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Protein

Probable ATP-dependent RNA helicase DDX28

Gene

DDX28

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function (PubMed:25683708, PubMed:25683715). May be involved in RNA processing or transport. Has RNA and Mg2+-dependent ATPase activity (PubMed:11350955).3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi172 – 1798ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: GO_Central
  • poly(A) RNA binding Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

  • mitochondrial large ribosomal subunit assembly Source: UniProtKB
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding, rRNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX28 (EC:3.6.4.13)
Alternative name(s):
Mitochondrial DEAD box protein 28
Gene namesi
Name:DDX28
Synonyms:MDDX28
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:17330. DDX28.

Subcellular locationi

  • Nucleus 2 Publications
  • Mitochondrion 1 Publication
  • Mitochondrion matrixmitochondrion nucleoid 1 Publication
  • Mitochondrion matrix 1 Publication

  • Note: Transported between these two compartments. Nuclear localization depends on active RNA polymerase II transcription. Localizes to mitochondrial RNA granules found in close proximity to the mitochondrial nucleoids.2 Publications

GO - Cellular componenti

  • cytoplasm Source: HPA
  • mitochondrial nucleoid Source: UniProtKB
  • mitochondrion Source: LIFEdb
  • nucleolus Source: HPA
  • nucleus Source: HPA
  • ribonucleoprotein granule Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Mitochondrion nucleoid, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA27214.

Polymorphism and mutation databases

BioMutaiDDX28.
DMDMi296434476.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 540540Probable ATP-dependent RNA helicase DDX28PRO_0000055033Add
BLAST

Proteomic databases

EPDiQ9NUL7.
MaxQBiQ9NUL7.
PaxDbiQ9NUL7.
PRIDEiQ9NUL7.

PTM databases

iPTMnetiQ9NUL7.
PhosphoSiteiQ9NUL7.

Expressioni

Tissue specificityi

Expressed in all tissues tested, including brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, leukocytes, colon, small intestine, ovary and prostate.1 Publication

Gene expression databases

BgeeiQ9NUL7.
CleanExiHS_DDX28.
GenevisibleiQ9NUL7. HS.

Organism-specific databases

HPAiHPA041911.
HPA053585.

Interactioni

Subunit structurei

Monomer. Found in a complex with GRSF1, DHX30, FASTKD2 and FASTKD5. Associates with the 16S mitochondrial rRNA (16S mt-rRNA) and with the mitochondrial ribosome large subunit (39S).2 Publications

Protein-protein interaction databases

BioGridi120907. 45 interactions.
IntActiQ9NUL7. 12 interactions.
MINTiMINT-4992126.
STRINGi9606.ENSP00000332340.

Structurei

3D structure databases

ProteinModelPortaliQ9NUL7.
SMRiQ9NUL7. Positions 113-505.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini159 – 351193Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini377 – 536160Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi3 – 1816Mitochondrial targeting signalSequence analysisAdd
BLAST
Motifi126 – 15631Q motifAdd
BLAST
Motifi180 – 19112Nuclear export signalSequence analysisAdd
BLAST
Motifi286 – 2894DEAD
Motifi520 – 5234Nuclear localization signalSequence analysis

Sequence similaritiesi

Belongs to the DEAD box helicase family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0330. Eukaryota.
ENOG410XQU7. LUCA.
GeneTreeiENSGT00730000110914.
HOGENOMiHOG000008689.
HOVERGENiHBG081424.
InParanoidiQ9NUL7.
OMAiQRLISCK.
OrthoDBiEOG7TMZT1.
PhylomeDBiQ9NUL7.
TreeFamiTF324977.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9NUL7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALTRPVRLF SLVTRLLLAP RRGLTVRSPD EPLPVVRIPV ALQRQLEQRQ
60 70 80 90 100
SRRRNLPRPV LVRPGPLLVS ARRPELNQPA RLTLGRWERA PLASQGWKSR
110 120 130 140 150
RARRDHFSIE RAQQEAPAVR KLSSKGSFAD LGLEPRVLHA LQEAAPEVVQ
160 170 180 190 200
PTTVQSSTIP SLLRGRHVVC AAETGSGKTL SYLLPLLQRL LGQPSLDSLP
210 220 230 240 250
IPAPRGLVLV PSRELAQQVR AVAQPLGRSL GLLVRDLEGG HGMRRIRLQL
260 270 280 290 300
SRQPSADVLV ATPGALWKAL KSRLISLEQL SFLVLDEADT LLDESFLELV
310 320 330 340 350
DYILEKSHIA EGPADLEDPF NPKAQLVLVG ATFPEGVGQL LNKVASPDAV
360 370 380 390 400
TTITSSKLHC IMPHVKQTFL RLKGADKVAE LVHILKHRDR AERTGPSGTV
410 420 430 440 450
LVFCNSSSTV NWLGYILDDH KIQHLRLQGQ MPALMRVGIF QSFQKSSRDI
460 470 480 490 500
LLCTDIASRG LDSTGVELVV NYDFPPTLQD YIHRAGRVGR VGSEVPGTVI
510 520 530 540
SFVTHPWDVS LVQKIELAAR RRRSLPGLAS SVKEPLPQAT
Length:540
Mass (Da):59,581
Last modified:May 18, 2010 - v2
Checksum:i1FAA4477853893B5
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti4 – 41T → A.3 Publications
Corresponds to variant rs237831 [ dbSNP | Ensembl ].
VAR_052163

