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Protein

Probable ATP-dependent RNA helicase DDX41

Gene

Ddx41

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. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi225 – 2328ATPPROSITE-ProRule annotation
Zinc fingeri580 – 59718CCHC-typeAdd
BLAST

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: MGI
  • helicase activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • poly(A) RNA binding Source: MGI

GO - Biological processi

  • cellular response to interferon-beta Source: MGI
  • defense response to virus Source: MGI
  • mRNA processing Source: UniProtKB-KW
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • RNA splicing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-3134975. Regulation of innate immune responses to cytosolic DNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX41 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 41
Gene namesi
Name:Ddx41
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1920185. Ddx41.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: MGI
  • endoplasmic reticulum Source: MGI
  • membrane Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 622622Probable ATP-dependent RNA helicase DDX41PRO_0000054971Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei21 – 211PhosphoserineCombined sources
Modified residuei23 – 231PhosphoserineCombined sources
Modified residuei33 – 331PhosphotyrosineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ91VN6.
MaxQBiQ91VN6.
PaxDbiQ91VN6.
PRIDEiQ91VN6.

PTM databases

iPTMnetiQ91VN6.
PhosphoSiteiQ91VN6.

Expressioni

Gene expression databases

BgeeiQ91VN6.
CleanExiMM_DDX41.
GenevisibleiQ91VN6. MM.

Interactioni

Subunit structurei

Identified in the spliceosome C complex.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Tmem173Q3TBT34EBI-2551902,EBI-3862093
Trim21Q621916EBI-2551902,EBI-6840982

Protein-protein interaction databases

BioGridi215656. 6 interactions.
IntActiQ91VN6. 6 interactions.
MINTiMINT-4120996.
STRINGi10090.ENSMUSP00000021956.

Structurei

3D structure databases

ProteinModelPortaliQ91VN6.
SMRiQ91VN6. Positions 161-566.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini212 – 396185Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini407 – 567161Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi181 – 20929Q motifAdd
BLAST
Motifi344 – 3474DEAD box

Sequence similaritiesi

Contains 1 CCHC-type zinc finger.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri580 – 59718CCHC-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0341. Eukaryota.
ENOG410XQQC. LUCA.
GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268792.
HOVERGENiHBG015893.
InParanoidiQ91VN6.
KOiK13116.
OMAiIMFALEQ.
OrthoDBiEOG7V49Z1.
TreeFamiTF300340.

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. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q91VN6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDSEPERKR ARADEATAGG SRSEDEDEDD EDYVPYVPLR QRRQLLLQKL
60 70 80 90 100
LQRRRKGATE EEQQDSGSEP RGDEDDIPLG PQSNVSLLDQ HQHLKEKAEA
110 120 130 140 150
RKESAKEKQL KEEEKILESV AEGRALMSVK EMAKGITYDD PIKTSWTPPR
160 170 180 190 200
YVLSMSEERH ERVRKKYHIL VEGDGIPPPI KSFKEMKFPA AILRGLKKKG
210 220 230 240 250
ILHPTPIQIQ GIPTILSGRD MIGIAFTGSG KTLVFTLPVI MFCLEQEKRL
260 270 280 290 300
PFSKREGPYG LIICPSRELA RQTHGILEYY CRLLQEDSSP LLRCALCIGG
310 320 330 340 350
MSVKEQMETI RHGVHMMVAT PGRLMDLLQK KMVSLDICRY LALDEADRMI
360 370 380 390 400
DMGFEGDIRT IFSYFKGQRQ TLLFSATMPK KIQNFAKSAL VKPVTINVGR
410 420 430 440 450
AGAASLDVIQ EVEYVKEEAK MVYLLECLQK TPPPVLIFAE KKADVDAIHE
460 470 480 490 500
YLLLKGVEAV AIHGGKDQEE RTKAIEAFRE GKKDVLVATD VASKGLDFPA
510 520 530 540 550
IQHVINYDMP EEIENYVHRI GRTGRSGNTG IATTFINKAC DESVLMDLKA
560 570 580 590 600
LLLEAKQKVP PVLQVLHCGD ESMLDIGGER GCAFCGGLGH RITDCPKLEA
610 620
MQTKQVSNIG RKDYLAHSSM DF
Length:622
Mass (Da):69,820
Last modified:July 27, 2011 - v2
Checksum:i85829CA9BDD0F4E1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti562 – 5621V → G in AAH11308 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK156957 mRNA. Translation: BAE33914.1.
BC011308 mRNA. Translation: AAH11308.1.
CCDSiCCDS26549.1.
RefSeqiNP_598820.2. NM_134059.2.
UniGeneiMm.205045.

Genome annotation databases

EnsembliENSMUST00000021956; ENSMUSP00000021956; ENSMUSG00000021494.
GeneIDi72935.
KEGGimmu:72935.
UCSCiuc007qro.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK156957 mRNA. Translation: BAE33914.1.
BC011308 mRNA. Translation: AAH11308.1.
CCDSiCCDS26549.1.
RefSeqiNP_598820.2. NM_134059.2.
UniGeneiMm.205045.

3D structure databases

ProteinModelPortaliQ91VN6.
SMRiQ91VN6. Positions 161-566.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi215656. 6 interactions.
IntActiQ91VN6. 6 interactions.
MINTiMINT-4120996.
STRINGi10090.ENSMUSP00000021956.

PTM databases

iPTMnetiQ91VN6.
PhosphoSiteiQ91VN6.

Proteomic databases

EPDiQ91VN6.
MaxQBiQ91VN6.
PaxDbiQ91VN6.
PRIDEiQ91VN6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000021956; ENSMUSP00000021956; ENSMUSG00000021494.
GeneIDi72935.
KEGGimmu:72935.
UCSCiuc007qro.2. mouse.

Organism-specific databases

CTDi51428.
MGIiMGI:1920185. Ddx41.

Phylogenomic databases

eggNOGiKOG0341. Eukaryota.
ENOG410XQQC. LUCA.
GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268792.
HOVERGENiHBG015893.
InParanoidiQ91VN6.
KOiK13116.
OMAiIMFALEQ.
OrthoDBiEOG7V49Z1.
TreeFamiTF300340.

Enzyme and pathway databases

ReactomeiR-MMU-3134975. Regulation of innate immune responses to cytosolic DNA.

Miscellaneous databases

ChiTaRSiDdx41. mouse.
PROiQ91VN6.
SOURCEiSearch...

Gene expression databases

BgeeiQ91VN6.
CleanExiMM_DDX41.
GenevisibleiQ91VN6. 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. 2 hits.
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: NOD.
    Tissue: Spleen.
  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].
    Strain: NMRI.
    Tissue: Mammary tumor.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21; SER-23 AND TYR-33, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiDDX41_MOUSE
AccessioniPrimary (citable) accession number: Q91VN6
Secondary accession number(s): Q3U0E0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2005
Last sequence update: July 27, 2011
Last modified: June 8, 2016
This is version 125 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.