Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

ATP-dependent RNA helicase DDX1

Gene

Ddx1

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

Functioni

Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi46 – 538ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Exonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, Transcription, Transcription regulation, tRNA processing

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DDX1 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 1
Gene namesi
Name:Ddx1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 12

Organism-specific databases

MGIiMGI:2144727. Ddx1.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity
  • Cytoplasmic granule By similarity

  • Note: Localized with MBNL1, TIAL1 and YBX1 in stress granules upon stress. Localized with CSTF2 in cleavage bodies. Forms large aggregates called DDX1 bodies. Relocalized into multiple foci (IR-induced foci or IRIF) after IR treatment, a process that depends on the presence of chromosomal DNA and/or RNA-DNA duplexes. Relocalized at sites of DNA double-strand breaks (DSBs) in an ATM-dependent manner after IR treatment. Colocalized with RELA in the nucleus upon TNF-alpha induction. Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 740740ATP-dependent RNA helicase DDX1PRO_0000054987Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei239 – 2391N6-acetyllysineBy similarity
Modified residuei268 – 2681N6-acetyllysineBy similarity
Modified residuei281 – 2811N6-acetyllysineBy similarity
Modified residuei481 – 4811PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ91VR5.
MaxQBiQ91VR5.
PaxDbiQ91VR5.
PeptideAtlasiQ91VR5.
PRIDEiQ91VR5.

2D gel databases

REPRODUCTION-2DPAGEQ91VR5.

PTM databases

iPTMnetiQ91VR5.
PhosphoSiteiQ91VR5.
SwissPalmiQ91VR5.

Expressioni

Tissue specificityi

Testis-specific. Expressed in the germ line stem cells, spermatogonia and spermatocytes of the testis. Also expressed in the seminoma and nonseminoma types of testicular germ cell tumors (TGCTs) (at protein level).1 Publication

Developmental stagei

Expressed in the testis from 11.5 to 19.5 dpc.1 Publication

Gene expression databases

BgeeiQ91VR5.
CleanExiMM_DDX1.
GenevisibleiQ91VR5. MM.

Interactioni

Subunit structurei

Interacts with MBNL1. Interacts with CSTF2. Interacts with HNRNPK. Interacts with ATM. Interacts with RELA (via C-terminal). Component of the tRNA-splicing ligase complex (By similarity). Interacts with PHF5A (via C-terminus).By similarity1 Publication

Protein-protein interaction databases

BioGridi222684. 7 interactions.
IntActiQ91VR5. 4 interactions.
STRINGi10090.ENSMUSP00000065987.

Structurei

3D structure databases

ProteinModelPortaliQ91VR5.
SMRiQ91VR5. Positions 25-70, 96-253, 258-674.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 428427Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini70 – 247178B30.2/SPRYPROSITE-ProRule annotationAdd
BLAST
Domaini493 – 681189Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 525525Necessary for interaction with RELABy similarityAdd
BLAST
Regioni1 – 295295Necessary for interaction with HNRNPKBy similarityAdd
BLAST
Regioni525 – 740216Necessary for interaction with HNRNPKBy similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi370 – 3734DEAD box

Domaini

The helicase domain is involved in the stimulation of RELA transcriptional activity.By similarity

Sequence similaritiesi

Contains 1 B30.2/SPRY domain.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0349. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000251633.
HOVERGENiHBG005462.
InParanoidiQ91VR5.
KOiK13177.
OMAiTLNNVKQ.
OrthoDBiEOG7RNJZJ.
PhylomeDBiQ91VR5.
TreeFamiTF106114.

