ID   DDX28_HUMAN             Reviewed;         540 AA.
AC   Q9NUL7;
DT   10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT   18-MAY-2010, sequence version 2.
DT   07-APR-2021, entry version 164.
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; Synonyms=MDDX28;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, FUNCTION, TISSUE
RP   SPECIFICITY, AND VARIANT ALA-4.
RC   TISSUE=Testis;
RX   PubMed=11350955; DOI=10.1074/jbc.m011629200;
RA   Valgardsdottir R., Brede G., Eide L.G., Frengen E., Prydz H.;
RT   "Cloning and characterization of MDDX28, a putative dead-box helicase with
RT   mitochondrial and nuclear localization.";
RL   J. Biol. Chem. 276:32056-32063(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT ALA-4.
RC   TISSUE=Placenta;
RX   PubMed=14702039; DOI=10.1038/ng1285;
RA   Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA   Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA   Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA   Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA   Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA   Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA   Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA   Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA   Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA   Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA   Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA   Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA   Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA   Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA   Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA   Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA   Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA   Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA   Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA   Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA   Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA   Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA   Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA   Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA   Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA   Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA   Isogai T., Sugano S.;
RT   "Complete sequencing and characterization of 21,243 full-length human
RT   cDNAs.";
RL   Nat. Genet. 36:40-45(2004).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=15616553; DOI=10.1038/nature03187;
RA   Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G.,
RA   Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E.,
RA   Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J., Buckingham J.M.,
RA   Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C.,
RA   Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M.,
RA   Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M.,
RA   Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D.,
RA   Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L.,
RA   Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E.,
RA   Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H.,
RA   Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y.,
RA   Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J.,
RA   Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D.,
RA   Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S.,
RA   Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A.,
RA   Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M.,
RA   Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H.,
RA   Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A.,
RA   Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J.,
RA   DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J.,
RA   Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M.,
RA   Myers R.M., Rubin E.M., Pennacchio L.A.;
RT   "The sequence and analysis of duplication-rich human chromosome 16.";
RL   Nature 432:988-994(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT ALA-4.
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).
RN   [5]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA   Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA   Bennett K.L., Superti-Furga G., Colinge J.;
RT   "Initial characterization of the human central proteome.";
RL   BMC Syst. Biol. 5:17-17(2011).
RN   [6]
RP   FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, RNA-BINDING, ASSOCIATION WITH
RP   MITOCHONDRIAL RIBOSOME LARGE SUBUNIT, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=25683708; DOI=10.1016/j.celrep.2015.01.033;
RA   Tu Y.T., Barrientos A.;
RT   "The human mitochondrial DEAD-box protein DDX28 resides in RNA granules and
RT   functions in mitoribosome assembly.";
RL   Cell Rep. 10:854-864(2015).
RN   [7]
RP   FUNCTION, IDENTIFICATION IN A COMPLEX WITH GRSF1; DDX30; FASTKD2 AND
RP   FASTKD5, SUBCELLULAR LOCATION, RNA-BINDING, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=25683715; DOI=10.1016/j.celrep.2015.01.030;
RA   Antonicka H., Shoubridge E.A.;
RT   "Mitochondrial RNA granules are centers for post-transcriptional RNA
RT   processing and ribosome biogenesis.";
RL   Cell Rep. 10:920-932(2015).
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 (PubMed:25683708, PubMed:25683715). May
CC       be involved in RNA processing or transport. Has RNA and Mg(2+)-
CC       dependent ATPase activity (PubMed:11350955).
CC       {ECO:0000269|PubMed:11350955, ECO:0000269|PubMed:25683708,
CC       ECO:0000269|PubMed:25683715}.
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:0000269|PubMed:25683708, ECO:0000269|PubMed:25683715}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11350955,
CC       ECO:0000269|PubMed:25683708}. Mitochondrion
CC       {ECO:0000269|PubMed:11350955}. Mitochondrion matrix, mitochondrion
CC       nucleoid {ECO:0000269|PubMed:25683715}. Mitochondrion matrix
CC       {ECO:0000269|PubMed:25683708}. Note=Transported between these two
CC       compartments. Nuclear localization depends on active RNA polymerase II
CC       transcription. Localizes to mitochondrial RNA granules found in close
CC       proximity to the mitochondrial nucleoids. {ECO:0000269|PubMed:25683708,
CC       ECO:0000269|PubMed:25683715}.
CC   -!- TISSUE SPECIFICITY: Expressed in all tissues tested, including brain,
CC       placenta, lung, liver, skeletal muscle, kidney, pancreas, leukocytes,
CC       colon, small intestine, ovary and prostate.
CC       {ECO:0000269|PubMed:11350955}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. {ECO:0000305}.
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DR   EMBL; AF329821; AAG59833.1; -; Genomic_DNA.
DR   EMBL; AK002144; BAA92106.1; -; mRNA.
DR   EMBL; AC130462; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC024273; AAH24273.1; -; mRNA.
DR   CCDS; CCDS10858.1; -.
DR   RefSeq; NP_060850.2; NM_018380.3.
DR   SMR; Q9NUL7; -.
DR   BioGRID; 120907; 177.
DR   CORUM; Q9NUL7; -.
