ID C3H4_ORYSJ Reviewed; 1007 AA.
AC Q1EHT7; A0A0P0V0I9; Q0JNY6;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 1.
DT 24-JAN-2024, entry version 99.
DE RecName: Full=Zinc finger CCCH domain-containing protein 4;
DE Short=OsC3H4;
DE EC=3.6.4.-;
GN OrderedLocusNames=Os01g0256800, LOC_Os01g15300; ORFNames=P0711E10.43;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP NOMENCLATURE.
RX PubMed=18221561; DOI=10.1186/1471-2164-9-44;
RA Wang D., Guo Y., Wu C., Yang G., Li Y., Zheng C.;
RT "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.";
RL BMC Genomics 9:44-44(2008).
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF04542.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AP000570; BAE95808.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF04542.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP014957; BAS71395.1; -; Genomic_DNA.
DR EMBL; AK100311; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015623489.1; XM_015768003.1.
DR AlphaFoldDB; Q1EHT7; -.
DR SMR; Q1EHT7; -.
DR STRING; 39947.Q1EHT7; -.
DR PaxDb; 39947-Q1EHT7; -.
DR EnsemblPlants; Os01t0256800-01; Os01t0256800-01; Os01g0256800.
DR GeneID; 9270656; -.
DR Gramene; Os01t0256800-01; Os01t0256800-01; Os01g0256800.
DR KEGG; osa:9270656; -.
DR eggNOG; KOG0920; Eukaryota.
DR HOGENOM; CLU_007384_0_0_1; -.
DR InParanoid; Q1EHT7; -.
DR OMA; INPPMYL; -.
DR OrthoDB; 1213822at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q1EHT7; baseline and differential.
DR Genevisible; Q1EHT7; OS.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004386; F:helicase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IEA:EnsemblPlants.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0000462; P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR CDD; cd17917; DEXHc_RHA-like; 1.
DR CDD; cd18791; SF2_C_RHA; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR Gene3D; 4.10.1000.10; Zinc finger, CCCH-type; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR041367; Znf-CCCH_4.
DR InterPro; IPR000571; Znf_CCCH.
DR InterPro; IPR036855; Znf_CCCH_sf.
DR PANTHER; PTHR18934; ATP-DEPENDENT RNA HELICASE; 1.
DR PANTHER; PTHR18934:SF221; DEXH-BOX ATP-DEPENDENT RNA HELICASE DEXH8; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF18044; zf-CCCH_4; 1.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00356; ZnF_C3H1; 2.
DR SUPFAM; SSF90229; CCCH zinc finger; 2.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50103; ZF_C3H1; 2.
PE 2: Evidence at transcript level;
KW ATP-binding; DNA-binding; Helicase; Hydrolase; Metal-binding;
KW Nucleotide-binding; Reference proteome; Repeat; Zinc; Zinc-finger.
FT CHAIN 1..1007
FT /note="Zinc finger CCCH domain-containing protein 4"
FT /id="PRO_0000346803"
FT DOMAIN 28..192
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 250..420
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 723..750
FT /note="C3H1-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 751..778
FT /note="C3H1-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT MOTIF 139..142
FT /note="DEAH box"
FT BINDING 41..48
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 727
FT /note="E -> V (in Ref. 5; AK100311)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1007 AA; 113227 MW; 941D3EE50D54B0EC CRC64;
MAEAEEKRVG VGEARAPLAV EALRGKIVEK VKGNRVTLIV GDTGCGKSSM VPQFLLEENM
EPILCTQPRR FAVVAIAQMI AESRNCQVGE EVGYHIGHSN VSNLNSKRSR IVFKTAGVVL
EQMRDKGIAA LNYKVIILDE IHERSVESDL VLACVKQFMM KKNDLRLILM SATADITRYK
DYFRDLGRGE RVEVIAIPSS PRSSIFQRKV LYLEQIVDIL KMDSESLSTK YCSGPNTAAD
AGLKPDVYEL IHRLLLHIHQ NEPDIGKSIL VFLPTYYALE QQWIRLLSAS SMFKVHILHR
SIDTDEALQT MKVSKSCRKV ILATNIAESS VTIPGVAYVI DSCRSLQVYW DPIRKTDSAE
LVWVSKSQAE QRKGRTGRTC DGQIYRLVTG PFYNSLTDHE YPAILRLSLR EQVLMICCAE
SRAMNDPHVL LQKVLDPPDS DVVEDALESL VQIRALDKPT SPRGRHEPTF YGCLLNSLPL
SFDASVLALK FGDTGSICEG ILISIMLDIQ PLPIVQPFGH QQLCKMYRNN YFEEEGIDLQ
TGKKEAALVG NLCAFQFWQR MFKDKYRLDC LINVVNTHEP KASNGFVAKP EDEWCAFHNL
VPTALNYISE IYDDIMGTLH RFRPSFLVKI NPPMYLQPSE FHHMCLRHEV LELENVNSLP
LEAENSHLDS HRRCAATPYV SPADFGTTTV VKTLKTLIKE MKTQSAADRV TYRELVHGYV
QPALENEMCV FFLNGSCNRG DTCHFSHSSR APRPICKFFL TLQGCRNGNS CSFSHDSGSL
VSSSITSGIC SQENRATSVC CKRLLPAAGD GHILVMNDKS LQFACKLCNY YDPTKIIACT
PGPHSFESDS VTKGLKILQN LADPSYLFIG GEHKLSVPWT KLSRVFWFAD IDSNESISEQ
VVLQKFFQHI AIKTLSEKMS DLQVIVIMNN AKFVQLQVER LARECFLFLG ESFMFDEATL
GWFSDTPNYP RGMQVSAPVA YIFSMHPPTG IQFGDYASEL RKVLYSN
//
