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Protein

Probable ATP-dependent RNA helicase DDX4

Gene

Ddx4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable ATP-dependent RNA helicase required during spermatogenesis to repress transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Involved in the secondary piRNAs metabolic process, the production of piRNAs in fetal male germ cells through a ping-pong amplification cycle.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi305 – 3128ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • cell differentiation Source: UniProtKB-KW
  • DNA methylation involved in gamete generation Source: UniProtKB
  • gene silencing by RNA Source: UniProtKB-KW
  • male meiosis Source: UniProtKB
  • male meiosis I Source: MGI
  • multicellular organism development Source: UniProtKB-KW
  • piRNA metabolic process Source: UniProtKB
  • regulation of protein localization Source: MGI
  • RNA secondary structure unwinding Source: GO_Central
  • spermatogenesis Source: UniProtKB
  • sperm motility Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Helicase, Hydrolase

Keywords - Biological processi

Differentiation, Meiosis, RNA-mediated gene silencing, Spermatogenesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-MMU-5601884. PIWI-interacting RNA (piRNA) biogenesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX4 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 4
Mvh1 Publication
Vasa homolog1 Publication
Gene namesi
Name:Ddx4
Synonyms:Vasa
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:102670. Ddx4.

Subcellular locationi

GO - Cellular componenti

  • chromatoid body Source: MGI
  • cytoplasm Source: MGI
  • cytosol Source: Reactome
  • intracellular ribonucleoprotein complex Source: MGI
  • nucleus Source: MGI
  • perinuclear region of cytoplasm Source: MGI
  • pi-body Source: UniProtKB
  • piP-body Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Mice are viable but show male sterility due to defects in spermatogenesis. Retrotransposons are derepressed due to DNA demethylation. Defects are caused by impaired piRNA expression.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 702702Probable ATP-dependent RNA helicase DDX4PRO_0000054979Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei195 – 1951PhosphoserineBy similarity
Modified residuei199 – 1991PhosphoserineCombined sources
Modified residuei700 – 7001PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ61496.
MaxQBiQ61496.
PaxDbiQ61496.
PeptideAtlasiQ61496.
PRIDEiQ61496.

2D gel databases

REPRODUCTION-2DPAGEIPI00121394.
Q61496.

PTM databases

iPTMnetiQ61496.
PhosphoSiteiQ61496.

Expressioni

Tissue specificityi

Testis-specific.1 Publication

Developmental stagei

Expressed in spermatogenic cells from the spermatocyte stage to the round spermatid stage.1 Publication

Gene expression databases

BgeeiQ61496.
CleanExiMM_DDX4.
ExpressionAtlasiQ61496. baseline and differential.
GenevisibleiQ61496. MM.

Interactioni

Subunit structurei

Found in a mRNP complex, at least composed of TDRD1, TDRD6, TDRD7 and DDX4 (PubMed:17141210). N-terminus interacts with RANBP9 (PubMed:14648869). Interacts with PIWIL2 and MAEL (PubMed:14736746, PubMed:16787967). Interacts with ARNTL/BMAL1 and CLOCK (PubMed:22900038).5 Publications

Protein-protein interaction databases

BioGridi199085. 5 interactions.
DIPiDIP-61113N.
STRINGi10090.ENSMUSP00000096769.

Structurei

3D structure databases

ProteinModelPortaliQ61496.
SMRiQ61496. Positions 219-648.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini292 – 475184Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini503 – 648146Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi261 – 28929Q motifAdd
BLAST
Motifi419 – 4224DEAD box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi58 – 207150Gly-richAdd
BLAST

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0335. Eukaryota.
ENOG410XNTI. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000268804.
HOVERGENiHBG015893.
InParanoidiQ61496.
KOiK13982.
PhylomeDBiQ61496.

