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

Nucleolar RNA helicase 2

Gene

Ddx21

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

Functioni

RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes. In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77'. Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase). Involved in rRNA processing.By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi302 – 309ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • 7SK snRNA binding Source: UniProtKB
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: UniProtKB
  • double-stranded RNA binding Source: MGI
  • poly(A) RNA binding Source: MGI
  • RNA binding Source: MGI
  • RNA helicase activity Source: MGI
  • rRNA binding Source: UniProtKB
  • snoRNA binding Source: UniProtKB

GO - Biological processi

  • osteoblast differentiation Source: MGI
  • response to exogenous dsRNA Source: MGI
  • response to virus Source: MGI
  • RNA secondary structure unwinding Source: GO_Central
  • rRNA processing Source: UniProtKB-KW
  • transcription from RNA polymerase II promoter Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

rRNA processing, Transcription

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-5250924. B-WICH complex positively regulates rRNA expression.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleolar RNA helicase 2Curated (EC:3.6.4.13By similarity)
Alternative name(s):
DEAD box protein 21
Gu-alpha
Nucleolar RNA helicase Gu
Nucleolar RNA helicase II
RH II/Gu
Gene namesi
Name:Ddx21
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1860494. Ddx21.

Subcellular locationi

  • Nucleusnucleolus By similarity
  • Nucleusnucleoplasm By similarity

  • Note: Present both in nucleolus and nucleoplasm. Interaction with JUN promotes translocation from the nucleolus to the nucleoplasm. Interaction with WDR46 is required for localization to the nucleolus.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550281 – 851Nucleolar RNA helicase 2Add BLAST851

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei7PhosphoserineBy similarity1
Modified residuei13PhosphoserineBy similarity1
Modified residuei39N6-acetyllysineCombined sources1
Modified residuei118PhosphoserineCombined sources1
Modified residuei144PhosphoserineCombined sources1
Modified residuei155PhosphoserineCombined sources1
Modified residuei181PhosphoserineCombined sources1
Modified residuei192PhosphoserineCombined sources1
Modified residuei218PhosphoserineCombined sources1
Modified residuei236PhosphoserineCombined sources1
Modified residuei243PhosphoserineCombined sources1
Modified residuei244PhosphoserineCombined sources1
Modified residuei245PhosphoserineCombined sources1
Modified residuei368PhosphothreonineBy similarity1
Modified residuei639PhosphoserineBy similarity1
Modified residuei847N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9JIK5.
MaxQBiQ9JIK5.
PaxDbiQ9JIK5.
PeptideAtlasiQ9JIK5.
PRIDEiQ9JIK5.

PTM databases

iPTMnetiQ9JIK5.
PhosphoSitePlusiQ9JIK5.
SwissPalmiQ9JIK5.

Expressioni

Tissue specificityi

Highly expressed in liver and testis. Expressed at lower level in brain, lungs, and skeletal muscle.1 Publication

Gene expression databases

BgeeiENSMUSG00000020075.
CleanExiMM_DDX21.
GenevisibleiQ9JIK5. MM.

Interactioni

Subunit structurei

Component of the B-WICH complex, at least composed of SMARCA5/SNF2H, BAZ1B/WSTF, SF3B1, DEK, MYO1C, ERCC6, MYBBP1A and DDX21. Interacts with C1QBP. Interacts with JUN. Interacts with WDR46.By similarity

Protein-protein interaction databases

BioGridi207838. 5 interactors.
DIPiDIP-48574N.
IntActiQ9JIK5. 4 interactors.
MINTiMINT-1867885.
STRINGi10090.ENSMUSP00000042691.

Structurei

Secondary structure

1851
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi845 – 849Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZINX-ray2.00B/C839-851[»]
ProteinModelPortaliQ9JIK5.
SMRiQ9JIK5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati117 – 1531-1Add BLAST37
Repeati154 – 1901-2Add BLAST37
Repeati191 – 2271-3Add BLAST37
Domaini289 – 468Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST180
Domaini501 – 645Helicase C-terminalPROSITE-ProRule annotationAdd BLAST145
Repeati807 – 8112-15
Repeati817 – 8232-27
Repeati829 – 8332-35

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 2273 X 37 AA tandem repeatsAdd BLAST111
Regioni807 – 8333 X 5 AA repeatsAdd BLAST27

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi258 – 286Q motifPROSITE-ProRule annotationAdd BLAST29
Motifi411 – 414DEAD boxPROSITE-ProRule annotation4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi95 – 98Poly-Lys4

Domaini

The helicase and foldase activities reside in two separate domains, the helicase in the N-terminus and the foldase in the C-terminus.By similarity
The 3 X 5 AA repeats seem to be critical for the RNA folding activity.By similarity