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF329821 Genomic DNA. Translation: AAG59833.1.
AK002144 mRNA. Translation: BAA92106.1.
AC130462 Genomic DNA. No translation available.
BC024273 mRNA. Translation: AAH24273.1.
CCDSiCCDS10858.1.
RefSeqiNP_060850.2. NM_018380.3.
UniGeneiHs.458313.

Genome annotation databases

EnsembliENST00000332395; ENSP00000332340; ENSG00000182810.
GeneIDi55794.
KEGGihsa:55794.
UCSCiuc002evh.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF329821 Genomic DNA. Translation: AAG59833.1.
AK002144 mRNA. Translation: BAA92106.1.
AC130462 Genomic DNA. No translation available.
BC024273 mRNA. Translation: AAH24273.1.
CCDSiCCDS10858.1.
RefSeqiNP_060850.2. NM_018380.3.
UniGeneiHs.458313.

3D structure databases

ProteinModelPortaliQ9NUL7.
SMRiQ9NUL7. Positions 113-505.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120907. 45 interactions.
IntActiQ9NUL7. 12 interactions.
MINTiMINT-4992126.
STRINGi9606.ENSP00000332340.

PTM databases

iPTMnetiQ9NUL7.
PhosphoSiteiQ9NUL7.

Polymorphism and mutation databases

BioMutaiDDX28.
DMDMi296434476.

Proteomic databases

EPDiQ9NUL7.
MaxQBiQ9NUL7.
PaxDbiQ9NUL7.
PRIDEiQ9NUL7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000332395; ENSP00000332340; ENSG00000182810.
GeneIDi55794.
KEGGihsa:55794.
UCSCiuc002evh.3. human.

Organism-specific databases

CTDi55794.
GeneCardsiDDX28.
HGNCiHGNC:17330. DDX28.
HPAiHPA041911.
HPA053585.
MIMi607618. gene.
neXtProtiNX_Q9NUL7.
PharmGKBiPA27214.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0330. Eukaryota.
ENOG410XQU7. LUCA.
GeneTreeiENSGT00730000110914.
HOGENOMiHOG000008689.
HOVERGENiHBG081424.
InParanoidiQ9NUL7.
OMAiQRLISCK.
OrthoDBiEOG7TMZT1.
PhylomeDBiQ9NUL7.
TreeFamiTF324977.

Miscellaneous databases

GenomeRNAii55794.
NextBioi60915.
PROiQ9NUL7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NUL7.
CleanExiHS_DDX28.
GenevisibleiQ9NUL7. HS.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of MDDX28, a putative dead-box helicase with mitochondrial and nuclear localization."
    Valgardsdottir R., Brede G., Eide L.G., Frengen E., Prydz H.
    J. Biol. Chem. 276:32056-32063(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, FUNCTION, TISSUE SPECIFICITY, VARIANT ALA-4.
    Tissue: Testis.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ALA-4.
    Tissue: Placenta.
  3. "The sequence and analysis of duplication-rich human chromosome 16."
    Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J.
    , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
    Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ALA-4.
    Tissue: Brain.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  6. "The human mitochondrial DEAD-box protein DDX28 resides in RNA granules and functions in mitoribosome assembly."
    Tu Y.T., Barrientos A.
    Cell Rep. 0:0-0(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, RNA-BINDING, ASSOCIATION WITH MITOCHONDRIAL RIBOSOME LARGE SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis."
    Antonicka H., Shoubridge E.A.
    Cell Rep. 0:0-0(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN A COMPLEX WITH GRSF1; DDX30; FASTKD2 AND FASTKD5, SUBCELLULAR LOCATION, RNA-BINDING, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiDDX28_HUMAN
AccessioniPrimary (citable) accession number: Q9NUL7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: May 18, 2010
Last modified: April 13, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.