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Protein

ATP-dependent RNA helicase A

Gene

DHX9

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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 (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi408 – 4158ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Helicase, Hydrolase

Keywords - Biological processi

Biological rhythms

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase A (EC:3.6.4.13)
Short name:
RHA
Alternative name(s):
DEAH box protein 9
Nuclear DNA helicase II
Short name:
NDH II
Gene namesi
Name:DHX9
Synonyms:DDX9, NDH2
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Unplaced

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleusnucleolus By similarity

  • Note: Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Can shuttle between nucleus and cytoplasm (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 – 12871287ATP-dependent RNA helicase APRO_0000055156Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei143 – 1431N6-acetyllysineBy similarity
Modified residuei188 – 1881N6-acetyllysineBy similarity
Modified residuei196 – 1961N6-acetyllysineBy similarity
Modified residuei318 – 3181PhosphoserineBy similarity
Modified residuei1021 – 10211N6-acetyllysineBy similarity

Post-translational modificationi

Methylated. HRMT1L2 mediated methylation of undefined Arg residues in the NTD is required for nuclear localization (By similarity).By similarity
May be phosphorylated by PRKDC/XRCC7. Phosphorylated by EIF2AK2/PKR and this phosphorylation perturbs its association with dsRNA.By similarity

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ28141.
PRIDEiQ28141.

Interactioni

Subunit structurei

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) (By similarity).By similarity

Protein-protein interaction databases

BioGridi158477. 1 interaction.
IntActiQ28141. 2 interactions.
STRINGi9913.ENSBTAP00000026409.

Structurei

3D structure databases

ProteinModelPortaliQ28141.
SMRiQ28141. Positions 4-95, 163-257.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 7169DRBM 1PROSITE-ProRule annotationAdd
BLAST
Domaini177 – 24973DRBM 2PROSITE-ProRule annotationAdd
BLAST
Domaini395 – 561167Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini633 – 806174Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 247247Interaction with CREBBPBy similarityAdd
BLAST
Regioni227 – 32296Interaction with BRCA1By similarityAdd
BLAST
Regioni328 – 37750MTADBy similarityAdd
BLAST
Regioni1148 – 1277130NTDBy similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi508 – 5114DEIH box
Motifi583 – 59210Nuclear localization signalSequence analysis

Domaini

The MTAD domain mediates interaction with the RNA polymerase II holoenzyme. The NTD domain is necessary and sufficient for nucleo-cytoplasmic shuttling and interaction with HRMT1L2 and SMN1 (By similarity).By similarity

Sequence similaritiesi

Contains 2 DRBM (double-stranded RNA-binding) domains.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0920. Eukaryota.
COG1643. LUCA.
HOGENOMiHOG000247063.
HOVERGENiHBG039429.
InParanoidiQ28141.
KOiK13184.

