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O70133 (DHX9_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 131. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ATP-dependent RNA helicase A

Short name=RHA
EC=3.6.4.13
Alternative name(s):
DEAH box protein 9
Short name=mHEL-5
Nuclear DNA helicase II
Short name=NDH II
Gene names
Name:Dhx9
Synonyms:Ddx9
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1380 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the CRD-mediated complex that promotes MYC mRNA stability. Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alterations of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. As component of a large PER complex is involved in the inhibition of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms. Ref.10

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

Interacts with ZIC2, IGF2BP1, IGF2BP2, IGF2BP3, MBD2, HRMT1L2/PRMT1, RELA and LARP6. Can also interact with XRCC5 and with TOP2A in an RNA dependent manner; these interactions may be indirect. Interaction with TOP2A is promoted by UBC9. Interacts with histone H2AFX and this requires phosphorylation of H2AFX on 'Ser-139'. Interacts (via N-terminus) with EIF2AK2/PKR and this interaction is dependent upon the activation of the kinase. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. May act to directly link BRCA1, CREBBP or SMN1 and the RNA polymerase II complex. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. The large PER complex involved in the repression of transcriptional termination is composed of at least PER2, CDK9, DDX5, DHX9, NCBP1 and POLR2A (active). Ref.9 Ref.10 Ref.13

Subcellular location

Nucleusnucleolus. Cytoplasm By similarity. Note: Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Can shuttle between nucleus and cytoplasm By similarity. Ref.6

Domain

The MTAD domain mediates interaction with the RNA polymerase II holoenzyme By similarity.

Post-translational modification

Methylated By similarity.

May be phosphorylated by PRKDC/XRCC7 By similarity. Phosphorylated by EIF2AK2/PKR and this phosphorylation perturbs its association with dsRNA. Ref.9

Sequence similarities

Belongs to the DEAD box helicase family. DEAH subfamily.

Contains 2 DRBM (double-stranded RNA-binding) domains.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Sequence caution

The sequence AAH89159.1 differs from that shown. Reason: Frameshift at positions 447 and 448.

The sequence AAR87796.1 differs from that shown. Reason: Intron retention.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O70133-1)

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.
Isoform 2 (identifier: O70133-2)

The sequence of this isoform differs from the canonical sequence as follows:
     123-123: E → EA
Note: Contains a phosphoserine at position 137.
Isoform 3 (identifier: O70133-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-216: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 13801380ATP-dependent RNA helicase A
PRO_0000055158

Regions

Domain3 – 7169DRBM 1
Domain182 – 25473DRBM 2
Domain400 – 566167Helicase ATP-binding
Domain638 – 811174Helicase C-terminal
Nucleotide binding413 – 4208ATP By similarity
Region1 – 253253Interaction with CREBBP By similarity
Region233 – 32896Interaction with BRCA1 By similarity
Region333 – 38250MTAD By similarity
Motif513 – 5164DEAH box
Motif588 – 59710Nuclear localization signal Potential
Compositional bias1171 – 1380210Arg/Gly/Ser/Tyr-rich

Amino acid modifications

Modified residue1481N6-acetyllysine Ref.11
Modified residue1931N6-acetyllysine By similarity
Modified residue2011N6-acetyllysine By similarity
Modified residue3231Phosphoserine By similarity
Modified residue10261N6-acetyllysine By similarity

Natural variations

Alternative sequence1 – 216216Missing in isoform 3.
VSP_014778
Alternative sequence1231E → EA in isoform 2.
VSP_014779

Experimental info

Sequence conflict461A → R in AAC05725. Ref.1
Sequence conflict1361S → A in AAC05725. Ref.1
Sequence conflict1361S → A in AAC05301. Ref.1
Sequence conflict1871L → V Ref.2
Sequence conflict1891Q → H in AAC05725. Ref.1
Sequence conflict2111R → G in BAB28848. Ref.4
Sequence conflict2351S → C in AAC05725. Ref.1
Sequence conflict2571V → C in AAC05725. Ref.1
Sequence conflict2811S → P in AAC05725. Ref.1
Sequence conflict6741N → M in AAB72087. Ref.5
Sequence conflict7481T → I in AAB72087. Ref.5
Sequence conflict8311I → V in AAB72087. Ref.5

Secondary structure

........................ 1380
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 19, 2005. Version 2.
Checksum: 005D641CD9A4F0C9

FASTA1,380149,475
        10         20         30         40         50         60 
MGDIKNFLYA WCGKRKMTPA YEIRAVGNKN RQKFMCEVRV EGFNYAGMGN STNKKDAQSN 

        70         80         90        100        110        120 
AARDFVNYLV RINEVKSEEV PAVGIVPPPP ILSDTSDSTA SAAEGLPAPM GGPLPPHLAL 