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.
IPR000629. RNA-helicase_DEAD-box_CS.
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. 2 hits.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q61496-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGDEDWEAEI LKPHVSSYVP VFEKDKYSSG ANGDTFNRTS ASSDIGESSK
60 70 80 90 100
KENTSTTGGF GRGKGFGNRG FLNNKFEEGD SSGFWKESNN DCEDNQTRSR
110 120 130 140 150
GFSKRGGCQD GNDSEASGPF RRGGRGSFRG CRGGFGLGRP NSESDQDQGT
160 170 180 190 200
QRGGGLFGSR KPAASDSGNG DTYQSRSGSG RGGYKGLNEE VVTGSGKNSW
210 220 230 240 250
KSETEGGESS DSQGPKVTYI PPPPPEDEDS IFAHYQTGIN FDKYDTILVE
260 270 280 290 300
VSGHDAPPAI LTFEEANLCQ TLNNNIAKAG YTKLTPVQKY SIPIVLAGRD
310 320 330 340 350
LMACAQTGSG KTAAFLLPIL AHMMRDGITA SRFKELQEPE CIIVAPTREL
360 370 380 390 400
INQIYLEARK FSFGTCVRAV VIYGGTQFGH SVRQIVQGCN ILCATPGRLM
410 420 430 440 450
DIIGKEKIGL KQVKYLVLDE ADRMLDMGFG PEMKKLISCP GMPSKEQRQT
460 470 480 490 500
LLFSATFPEE IQRLAGDFLK SSYLFVAVGQ VGGACRDVQQ TILQVGQYSK
510 520 530 540 550
REKLVEILRN IGDERTMVFV ETKKKADFIA TFLCQEKIST TSIHGDREQR
560 570 580 590 600
EREQALGDFR CGKCPVLVAT SVAARGLDIE NVQHVINFDL PSTIDEYVHR
610 620 630 640 650
IGRTGRCGNT GRAISFFDTD SDNHLAQPLV KVLSDAQQDV PAWLEEIAFS
660 670 680 690 700
TYVPPSFSSS TRGGAVFASV DTRKNYQGKH TLNTAGISSS QAPNPVDDES

WD
Length:702
Mass (Da):76,470
Last modified:January 23, 2002 - v2
Checksum:i5D1E4CC0BDF39748
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti152 – 1521R → C in BAA03584 (PubMed:7991615).Curated
Sequence conflicti156 – 1605LFGSR → FLVLG in BAA03584 (PubMed:7991615).Curated
Sequence conflicti277 – 2771A → R in BAA03584 (PubMed:7991615).Curated
Sequence conflicti291 – 2911S → T in BAA03584 (PubMed:7991615).Curated
Sequence conflicti368 – 3692RA → IS in BAA03584 (PubMed:7991615).Curated
Sequence conflicti423 – 4231R → S in BAA03584 (PubMed:7991615).Curated
Sequence conflicti430 – 4301G → A in BAA03584 (PubMed:7991615).Curated
Sequence conflicti433 – 4331M → I in BAA03584 (PubMed:7991615).Curated
Sequence conflicti448 – 4481R → H in BAA03584 (PubMed:7991615).Curated
Sequence conflicti472 – 4721S → N in BAA03584 (PubMed:7991615).Curated
Sequence conflicti499 – 50911SKREKLVEILR → QKEKSLLRFYE in BAA03584 (PubMed:7991615).CuratedAdd
BLAST
Sequence conflicti540 – 5401T → S in BAA03584 (PubMed:7991615).Curated
Sequence conflicti680 – 70223HTLNT…DESWD → AHVEYSGDFFFTSSQSS in BAA03584 (PubMed:7991615).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK014844 mRNA. Translation: BAB29578.1.
D14859 mRNA. Translation: BAA03584.1.
CCDSiCCDS26774.1.
RefSeqiNP_034159.1. NM_010029.2.
UniGeneiMm.12818.

