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Protein

ATP-dependent RNA helicase DDX42

Gene

Ddx42

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi297 – 3048ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DDX42 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 42
Gene namesi
Name:Ddx42
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1919297. Ddx42.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 929929ATP-dependent RNA helicase DDX42PRO_0000280059Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei5 – 51N6-acetyllysineBy similarity
Modified residuei96 – 961PhosphoserineBy similarity
Modified residuei104 – 1041PhosphoserineCombined sources
Modified residuei109 – 1091PhosphoserineCombined sources
Modified residuei111 – 1111PhosphoserineCombined sources
Modified residuei185 – 1851PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ810A7.
MaxQBiQ810A7.
PaxDbiQ810A7.
PRIDEiQ810A7.

PTM databases

iPTMnetiQ810A7.
PhosphoSiteiQ810A7.

Expressioni

Gene expression databases

BgeeiQ810A7.
CleanExiMM_DDX42.
GenevisibleiQ810A7. MM.

Interactioni

Subunit structurei

Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42/SF3B125. Interacts (via the C-terminus) with TP53BP2; the interaction is not inhibitied by TP53BP2 ubiquitination and is independent of p53/TP53 (By similarity).By similarity

Protein-protein interaction databases

BioGridi215115. 1 interaction.
IntActiQ810A7. 2 interactions.
MINTiMINT-4113292.
STRINGi10090.ENSMUSP00000021046.

Structurei

3D structure databases

ProteinModelPortaliQ810A7.
SMRiQ810A7. Positions 211-632.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini284 – 459176Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini487 – 632146Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni739 – 82890Necessary for interaction with TP53BP2By similarityAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili116 – 15742Sequence analysisAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi253 – 28129Q motifAdd
BLAST
Motifi407 – 4104DEAD box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi43 – 464Poly-Ser
Compositional biasi175 – 1784Poly-Glu
Compositional biasi654 – 6596Poly-Gly
Compositional biasi675 – 6784Poly-Asn
Compositional biasi784 – 87895Gly-richAdd
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0334. Eukaryota.
ENOG410XSQV. LUCA.
GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268793.
HOVERGENiHBG081425.
InParanoidiQ810A7.
KOiK12835.
OMAiGNNNNVM.
OrthoDBiEOG7TMZR2.
PhylomeDBiQ810A7.
TreeFamiTF300351.

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. 1 hit.
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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q810A7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MNWNKGGPGT KRGFGFGGFA ISAGKKEEAK LPQQSHSAFG AASSSSGFGK
60 70 80 90 100
SAPPQLPSFY KIGSKRANFD EENAYFEDEE EDSSNVDLPY IPAENSPTRQ
110 120 130 140 150
QFHSKPADSD SDDDPLEAFM AEVEDQAARD MKRLEEKDKE RKNVKGIRDD
160 170 180 190 200
IEEEDDQEAY FRYMAENPTA GVVQEEEEDN LEYDSDGNPI APSKKIIDPL
210 220 230 240 250
PPIDHSEIDY PPFEKNFYNE HEEITNLTPQ QLIDLRHKLN LRVSGAAPPR
260 270 280 290 300
PGSSFAHFGF DEQLMHQIRK SEYTQPTPIQ CQGVPVALSG RDMIGIAKTG
310 320 330 340 350
SGKTAAFIWP MLIHIMDQKE LEPGDGPIAV IVCPTRELCQ QIHAECKRFG
360 370 380 390 400
KAYNLRSVAV YGGGSMWEQA KALQEGAEIV VCTPGRLIDH VKKKATNLQR
410 420 430 440 450
VSYLVFDEAD RMFDMGFEYQ VRSIASHVRP DRQTLLFSAT FRKKIEKLAR
460 470 480 490 500
DILIDPIRVV QGDIGEANED VTQIVEILHS GPSKWNWLTR RLVEFTSSGS
510 520 530 540 550
VLLFVTKKAN AEELASNLKQ EGHNLGLLHG DMDQSERNKV ISDFKKKDIP
560 570 580 590 600
VLVATDVAAR GLDIPSIKTV INYDVARDID THTHRIGRTG RAGEKGVAYT
610 620 630 640 650
LLTPKDSNFA GDLVRNLEGA NQHVSKELLD LAMQNAWFRK SRFKGGKGKK
660 670 680 690 700
LNIGGGGLGY RERPGLGSEN SDRGNNNNVM SNYEAYKPST GAMGDRLTAM
710 720 730 740 750
KAAFQSQYKS HFVAASLSNQ KAGTSSAGAS GWTSAGSLNS VPTNSAQQGH
760 770 780 790 800
NSPDNPMTSS TKNIPGFNNS GNISSAPVTY PSIGAQGVNN TASGNNSREG
810 820 830 840 850
IGGGNGKRER YTENRGGSRH SHGDGGNRHG DGGRHGDGYR YPESGSRHTD
860 870 880 890 900
GHRHGETRHG GSAGRHGESR GANDGRNGES RKEGFNRENK MDPKVDSSRM
910 920
DKVDSKTDKT PDGFAVPEPP KRKKSRWDS
Length:929
Mass (Da):101,965
Last modified:October 17, 2006 - v3
Checksum:i0E8F3D30D07BDFCF
GO
Isoform 2 (identifier: Q810A7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-119: Missing.