       130        140        150        160        170        180 
KAEENNSGVE SSGYGSPGPT WDRGANLKDY YSRKEEQEVQ ATLESEEVDL NAGLHGNWTL 

       190        200        210        220        230        240 
ENAKARLNQY FQKEKIQGEY KYTQVGPDHN RSFIAEMTIY IKQLGRRIFA REHGSNKKLA 

       250        260        270        280        290        300 
AQSCALSLVR QLYHLGVIEA YSGLTKKKEG ERVEPYKVFL SPDLELQLQN VVQELDLEIV 

       310        320        330        340        350        360 
PPPVDPSMPV ILNIGKLAHF EPSQRQNAVG VVPWSPPQSN WNPWTSSNID EGPLAYASTE 

       370        380        390        400        410        420 
QISMDLKNEL TYQMEQDHNL QSVLQERELL PVKKFEAEIL EAISSNSVVI IRGATGCGKT 

       430        440        450        460        470        480 
TQVPQYILDD FIQNDRAAEC NIVVTQPRRI SAVAVAERVA YERGEEPGKS CGYSVRFESI 

       490        500        510        520        530        540 
LPRPHASIMF CTVGVLLRKL EAGIRGISHV IVDEIHERDI NTDFLLVVLR DVVLAYPEVR 

       550        560        570        580        590        600 
IVLMSATIDT TMFCEYFFNC PIIEVYGRTF PVQEYFLEDC IQMTQFIPPP KDKKKKDKED 

       610        620        630        640        650        660 
DGGEDDDANC NLICGDEYGP ETKLSMSQLN EKETPFELIE ALLKYIETLN VPGAVLVFLP 

       670        680        690        700        710        720 
GWNLIYTMQK HLENNSHFGS HRYQILPLHS QIPREEQRKV FDPVPDGVTK VILSTNIAET 

       730        740        750        760        770        780 
SITINDVVYV IDSCKQKVKL FTAHNNMTNY ATVWASKTNL EQRKGRAGRV RPGFCFHLCS 

       790        800        810        820        830        840 
RARFDRLETH MTPEMFRTPL HEIALSIKLL RLGGIGQFLA KAIEPPPLDA IIEAEHTLRE 

       850        860        870        880        890        900 
LDALDANDEL TPLGRILAKL PIEPRFGKMM IMGCIFYVGD AVCTISAATC FPEPFISEGK 

       910        920        930        940        950        960 
RLGYIHRNFA GNRFSDHVAL LSVFQAWDDA RMSGEEAEIR FCEQKRLNMA TLRMTWEAKV 

       970        980        990       1000       1010       1020 
QLKEILINSG FPEDCLLTQV FTNTGPDNNL DVVISLLAFG VYPNVCYHKE KRKILTTEGR 

      1030       1040       1050       1060       1070       1080 
NALIHKSSVN CPFSSQDMKY PSPFFVFGEK IRTRAISAKG MTLVTPLQLL LFASKKVQSD 

      1090       1100       1110       1120       1130       1140 
GQIVFIDDWI RLQISHEAAA CITIRAAMEA LVVEVSKQPN IISQLDPVNE HMLNTIRQIS 

      1150       1160       1170       1180       1190       1200 
RPSAAGINLM IGSVRYGDGP RPPKMARYDN GSGYRRGYGG GGYGGGGYGG GYGSGGFGGG 

      1210       1220       1230       1240       1250       1260 
FGSGGGFGGG FNSGGGGFGS GGGGFGSGGG GFGGGGGGFS GGGGGGFGGG RGGGGGGFGG 

      1270       1280       1290       1300       1310       1320 
SGGFGNGGGG YGVGGGGYGG GGGGGYGGGS GGYGGGGYGG GEGYSISPNS YRGNYGGGGG 

      1330       1340       1350       1360       1370       1380 
GYRGGSQGGY RNNFGGDYRG SSGDYRGSGG GYRGSGGFQR RGYGGGYFGQ GRGGGGGGGY 

« Hide

Isoform 2 [UniParc].

Checksum: 0AB5502F91DEFB73
Show »

FASTA1,381149,546
Isoform 3 [UniParc].