Genome annotation databases

EnsembliENSMUST00000075748; ENSMUSP00000075157; ENSMUSG00000021758.
GeneIDi13206.
KEGGimmu:13206.
UCSCiuc007rwm.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK014844 mRNA. Translation: BAB29578.1.
D14859 mRNA. Translation: BAA03584.1.
CCDSiCCDS26774.1.
RefSeqiNP_034159.1. NM_010029.2.
UniGeneiMm.12818.

3D structure databases

ProteinModelPortaliQ61496.
SMRiQ61496. Positions 219-648.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi199085. 5 interactions.
DIPiDIP-61113N.
STRINGi10090.ENSMUSP00000096769.

PTM databases

iPTMnetiQ61496.
PhosphoSiteiQ61496.

2D gel databases

REPRODUCTION-2DPAGEIPI00121394.
Q61496.

Proteomic databases

EPDiQ61496.
MaxQBiQ61496.
PaxDbiQ61496.
PeptideAtlasiQ61496.
PRIDEiQ61496.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000075748; ENSMUSP00000075157; ENSMUSG00000021758.
GeneIDi13206.
KEGGimmu:13206.
UCSCiuc007rwm.2. mouse.

Organism-specific databases

CTDi54514.
MGIiMGI:102670. Ddx4.

Phylogenomic databases

eggNOGiKOG0335. Eukaryota.
ENOG410XNTI. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000268804.
HOVERGENiHBG015893.
InParanoidiQ61496.
KOiK13982.
PhylomeDBiQ61496.

Enzyme and pathway databases

ReactomeiR-MMU-5601884. PIWI-interacting RNA (piRNA) biogenesis.

Miscellaneous databases

ChiTaRSiDdx4. mouse.
PROiQ61496.
SOURCEiSearch...

Gene expression databases

BgeeiQ61496.
CleanExiMM_DDX4.
ExpressionAtlasiQ61496. baseline and differential.
GenevisibleiQ61496. 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.
IPR000629. RNA-helicase_DEAD-box_CS.
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. 2 hits.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. 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. "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: Testis.
  2. "Isolation of a DEAD-family protein gene that encodes a murine homolog of Drosophila vasa and its specific expression in germ cell lineage."
    Fujiwara Y., Komiya T., Kawabata H., Sato M., Fujimoto H., Furusawa M., Noce T.
    Proc. Natl. Acad. Sci. U.S.A. 91:12258-12262(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-702, DEVELOPMENTAL STAGE.
    Strain: BALB/cJ.
    Tissue: Testis.
  3. Cited for: INTERACTION WITH PIWIL2.
  4. "Mouse RanBPM is a partner gene to a germline specific RNA helicase, mouse vasa homolog protein."
    Shibata N., Tsunekawa N., Okamoto-Ito S., Akasu R., Tokumasu A., Noce T.
    Mol. Reprod. Dev. 67:1-7(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RANBP9.
    Tissue: Testis.
  5. "Mouse MAELSTROM: the link between meiotic silencing of unsynapsed chromatin and microRNA pathway?"
    Costa Y., Speed R.M., Gautier P., Semple C.A., Maratou K., Turner J.M.A., Cooke H.J.
    Hum. Mol. Genet. 15:2324-2334(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH MAEL.
  6. "Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice."
    Hosokawa M., Shoji M., Kitamura K., Tanaka T., Noce T., Chuma S., Nakatsuji N.
    Dev. Biol. 301:38-52(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A MRNP COMPLEX.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-199 AND SER-700, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Testis.
  8. Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
  9. "Circadian proteins CLOCK and BMAL1 in the chromatoid body, a RNA processing granule of male germ cells."
    Peruquetti R.L., de Mateo S., Sassone-Corsi P.
    PLoS ONE 7:E42695-E42695(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH CLOCK AND ARNTL/BMAL1.

Entry informationi

Entry nameiDDX4_MOUSE
AccessioniPrimary (citable) accession number: Q61496
Secondary accession number(s): Q9D5X7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2002
Last modified: July 6, 2016
This is version 138 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.