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR001870. B30.2/SPRY.
IPR013320. ConA-like_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
IPR003877. SPRY_dom.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00622. SPRY. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00449. SPRY. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
SSF52540. SSF52540. 3 hits.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 2 hits.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q91VR5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAFSEMGVM PEIAQAVEEM DWLLPTDIQA ESIPLILGGG DVLMAAETGS
60 70 80 90 100
GKTGAFSIPV IQIVYETLKD QQEGKKGKTT IKTGASVLNK WQMNPYDRGS
110 120 130 140 150
AFAIGSDGLC CQSREVKEWH GCRGTRGLLK GKHYYEVSCH DQGLCRVGWS
160 170 180 190 200
TMQASLDLGT DKFGFGFGGT GKKSHNKQFD NYGEEFTMHD TIGCYLDIDK
210 220 230 240 250
GHVKFSKNGK DLGLAFEIPA HIKNQALFPA CVLKNAELKF NFGEEEFKFP
260 270 280 290 300
PKDGFVALSK APDNYIVKSQ HTGNAQVSQT KFLPNAPKAL IVEPSRELAE
310 320 330 340 350
QTLNNVKQFK KYIDNPKLRE LLIIGGVAAR DQLSVLDNGV DIVVGTPGRL
360 370 380 390 400
DDLVSTGKLN LSQVRFLVLD EADGLLSQGY SDFINRMHNQ IPQITCDGKR
410 420 430 440 450
LQVIVCSATL HSFDVKKLSE KIMHFPTWVD LKGEDSVPDT VHHVVVPVNP
460 470 480 490 500
KTDKLWERLG KNHIRTDDVH AKDNTRPGAN SPEMWSEAIK ILKGEYAVRA
510 520 530 540 550
IKEHKMDQAI IFCRTKIDCD NLEQYFMQQG GGPDKKGHQF SCVCLHGDRK
560 570 580 590 600
PHERKQNLER FKKGDVRFLI CTDVAARGID IHGVPYVINV TLPDEKQNYV
610 620 630 640 650
HRIGRVGRAE RMGLAISLVA TEKEKVWYHV CSNRGKGCYN TRLKEDGGCT
660 670 680 690 700
IWYNEMQLLS EIEEHLNCTI SQVEPDIKVP VDEFDGKVTY GQKRAAGGGN
710 720 730 740
YKGHVDVLAP TVQELAALEK EAQTSFLHLG YLPNQLFRTF
Length:740
Mass (Da):82,500
Last modified:December 1, 2001 - v1
Checksum:i76457FBB75A3CEC2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK028341 mRNA. Translation: BAC25893.1.
AK153335 mRNA. Translation: BAE31914.1.
AK160982 mRNA. Translation: BAE36130.1.
BC010624 mRNA. Translation: AAH10624.1.
CCDSiCCDS25819.1.
RefSeqiNP_598801.1. NM_134040.1.
UniGeneiMm.251255.

Genome annotation databases

EnsembliENSMUST00000071103; ENSMUSP00000065987; ENSMUSG00000037149.
GeneIDi104721.
KEGGimmu:104721.
UCSCiuc007nbh.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK028341 mRNA. Translation: BAC25893.1.
AK153335 mRNA. Translation: BAE31914.1.
AK160982 mRNA. Translation: BAE36130.1.
BC010624 mRNA. Translation: AAH10624.1.
CCDSiCCDS25819.1.
RefSeqiNP_598801.1. NM_134040.1.
UniGeneiMm.251255.

3D structure databases

ProteinModelPortaliQ91VR5.
SMRiQ91VR5. Positions 25-70, 96-253, 258-674.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi222684. 7 interactions.
IntActiQ91VR5. 4 interactions.
STRINGi10090.ENSMUSP00000065987.

PTM databases

iPTMnetiQ91VR5.
PhosphoSiteiQ91VR5.
SwissPalmiQ91VR5.

2D gel databases

REPRODUCTION-2DPAGEQ91VR5.

Proteomic databases

EPDiQ91VR5.
MaxQBiQ91VR5.
PaxDbiQ91VR5.
PeptideAtlasiQ91VR5.
PRIDEiQ91VR5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000071103; ENSMUSP00000065987; ENSMUSG00000037149.
GeneIDi104721.
KEGGimmu:104721.
UCSCiuc007nbh.1. mouse.

Organism-specific databases

CTDi1653.
MGIiMGI:2144727. Ddx1.

Phylogenomic databases

eggNOGiKOG0349. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000251633.
HOVERGENiHBG005462.
InParanoidiQ91VR5.
KOiK13177.
OMAiTLNNVKQ.
OrthoDBiEOG7RNJZJ.
PhylomeDBiQ91VR5.
TreeFamiTF106114.

Miscellaneous databases

PROiQ91VR5.
SOURCEiSearch...

Gene expression databases

BgeeiQ91VR5.
CleanExiMM_DDX1.
GenevisibleiQ91VR5. MM.

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR001870. B30.2/SPRY.
IPR013320. ConA-like_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
IPR003877. SPRY_dom.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00622. SPRY. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00449. SPRY. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
SSF52540. SSF52540. 3 hits.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 2 hits.
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: Bone marrow and Head.
  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: FVB/N-3.
    Tissue: Mammary tumor.
  3. "PHF5A represents a bridge protein between splicing proteins and ATP-dependent helicases and is differentially expressed during mouse spermatogenesis."
    Rzymski T., Grzmil P., Meinhardt A., Wolf S., Burfeind P.
    Cytogenet. Genome Res. 121:232-244(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PHF5A.
  4. "DDX1 is required for testicular tumorigenesis, partially through the transcriptional activation of 12p stem cell genes."
    Tanaka K., Okamoto S., Ishikawa Y., Tamura H., Hara T.
    Oncogene 28:2142-2151(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-481, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiDDX1_MOUSE
AccessioniPrimary (citable) accession number: Q91VR5
Secondary accession number(s): Q3TU41
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2005
Last sequence update: December 1, 2001
Last modified: July 6, 2016
This is version 133 of the entry and version 1 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.