Checksum: DA64E679A88D87C2
Show »

FASTA1,164125,615

References

« Hide 'large scale' references
[1]"Molecular analysis of the cDNA and genomic DNA encoding mouse RNA helicase A."
Lee C.-G., Eki T., Okumura K., da Costa Soares V., Hurwitz J.
Genomics 47:365-371(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-161.
Strain: 129/Sv.
[2]"Transcriptome analysis of mouse stem cells and early embryos."
Sharov A.A., Piao Y., Matoba R., Dudekula D.B., Qian Y., VanBuren V., Falco G., Martin P.R., Stagg C.A., Bassey U.C., Wang Y., Carter M.G., Hamatani T., Aiba K., Akutsu H., Sharova L., Tanaka T.S., Kimber W.L. expand/collapse author list , Yoshikawa T., Jaradat S.A., Pantano S., Nagaraja R., Boheler K.R., Taub D., Hodes R.J., Longo D.L., Schlessinger D., Keller J., Klotz E., Kelsoe G., Umezawa A., Vescovi A.L., Rossant J., Kunath T., Hogan B.L.M., Curci A., D'Urso M., Kelso J., Hide W., Ko M.S.H.
PLoS Biol. 1:410-419(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-756 (ISOFORM 3).
Strain: C57BL/6NCr.
[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] OF 1-756 (ISOFORM 1).
Strain: C57BL/6J.
Tissue: Embryonic germ cell.
[4]"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. expand/collapse author list , 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] OF 1-264 (ISOFORM 2).
Strain: C57BL/6J.
Tissue: Embryo.
[5]"mHEL-5."
Kisielow P., Miazek A.
Submitted (MAR-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE OF 386-919 (ISOFORMS 1/2/3).
Strain: C57BL/6.
[6]"Nucleolar localization of murine nuclear DNA helicase II (RNA helicase A)."
Zhang S., Herrmann C., Grosse F.
J. Cell Sci. 112:2693-2703(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[7]"Large-scale phosphorylation analysis of mouse liver."
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137 (ISOFORM 2), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[8]"Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis."
Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.
J. Proteome Res. 7:3957-3967(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137 (ISOFORM 2), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[9]"An antiviral response directed by PKR phosphorylation of the RNA helicase A."
Sadler A.J., Latchoumanin O., Hawkes D., Mak J., Williams B.R.
PLoS Pathog. 5:E1000311-E1000311(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH EIF2AK2, PHOSPHORYLATION.
[10]"Feedback regulation of transcriptional termination by the mammalian circadian clock PERIOD complex."
Padmanabhan K., Robles M.S., Westerling T., Weitz C.J.
Science 337:599-602(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN CIRCADIAN RHYTHMS, IDENTIFICATION IN A LARGE PER COMPLEX.
[11]"SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-148, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic fibroblast.
[12]"Solution structure of double-stranded RNA-binding motifs from hypothetical protein BAB28848."
RIKEN structural genomics initiative (RSGI)
Submitted (NOV-2004) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 4-262.
[13]"Functional role of Zic2 phosphorylation in transcriptional regulation."
Ishiguro A., Aruga J.
FEBS Lett. 582:154-158(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ZIC2.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U91922 mRNA. Translation: AAC05725.1.
AF023530 Genomic DNA. Translation: AAC05301.1.
AY512925 mRNA. Translation: AAR87796.1. Sequence problems.
BC089159 mRNA. Translation: AAH89159.1. Sequence problems.
AK013423 mRNA. Translation: BAB28848.1.
U92080 mRNA. Translation: AAB72087.1.
RefSeqNP_031868.2. NM_007842.2.
UniGeneMm.20000.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UILNMR-A163-262[»]
1WHQNMR-A4-89[»]
2RS6NMR-A4-89[»]
2RS7NMR-A163-262[»]
ProteinModelPortalO70133.
SMRO70133. Positions 4-89, 168-262, 331-1073.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid199088. 6 interactions.
IntActO70133. 8 interactions.
MINTMINT-1868227.

PTM databases

PhosphoSiteO70133.

Proteomic databases

MaxQBO70133.
PaxDbO70133.
PRIDEO70133.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID13211.
KEGGmmu:13211.

Organism-specific databases

CTD1660.
MGIMGI:108177. Dhx9.

Phylogenomic databases

eggNOGCOG1643.
HOGENOMHOG000247063.
HOVERGENHBG039429.
InParanoidO70133.
KOK13184.
PhylomeDBO70133.

Gene expression databases

CleanExMM_DHX9.
GenevestigatorO70133.

Family and domain databases

Gene3D3.30.160.20. 2 hits.
3.40.50.300. 2 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR014720. dsRNA-bd_dom.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF00270. DEAD. 1 hit.
PF00035. dsrm. 2 hits.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00358. DSRM. 2 hits.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 2 hits.
PROSITEPS00690. DEAH_ATP_HELICASE. 1 hit.
PS50137. DS_RBD. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSDHX9. mouse.
EvolutionaryTraceO70133.
NextBio283382.
PROO70133.
SOURCESearch...

Entry information

Entry nameDHX9_MOUSE
AccessionPrimary (citable) accession number: O70133
Secondary accession number(s): O35931 expand/collapse secondary AC list , O54703, Q5FWY1, Q6R5F7, Q9CSA2
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: July 19, 2005
Last modified: July 9, 2014
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

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