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0331. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268805.
HOVERGENiHBG051331.
InParanoidiQ9JIK5.
KOiK16911.
OMAiRFRGQRE.
OrthoDBiEOG091G04F8.
TreeFamiTF328622.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR012562. GUCT.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR012677. Nucleotide-bd_a/b_plait.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF08152. GUCT. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9JIK5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPGKLRSGAK LGSDGAEESM ETLPKPSEKK TRKEKTKSKT EEATEGMEEA
60 70 80 90 100
VSSKAKKTNK KGPSEDDVDP PKSRKAKKQE EEPQDDTAST SKTSKKKKEP
110 120 130 140 150
LEKQADSETK EIITEEPSEE EADMPKPKKM KKGKEANGDA GEKSPKLKNG
160 170 180 190 200
LSQPSEEEAD IPKPKKMKKG KEANGDAGEK SPKLKNGLSQ PSEEEVDIPK
210 220 230 240 250
PKKMKKGKEA SGDAGEKSPR LKDGLSQPSE PKSNSSDAPG EESSSETEKE
260 270 280 290 300
IPVEQKEGAF SNFPISEETV KLLKARGVNF LFPIQAKTFH HVYSGKDLIA
310 320 330 340 350
QARTGTGKTF SFAIPLIEKL QGGLQERKRG RAPQVLVLAP TRELANQVSK
360 370 380 390 400
DFSDITKKLS VACFYGGTPY GGQIERMRSG IDILVGTPGR IKDHLQNGKL
410 420 430 440 450
DLTKLKHVVL DEVDQMLDMG FADQVEEILC VAYKKDSEDN PQTLLFSATC
460 470 480 490 500
PHWVFNVAKK YMKSTYEQVD LIGKKTQKAA ITVEHLAIKC HWTERAAVIG
510 520 530 540 550
DVIRVYSGHQ GRTIIFCETK KDAQELSQNT CIKQDAQSLH GDIPQKQREI
560 570 580 590 600
TLKGFRNGNF GVLVATNVAA RGLDIPEVDL VVQSCPPKDV ESYIHRSGRT
610 620 630 640 650
GRAGRTGVCI CFYQNKEEYQ LAQVEQKAGI KFKRIGVPSA TEIIKASSKD
660 670 680 690 700
AIRLLDSVPP TAISHFKQSA EKLIEEKGAV EALAAALAHI SGATSVDQRS
710 720 730 740 750
LINSQAGFVT MILRCSIEMP NISYAWKELK EQLGESIDAK VKGMVFLKGK
760 770 780 790 800
LGVCFDVRTE AVTEIQEKWH DSRRWQLTVA TEQPELEGPP DGYRGRMGQR
810 820 830 840 850
DGSRGAFRGQ RGGSRNFRGQ GQRGGSRNFR GQRPGGGNRG QKRSFSKAFG

Q
Length:851
Mass (Da):93,551
Last modified:July 27, 2011 - v3
Checksum:i7066986F4CA0DCD7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1 – 46Missing in AAF61690 (PubMed:10860663).CuratedAdd BLAST46
Sequence conflicti790P → Q in AAD43959 (PubMed:10860663).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF220365 Genomic DNA. Translation: AAF61690.1.
AF159131 mRNA. Translation: AAD43959.3.
AK160095 mRNA. Translation: BAE35625.1.
CH466553 Genomic DNA. Translation: EDL32086.1.
BC043655 mRNA. Translation: AAH43655.1.
CCDSiCCDS23891.1.
RefSeqiNP_062426.2. NM_019553.2.
UniGeneiMm.413275.

Genome annotation databases

EnsembliENSMUST00000045866; ENSMUSP00000042691; ENSMUSG00000020075.
GeneIDi56200.
KEGGimmu:56200.
UCSCiuc007fhn.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF220365 Genomic DNA. Translation: AAF61690.1.
AF159131 mRNA. Translation: AAD43959.3.
AK160095 mRNA. Translation: BAE35625.1.
CH466553 Genomic DNA. Translation: EDL32086.1.
BC043655 mRNA. Translation: AAH43655.1.
CCDSiCCDS23891.1.
RefSeqiNP_062426.2. NM_019553.2.
UniGeneiMm.413275.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZINX-ray2.00B/C839-851[»]
ProteinModelPortaliQ9JIK5.
SMRiQ9JIK5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi207838. 5 interactors.
DIPiDIP-48574N.
IntActiQ9JIK5. 4 interactors.
MINTiMINT-1867885.
STRINGi10090.ENSMUSP00000042691.

PTM databases

iPTMnetiQ9JIK5.
PhosphoSitePlusiQ9JIK5.
SwissPalmiQ9JIK5.

Proteomic databases

EPDiQ9JIK5.
MaxQBiQ9JIK5.
PaxDbiQ9JIK5.
PeptideAtlasiQ9JIK5.
PRIDEiQ9JIK5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000045866; ENSMUSP00000042691; ENSMUSG00000020075.
GeneIDi56200.
KEGGimmu:56200.
UCSCiuc007fhn.1. mouse.

Organism-specific databases

CTDi9188.
MGIiMGI:1860494. Ddx21.

Phylogenomic databases

eggNOGiKOG0331. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268805.
HOVERGENiHBG051331.
InParanoidiQ9JIK5.
KOiK16911.
OMAiRFRGQRE.
OrthoDBiEOG091G04F8.
TreeFamiTF328622.

Enzyme and pathway databases

ReactomeiR-MMU-5250924. B-WICH complex positively regulates rRNA expression.

Miscellaneous databases

ChiTaRSiDdx21. mouse.
PROiQ9JIK5.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000020075.
CleanExiMM_DDX21.
GenevisibleiQ9JIK5. MM.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR012562. GUCT.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR012677. Nucleotide-bd_a/b_plait.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF08152. GUCT. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDX21_MOUSE
AccessioniPrimary (citable) accession number: Q9JIK5
Secondary accession number(s): Q3TVJ3, Q9WV45
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: July 27, 2011
Last modified: November 30, 2016
This is version 147 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.