DDX28_MOUSE
ID DDX28_MOUSE Reviewed; 540 AA.
AC Q9CWT6; Q0VBM0; Q3TQM0;
DT 10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Probable ATP-dependent RNA helicase DDX28;
DE EC=3.6.4.13;
DE AltName: Full=Mitochondrial DEAD box protein 28;
GN Name=Ddx28;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Corpora quadrigemina, and Embryonic stem cell;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: Plays an essential role in facilitating the proper assembly
CC of the mitochondrial large ribosomal subunit and its helicase activity
CC is essential for this function. May be involved in RNA processing or
CC transport. Has RNA and Mg(2+)-dependent ATPase activity (By
CC similarity). {ECO:0000250|UniProtKB:Q9NUL7}.
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 -!- SUBUNIT: Monomer. Found in a complex with GRSF1, DHX30, FASTKD2 and
CC FASTKD5. Associates with the 16S mitochondrial rRNA (16S mt-rRNA) and
CC with the mitochondrial ribosome large subunit (39S).
CC {ECO:0000250|UniProtKB:Q9NUL7}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9NUL7}.
CC Mitochondrion {ECO:0000250|UniProtKB:Q9NUL7}. Mitochondrion matrix,
CC mitochondrion nucleoid {ECO:0000250|UniProtKB:Q9NUL7}. Mitochondrion
CC matrix {ECO:0000250|UniProtKB:Q9NUL7}. Note=Transported between these
CC two compartments. Nuclear localization depends on active RNA polymerase
CC II transcription. Localizes to mitochondrial RNA granules found in
CC close proximity to the mitochondrial nucleoids (By similarity).
CC {ECO:0000250|UniProtKB:Q9NUL7}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. {ECO:0000305}.
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DR EMBL; AK010396; BAB26907.1; -; mRNA.
DR EMBL; AK163480; BAE37362.1; -; mRNA.
DR EMBL; BC120556; AAI20557.1; -; mRNA.
DR EMBL; BC120582; AAI20583.1; -; mRNA.
DR CCDS; CCDS22626.1; -.
DR RefSeq; NP_082314.2; NM_028038.3.
DR AlphaFoldDB; Q9CWT6; -.
DR SMR; Q9CWT6; -.
DR BioGRID; 215075; 1.
DR STRING; 10090.ENSMUSP00000058950; -.
DR iPTMnet; Q9CWT6; -.
DR PhosphoSitePlus; Q9CWT6; -.
DR EPD; Q9CWT6; -.
DR MaxQB; Q9CWT6; -.
DR PaxDb; Q9CWT6; -.
DR PeptideAtlas; Q9CWT6; -.
DR PRIDE; Q9CWT6; -.
DR ProteomicsDB; 279325; -.
DR Antibodypedia; 29712; 164 antibodies from 22 providers.
DR DNASU; 71986; -.
DR Ensembl; ENSMUST00000058579; ENSMUSP00000058950; ENSMUSG00000045538.
DR GeneID; 71986; -.
DR KEGG; mmu:71986; -.
DR UCSC; uc009nez.2; mouse.
DR CTD; 55794; -.
DR MGI; MGI:1919236; Ddx28.
DR VEuPathDB; HostDB:ENSMUSG00000045538; -.
DR eggNOG; KOG0330; Eukaryota.
DR GeneTree; ENSGT00940000161738; -.
DR HOGENOM; CLU_003041_1_3_1; -.
DR InParanoid; Q9CWT6; -.
DR OMA; CSKGWKH; -.
DR OrthoDB; 1223767at2759; -.
DR PhylomeDB; Q9CWT6; -.
DR TreeFam; TF324977; -.
DR BioGRID-ORCS; 71986; 22 hits in 78 CRISPR screens.
DR ChiTaRS; Ddx28; mouse.
DR PRO; PR:Q9CWT6; -.
DR Proteomes; UP000000589; Chromosome 8.
DR RNAct; Q9CWT6; protein.
DR Bgee; ENSMUSG00000045538; Expressed in manus and 211 other tissues.
DR Genevisible; Q9CWT6; MM.
DR GO; GO:0005829; C:cytosol; ISO:MGI.
DR GO; GO:0042645; C:mitochondrial nucleoid; ISS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; HDA:MGI.
DR GO; GO:0005730; C:nucleolus; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0035770; C:ribonucleoprotein granule; 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:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0019843; F:rRNA binding; ISS:UniProtKB.
DR GO; GO:1902775; P:mitochondrial large ribosomal subunit assembly; ISS:UniProtKB.
DR Gene3D; 3.40.50.300; -; 2.
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; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Helicase; Hydrolase; Mitochondrion; Mitochondrion nucleoid;
KW Nucleotide-binding; Nucleus; Reference proteome; Ribosome biogenesis;
KW RNA-binding; rRNA-binding.
FT CHAIN 1..540
FT /note="Probable ATP-dependent RNA helicase DDX28"
FT /id="PRO_0000055035"
FT DOMAIN 159..351
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 377..536
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT MOTIF 3..18
FT /note="Mitochondrial targeting signal"
FT /evidence="ECO:0000255"
FT MOTIF 126..156
FT /note="Q motif"
FT MOTIF 180..191
FT /note="Nuclear export signal"
FT /evidence="ECO:0000255"
FT MOTIF 286..289
FT /note="DEAD"
FT MOTIF 520..523
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT BINDING 172..179
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 13
FT /note="A -> V (in Ref. 1; BAB26907)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 540 AA; 59515 MW; A31891A909354A2E CRC64;
MALAGPSRLL ALAVRLLLEP RRNLVVRGSD QSLPVVRVPR ALQRRQEQRQ SGRGSLQRPV
LVRPGPLLVS ARRPELNQPA RLTLGRWERA PLASRGWKHR RSRQDHFSIE RVQQEAPALR
NLSSRGSFVD LGLEPRVLLA LQEAVPEVVQ PTSVQSKTIP PLLRGRHLLC AAETGSGKTL
SYLLPLFQRL LRGSDLDSRS FTAPRGLVLV PSRELAEQVQ AVAQSLGGYL GLQVIELGGG
LGMSRLKLQL YRRPAADVLV ATPGALWKAL KSQLISLQHL NFIVLDEVDT LLDESFLELV
DYILEKSPIA ESPAELEDPF NPKAQLVLVG ATFPEGLNQL LSKVTSPDSL TTITSSKLHC
LMPHVRQTFM RLKGADKVTE LVQILKQQDK ASKTEPSGTV LVFCNSASTV NWLGYILDDH
KIQHLRLQGQ MPASMRAGIF QSFQKGSQNI LVCTDIASRG LDSVHVEVVI NYDFPPTLQD
YIHRAGRVGR VGSEVPGSVI SFVTHPWDVS LVQKIELAAR RRRSLPGLAS SVGDPLPQKA
