DDX28_HUMAN
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 03-AUG-2022, entry version 169.
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 PDB; 7OI6; EM; 5.70 A; x=1-540.
DR PDBsum; 7OI6; -.
DR AlphaFoldDB; Q9NUL7; -.
DR SMR; Q9NUL7; -.
DR BioGRID; 120907; 261.
DR CORUM; Q9NUL7; -.
DR IntAct; Q9NUL7; 41.
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; 164 antibodies from 22 providers.
DR DNASU; 55794; -.
DR Ensembl; ENST00000332395.7; ENSP00000332340.6; ENSG00000182810.7.
DR GeneID; 55794; -.
DR KEGG; hsa:55794; -.
DR MANE-Select; ENST00000332395.7; ENSP00000332340.6; NM_018380.4; NP_060850.2.
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; -.
DR eggNOG; KOG0330; Eukaryota.
DR GeneTree; ENSGT00940000161738; -.
DR HOGENOM; CLU_003041_1_3_1; -.
DR InParanoid; Q9NUL7; -.
DR OMA; CSKGWKH; -.
DR OrthoDB; 1223767at2759; -.
DR PhylomeDB; Q9NUL7; -.
DR TreeFam; TF324977; -.
DR PathwayCommons; Q9NUL7; -.
DR SignaLink; Q9NUL7; -.
DR SIGNOR; Q9NUL7; -.
DR BioGRID-ORCS; 55794; 201 hits in 1083 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 165 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:0016887; F:ATP hydrolysis activity; IEA:RHEA.
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 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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Helicase; Hydrolase; Mitochondrion;
KW Mitochondrion nucleoid; Nucleotide-binding; Nucleus; Reference proteome;
KW Ribosome biogenesis; 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 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 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