Family and domain databases

Gene3Di3.30.160.20. 2 hits.
3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR014720. dsRBD_dom.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00035. dsrm. 2 hits.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00358. DSRM. 2 hits.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS50137. DS_RBD. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q28141-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGDVKNFLYA WCGKRKMTPS YEIRAVGNKN RQKFMCEVRV EGYNYTGMGN
60 70 80 90 100
STNKKDAQSN AARDFVNYLV RINELKSEEV PAVGVAPPTP SATDSSDTTA
110 120 130 140 150
EDGGVPGNLG GPLPPHLTLQ AENNSGGGGS GYVPTWDRGA NLKDYYSRKE
160 170 180 190 200
EQEVQATLES EEVDLNAGLH GNWTLENAKA RLNQYFQKEK IQGEYKYTQV
210 220 230 240 250
GPDHNRSFIA EMTIYIKQIG RRIFAREHGS NKKLAAQSCA LSLVRQLYHL
260 270 280 290 300
GVIEPYSGLT KKKEGETVEP YKVNLSQDLE HQLQNIVQEL NLEIVPIPED
310 320 330 340 350
PSVPVALNLG KLAQFEPSQR QNPVGVVPWS PPQSNWNPWT SSNIDEGPLA
360 370 380 390 400
YATPEQISMD LKNELMYQLE QDRDLQAVLQ ERELLPVKKF ESEILEAISQ
410 420 430 440 450
NPVVIIRGAT GCGKTTQVPQ FILDDCIQND RAAECNIVVT QPRRISAVSV
460 470 480 490 500
AERVAYERGE EPGKSCGYSV RFESILPRPH ASIMFCTVGV LLRKLEAGIR
510 520 530 540 550
GISHVIVDEI HERDINTDFL LVVLRDVVQA YPEVRIVLMS ATIDTSMFCE
560 570 580 590 600
YFFNCPIIEV YGRTFPVQEY FLEDCIQMTH FVPPPKDKKK KDKDDDGGED
610 620 630 640 650
DDANCNLICG DEYGAETRIS MAQLNEKETP FELIEALLLY IETLNVPGAV
660 670 680 690 700
LVFLPGWNLI YTMQKHLEMN PHFGSHRYQI LPLHSQIPRE EQRKVFDPVP
710 720 730 740 750
SGVTKIILST NIAETSITIN DVVYVIDSCK QKVKLFTAHN NMTNYATVWA
760 770 780 790 800
SKTNLEQRKG RAGRVRPGFC FHLCSRARFE RLETHMTPEM FRTPLHEIAL
810 820 830 840 850
SIKLLRLGGI GQFLAKAIEP PPLDAVIEAE HTLRELDALD ANDELTPLGR
860 870 880 890 900
ILAKLPIEPR FGKMMIMGCI FYVGDAICTI SAATCFPEPF ISEGKRLGYI
910 920 930 940 950
HRNFAGNRFS DHVALLSVFQ AWDDARMGGE EAEIRFCEHK RLNMATLRMT
960 970 980 990 1000
WEAKVQLKEI LINSGFPEEC LLTQVFTNTG PDNNLDVVIS LLAFGVYPNV
1010 1020 1030 1040 1050
CYHKEKRKIL TTEGRNALIH KSSVNCPFSS QDMKYPSPFF VFGEKIRTRA
1060 1070 1080 1090 1100
ISAKGMTLVT PLQLLLFASK KVQSDGQLVL VDDWIRLQIS HEAAACITAL
1110 1120 1130 1140 1150
RAAMEALVVE VTKQPGIISQ LDPVNERMLN TIRQISRPSA AGINLMIGTT
1160 1170 1180 1190 1200
RYGDGPRPPK MARYDNGSGY RRGGSSYSGG GYGLGGYGTG GYGGGGGYGG
1210 1220 1230 1240 1250
RGGYSGGGYG GGSNSFRGSY VGGGGGVGGG GGGFRGLSRG GYRGMSGGDY
1260 1270 1280
RGESGGGYRG SGGFQRGGGR GGYGGGYFGQ GRGGGGY
Length:1,287
Mass (Da):141,944
Last modified:November 1, 1997 - v1
Checksum:iDC908095AB683ED4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82829 mRNA. Translation: CAA58036.1.
PIRiI46032.
RefSeqiNP_776461.1. NM_174036.2.
UniGeneiBt.5544.

Genome annotation databases

GeneIDi281115.
KEGGibta:281115.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82829 mRNA. Translation: CAA58036.1.
PIRiI46032.
RefSeqiNP_776461.1. NM_174036.2.
UniGeneiBt.5544.

3D structure databases

ProteinModelPortaliQ28141.
SMRiQ28141. Positions 4-95, 163-257.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi158477. 1 interaction.
IntActiQ28141. 2 interactions.
STRINGi9913.ENSBTAP00000026409.

Proteomic databases

PaxDbiQ28141.
PRIDEiQ28141.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi281115.
KEGGibta:281115.

Organism-specific databases

CTDi1660.

Phylogenomic databases

eggNOGiKOG0920. Eukaryota.
COG1643. LUCA.
HOGENOMiHOG000247063.
HOVERGENiHBG039429.
InParanoidiQ28141.
KOiK13184.

Miscellaneous databases

NextBioi20805185.

Family and domain databases

Gene3Di3.30.160.20. 2 hits.
3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR014720. dsRBD_dom.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00035. dsrm. 2 hits.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00358. DSRM. 2 hits.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS50137. DS_RBD. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Molecular cloning of the gene encoding nuclear DNA helicase II. A bovine homologue of human RNA helicase A and Drosophila Mle protein."
    Zhang S., Maacke H., Grosse F.
    J. Biol. Chem. 270:16422-16427(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Thymus.

Entry informationi

Entry nameiDHX9_BOVIN
AccessioniPrimary (citable) accession number: Q28141
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: February 17, 2016
This is version 116 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. 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.