Show »
Length:810
Mass (Da):89,142
Checksum:iB16198868EA907D1
GO

Sequence cautioni

The sequence AAH43036.4 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti503 – 5031L → M in BAB25270 (PubMed:16141072).Curated
Sequence conflicti537 – 5371R → G in BAE42635 (PubMed:16141072).Curated
Sequence conflicti859 – 8591H → Y in BAC33675 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 119119Missing in isoform 2. 1 PublicationVSP_023519Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK007805 mRNA. Translation: BAB25270.3.
AK049311 mRNA. Translation: BAC33675.1.
AK169816 mRNA. Translation: BAE41388.1.
AK171730 mRNA. Translation: BAE42635.1.
AL604045 Genomic DNA. Translation: CAM23778.1.
BC043036 mRNA. Translation: AAH43036.4. Different initiation.
CCDSiCCDS48956.1. [Q810A7-1]
RefSeqiNP_082350.3. NM_028074.4. [Q810A7-1]
XP_006534344.1. XM_006534281.2. [Q810A7-1]
UniGeneiMm.41367.

Genome annotation databases

EnsembliENSMUST00000021046; ENSMUSP00000021046; ENSMUSG00000020705. [Q810A7-1]
GeneIDi72047.
KEGGimmu:72047.
UCSCiuc007lyk.2. mouse. [Q810A7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK007805 mRNA. Translation: BAB25270.3.
AK049311 mRNA. Translation: BAC33675.1.
AK169816 mRNA. Translation: BAE41388.1.
AK171730 mRNA. Translation: BAE42635.1.
AL604045 Genomic DNA. Translation: CAM23778.1.
BC043036 mRNA. Translation: AAH43036.4. Different initiation.
CCDSiCCDS48956.1. [Q810A7-1]
RefSeqiNP_082350.3. NM_028074.4. [Q810A7-1]
XP_006534344.1. XM_006534281.2. [Q810A7-1]
UniGeneiMm.41367.

3D structure databases

ProteinModelPortaliQ810A7.
SMRiQ810A7. Positions 211-632.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi215115. 1 interaction.
IntActiQ810A7. 2 interactions.
MINTiMINT-4113292.
STRINGi10090.ENSMUSP00000021046.

PTM databases

iPTMnetiQ810A7.
PhosphoSiteiQ810A7.

Proteomic databases

EPDiQ810A7.
MaxQBiQ810A7.
PaxDbiQ810A7.
PRIDEiQ810A7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000021046; ENSMUSP00000021046; ENSMUSG00000020705. [Q810A7-1]
GeneIDi72047.
KEGGimmu:72047.
UCSCiuc007lyk.2. mouse. [Q810A7-1]

Organism-specific databases

CTDi11325.
MGIiMGI:1919297. Ddx42.

Phylogenomic databases

eggNOGiKOG0334. Eukaryota.
ENOG410XSQV. LUCA.
GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268793.
HOVERGENiHBG081425.
InParanoidiQ810A7.
KOiK12835.
OMAiGNNNNVM.
OrthoDBiEOG7TMZR2.
PhylomeDBiQ810A7.
TreeFamiTF300351.

Miscellaneous databases

ChiTaRSiDdx42. mouse.
NextBioi335308.
PROiQ810A7.
SOURCEiSearch...

Gene expression databases

BgeeiQ810A7.
CleanExiMM_DDX42.
GenevisibleiQ810A7. 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. 1 hit.
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] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J and NOD.
    Tissue: Embryonic stem cell, Pancreas, Spleen and Thymus.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "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] (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Brain.
  4. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 616-626, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic brain.
  6. "A differential phosphoproteomic analysis of retinoic acid-treated P19 cells."
    Smith J.C., Duchesne M.A., Tozzi P., Ethier M., Figeys D.
    J. Proteome Res. 6:3174-3186(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Teratocarcinoma.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-109, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104 AND SER-109, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry."
    Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.
    Mol. Cell. Proteomics 8:904-912(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.
  10. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104; SER-109; SER-111 AND SER-185, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiDDX42_MOUSE
AccessioniPrimary (citable) accession number: Q810A7
Secondary accession number(s): Q3TAN3
, Q3TE60, Q8BWZ7, Q9D8Q2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: October 17, 2006
Last modified: May 11, 2016
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, 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.