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Protein

Probable ATP-dependent RNA helicase DDX28

Gene

Ddx28

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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. May be involved in RNA processing or transport. Has RNA and Mg2+-dependent ATPase activity (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

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

GO - Molecular functioni

GO - Biological processi

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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:1919236. Ddx28.

Subcellular locationi

  • Nucleus By similarity
  • Mitochondrion By similarity
  • Mitochondrion matrixmitochondrion nucleoid By similarity
  • Mitochondrion matrix By similarity

  • 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 (By similarity).By similarity

GO - Cellular componenti

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

Keywords - Cellular componenti

Mitochondrion, Mitochondrion nucleoid, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 540540Probable ATP-dependent RNA helicase DDX28PRO_0000055035Add
BLAST

Proteomic databases

EPDiQ9CWT6.
MaxQBiQ9CWT6.
PaxDbiQ9CWT6.
PRIDEiQ9CWT6.

PTM databases

PhosphoSiteiQ9CWT6.

Expressioni

Gene expression databases

BgeeiQ9CWT6.
CleanExiMM_DDX28.
GenevisibleiQ9CWT6. MM.

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).By similarity

Protein-protein interaction databases

BioGridi215075. 1 interaction.
STRINGi10090.ENSMUSP00000058950.

Structurei

3D structure databases

ProteinModelPortaliQ9CWT6.
SMRiQ9CWT6. Positions 127-507.
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.
InParanoidiQ9CWT6.
OMAiHILCAAE.
OrthoDBiEOG7TMZT1.
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.

Q9CWT6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALAGPSRLL ALAVRLLLEP RRNLVVRGSD QSLPVVRVPR ALQRRQEQRQ
60 70 80 90 100
SGRGSLQRPV LVRPGPLLVS ARRPELNQPA RLTLGRWERA PLASRGWKHR
110 120 130 140 150
RSRQDHFSIE RVQQEAPALR NLSSRGSFVD LGLEPRVLLA LQEAVPEVVQ
160 170 180 190 200
PTSVQSKTIP PLLRGRHLLC AAETGSGKTL SYLLPLFQRL LRGSDLDSRS
210 220 230 240 250
FTAPRGLVLV PSRELAEQVQ AVAQSLGGYL GLQVIELGGG LGMSRLKLQL
260 270 280 290 300
YRRPAADVLV ATPGALWKAL KSQLISLQHL NFIVLDEVDT LLDESFLELV
310 320 330 340 350
DYILEKSPIA ESPAELEDPF NPKAQLVLVG ATFPEGLNQL LSKVTSPDSL
360 370 380 390 400
TTITSSKLHC LMPHVRQTFM RLKGADKVTE LVQILKQQDK ASKTEPSGTV
410 420 430 440 450
LVFCNSASTV NWLGYILDDH KIQHLRLQGQ MPASMRAGIF QSFQKGSQNI
460 470 480 490 500
LVCTDIASRG LDSVHVEVVI NYDFPPTLQD YIHRAGRVGR VGSEVPGSVI
510 520 530 540
SFVTHPWDVS LVQKIELAAR RRRSLPGLAS SVGDPLPQKA
Length:540
Mass (Da):59,515
Last modified:July 27, 2011 - v2
Checksum:iA31891A909354A2E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti13 – 131A → V in BAB26907 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK010396 mRNA. Translation: BAB26907.1.
AK163480 mRNA. Translation: BAE37362.1.
BC120556 mRNA. Translation: AAI20557.1.
BC120582 mRNA. Translation: AAI20583.1.
CCDSiCCDS22626.1.
RefSeqiNP_082314.2. NM_028038.3.
UniGeneiMm.307515.

Genome annotation databases

EnsembliENSMUST00000058579; ENSMUSP00000058950; ENSMUSG00000045538.
GeneIDi71986.
KEGGimmu:71986.
UCSCiuc009nez.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK010396 mRNA. Translation: BAB26907.1.
AK163480 mRNA. Translation: BAE37362.1.
BC120556 mRNA. Translation: AAI20557.1.
BC120582 mRNA. Translation: AAI20583.1.
CCDSiCCDS22626.1.
RefSeqiNP_082314.2. NM_028038.3.
UniGeneiMm.307515.

3D structure databases

ProteinModelPortaliQ9CWT6.
SMRiQ9CWT6. Positions 127-507.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi215075. 1 interaction.
STRINGi10090.ENSMUSP00000058950.

PTM databases

PhosphoSiteiQ9CWT6.

Proteomic databases

EPDiQ9CWT6.
MaxQBiQ9CWT6.
PaxDbiQ9CWT6.
PRIDEiQ9CWT6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058579; ENSMUSP00000058950; ENSMUSG00000045538.
GeneIDi71986.
KEGGimmu:71986.
UCSCiuc009nez.2. mouse.

Organism-specific databases

CTDi55794.
MGIiMGI:1919236. Ddx28.

Phylogenomic databases

eggNOGiKOG0330. Eukaryota.
ENOG410XQU7. LUCA.
GeneTreeiENSGT00730000110914.
HOGENOMiHOG000008689.
HOVERGENiHBG081424.
InParanoidiQ9CWT6.
OMAiHILCAAE.
OrthoDBiEOG7TMZT1.
TreeFamiTF324977.

Miscellaneous databases

NextBioi335138.
PROiQ9CWT6.
SOURCEiSearch...

Gene expression databases

BgeeiQ9CWT6.
CleanExiMM_DDX28.
GenevisibleiQ9CWT6. MM.

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

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Corpora quadrigemina and Embryonic stem cell.
  2. "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].
    Tissue: Brain.

Entry informationi

Entry nameiDDX28_MOUSE
AccessioniPrimary (citable) accession number: Q9CWT6
Secondary accession number(s): Q0VBM0, Q3TQM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: July 27, 2011
Last modified: May 11, 2016
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.