DR   IntAct; Q9NUL7; 34.
DR   MINT; Q9NUL7; -.
DR   STRING; 9606.ENSP00000332340; -.
DR   iPTMnet; Q9NUL7; -.
DR   PhosphoSitePlus; Q9NUL7; -.
DR   BioMuta; DDX28; -.
DR   DMDM; 296434476; -.
DR   EPD; Q9NUL7; -.
DR   jPOST; Q9NUL7; -.
DR   MassIVE; Q9NUL7; -.
DR   MaxQB; Q9NUL7; -.
DR   PaxDb; Q9NUL7; -.
DR   PeptideAtlas; Q9NUL7; -.
DR   PRIDE; Q9NUL7; -.
DR   ProteomicsDB; 82692; -.
DR   Antibodypedia; 29712; 154 antibodies.
DR   Ensembl; ENST00000332395; ENSP00000332340; ENSG00000182810.
DR   GeneID; 55794; -.
DR   KEGG; hsa:55794; -.
DR   UCSC; uc002evh.3; human.
DR   CTD; 55794; -.
DR   DisGeNET; 55794; -.
DR   GeneCards; DDX28; -.
DR   HGNC; HGNC:17330; DDX28.
DR   HPA; ENSG00000182810; Low tissue specificity.
DR   MIM; 607618; gene.
DR   neXtProt; NX_Q9NUL7; -.
DR   OpenTargets; ENSG00000182810; -.
DR   PharmGKB; PA27214; -.
DR   VEuPathDB; HostDB:ENSG00000182810.6; -.
DR   eggNOG; KOG0330; Eukaryota.
DR   GeneTree; ENSGT00940000161738; -.
DR   HOGENOM; CLU_003041_1_3_1; -.
DR   InParanoid; Q9NUL7; -.
DR   OMA; CIMPHVK; -.
DR   OrthoDB; 1223767at2759; -.
DR   PhylomeDB; Q9NUL7; -.
DR   TreeFam; TF324977; -.
DR   PathwayCommons; Q9NUL7; -.
DR   SIGNOR; Q9NUL7; -.
DR   BioGRID-ORCS; 55794; 192 hits in 999 CRISPR screens.
DR   ChiTaRS; DDX28; human.
DR   GenomeRNAi; 55794; -.
DR   Pharos; Q9NUL7; Tbio.
DR   PRO; PR:Q9NUL7; -.
DR   Proteomes; UP000005640; Chromosome 16.
DR   RNAct; Q9NUL7; protein.
DR   Bgee; ENSG00000182810; Expressed in oocyte and 207 other tissues.
DR   Genevisible; Q9NUL7; HS.
DR   GO; GO:0005829; C:cytosol; IDA:HPA.
DR   GO; GO:0042645; C:mitochondrial nucleoid; IDA:UniProtKB.
DR   GO; GO:0005739; C:mitochondrion; IDA:LIFEdb.
DR   GO; GO:0005730; C:nucleolus; IDA:HPA.
DR   GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR   GO; GO:0035770; C:ribonucleoprotein granule; IDA:UniProtKB.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0019843; F:rRNA binding; IDA:UniProtKB.
DR   GO; GO:1902775; P:mitochondrial large ribosomal subunit assembly; IMP:UniProtKB.
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   1: Evidence at protein 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_0000055033"
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   NP_BIND         172..179
FT                   /note="ATP"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
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   VARIANT         4
FT                   /note="T -> A (in dbSNP:rs237831)"
FT                   /evidence="ECO:0000269|PubMed:11350955,
FT                   ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334"
FT                   /id="VAR_052163"
SQ   SEQUENCE   540 AA;  59581 MW;  1FAA4477853893B5 CRC64;
     MALTRPVRLF SLVTRLLLAP RRGLTVRSPD EPLPVVRIPV ALQRQLEQRQ SRRRNLPRPV
     LVRPGPLLVS ARRPELNQPA RLTLGRWERA PLASQGWKSR RARRDHFSIE RAQQEAPAVR
     KLSSKGSFAD LGLEPRVLHA LQEAAPEVVQ PTTVQSSTIP SLLRGRHVVC AAETGSGKTL
     SYLLPLLQRL LGQPSLDSLP IPAPRGLVLV PSRELAQQVR AVAQPLGRSL GLLVRDLEGG
     HGMRRIRLQL SRQPSADVLV ATPGALWKAL KSRLISLEQL SFLVLDEADT LLDESFLELV
     DYILEKSHIA EGPADLEDPF NPKAQLVLVG ATFPEGVGQL LNKVASPDAV TTITSSKLHC
     IMPHVKQTFL RLKGADKVAE LVHILKHRDR AERTGPSGTV LVFCNSSSTV NWLGYILDDH
     KIQHLRLQGQ MPALMRVGIF QSFQKSSRDI LLCTDIASRG LDSTGVELVV NYDFPPTLQD
     YIHRAGRVGR VGSEVPGTVI SFVTHPWDVS LVQKIELAAR RRRSLPGLAS SVKEPLPQAT
//