI:CHEBI:33697"
FT /ligand_part="N(6)-methyladenosine 5'-phosphate residue"
FT /ligand_part_id="ChEBI:CHEBI:74449"
FT /evidence="ECO:0000250|UniProtKB:Q96MU7"
FT MOD_RES 1089
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT MOD_RES 1090
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B2RR83"
FT MOD_RES 1092
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT MOD_RES 1202
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
FT MOD_RES 1263
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B2RR83"
FT MOD_RES 1267
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B2RR83"
FT MOD_RES 1281
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9H6S0"
SQ SEQUENCE 1430 AA; 160207 MW; BFEB6AAC79B7D5A8 CRC64;
MSRPSSVSPR QPAPGGGGGG GPSPCGPGGG GRAKGLKDIR IDEEVKIAVN IALERFRYGD
QREMEFPSSL TSTERAFIHR LSQSLGLVSK SKGKGANRYL TVKKKDGSET AHAMMTCNLT
HNTKHAVRSL IQRFPVTNKE RTELLPKTER GNVFAVEAEN REMSKTSGRL NNGIPQIPVK
RGESEFDSFR QSLPVFEKQE EIVKIIKENK VVLIVGETGS GKTTQIPQFL LDDCFKNGIP
CRIFCTQPRR LAAIAVAERV AAERRERIGQ TIGYQIRLES RVSPKTLLTF CTNGVLLRTL
MAGDSTLSTV THVIVDEVHE RDRFSDFLLT KLRDLLQKHP TLKLILSSAA LDVNLFIRYF
GSCPVIYIQG RPFEVKEMFL EDILRTTGYT NKEMLKYKKE KQQEEKQQTT LTEWYSAQEN
SFKPGSQRQR TVLNVTDEYD LLDDGGDAVF SQLTEKDVNC LEPWLVKEMD ACLSDIWLHK
DIDAFAQVFH LILTENVSVD YRHSETSATA LMVAAGRGFA SQVEQLISMG ANVHSKASNG
WMALDWAKHF GQTEIVDLLE SYSASLEFGN LDESSLVQTN GSDLSAEDRE LLKAYHHSFD
DEKVDLDLIM HLLYNICHSC DAGAVLIFLP GYDEIVGLRD RILFDDKRFA DNTHRYQVFM
LHSNMQTSDQ KKVLKNPPAG VRKIILSTNI AETSITVNDV VFVIDSGKVK EKSFDALNFV
TMLKMVWISK ASAIQRKGRA GRCRPGICFR LFSRLRFQNM LEFQTPELLR MPLQELCLHT
KLLAPVNCPV ADFLMKAPEP PPALIVRNAV QMLKTIDAMD TWEDLTELGY HLADLPVEPH
LGKMVLCAVV LKCLDPILTI ACTLAYRDPF VLPTQASQKR AAMLCRKRFT AGAFSDHMAL
LRAFQAWQKA RSDGWERAFC EKNFLSQATM EIIIGMRTQL LGQLRASGFV RARGGGDIRD
VNTNSENWAV VKAALVAGMY PNLVHVDREN LVLTGPKEKK VRFHPASVLS QPQYKKIPPA
NGQAAAIKAL PTDWLIYDEM TRAHRIANIR CCSAVTPVTI LVFCGPARLA SNALQEPSSF
RVDGIPNDSS DSEMEDKTTA NLAALKLDEW LHFKLEPEAA SLLLQLRQKW HSLFLRRMRA
PSKPWSQVDE ATIRAIIAVL STEEQSAGLQ QPSGIGQRPR PMSSEELPLA SSWRSNNSRK
SSADTEFSDE CTTAERVLMK SPSPALHPPQ KYKDRGILHP KRGTEDRSDQ SSVKSTDSSS
YPSPCASPSP PSSGKGSKSP SPRPNMPVRY FIMKSSNLRN LEISQQKGIW STTPSNERKL
NRAFWESSMV YLVFSVQGSG HFQGFSRMSS EIGREKSQDW GSAGLGGVFK VEWIRKESLP
FQFAHHLLNP WNDNKKVQIS RDGQELEPQV GEQLLQLWER LPLGEKNTTD
