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Protein

Nucleolar RNA helicase 2

Gene

DDX21

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). 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 (PubMed:25470060, PubMed:25477391). 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 (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292). May bind to specific miRNA hairpins (PubMed:28431233). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1 (By similarity).By similarity8 Publications

Miscellaneous

Autoantibodies against DDX21 are found in patients with watermelon stomach disease, which is characterized by prominent stripes of ectatic vascular tissue in the stomach similar to stripes on a watermelon.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi230 – 237ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processAntiviral defense, Immunity, Innate immunity, rRNA processing, Transcription
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleolar RNA helicase 2Curated (EC:3.6.4.131 Publication)
Alternative name(s):
DEAD box protein 21
Gu-alpha
Nucleolar RNA helicase Gu
Nucleolar RNA helicase II
RH II/Gu
Gene namesi
Name:DDX21
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

EuPathDBiHostDB:ENSG00000165732.12
HGNCiHGNC:2744 DDX21
MIMi606357 gene
neXtProtiNX_Q9NR30

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi339 – 340DE → HG in mutant DEV; loss of helicase activity. Defects in release of P-TEFb from inhibitory 7SK snRNP. 2 Publications2
Mutagenesisi375 – 376SA → LE in mutant SAT; ATPase defective. Defects in release of P-TEFb from inhibitory 7SK snRNP. 2 Publications2

Organism-specific databases

DisGeNETi9188
OpenTargetsiENSG00000165732
PharmGKBiPA27210

Polymorphism and mutation databases

BioMutaiDDX21
DMDMi76803555

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550271 – 783Nucleolar RNA helicase 2Add BLAST783

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei7PhosphoserineCombined sources1
Modified residuei13PhosphoserineCombined sources1
Modified residuei71PhosphoserineCombined sources1
Modified residuei89PhosphoserineCombined sources1
Cross-linki116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei121PhosphoserineCombined sources1 Publication1
Modified residuei147PhosphoserineBy similarity1
Modified residuei164PhosphoserineBy similarity1
Modified residuei171PhosphoserineBy similarity1
Modified residuei173PhosphoserineBy similarity1
Modified residuei296PhosphothreonineCombined sources1
Modified residuei567PhosphoserineCombined sources1
Modified residuei779N6-acetyllysineCombined sources1
Isoform 2 (identifier: Q9NR30-2)
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9NR30
MaxQBiQ9NR30
PaxDbiQ9NR30
PeptideAtlasiQ9NR30
PRIDEiQ9NR30
ProteomicsDBi82265
82266 [Q9NR30-2]
TopDownProteomicsiQ9NR30-1 [Q9NR30-1]

2D gel databases

SWISS-2DPAGEiQ9NR30

PTM databases

iPTMnetiQ9NR30
PhosphoSitePlusiQ9NR30
SwissPalmiQ9NR30

Expressioni

Gene expression databases

BgeeiENSG00000165732 Expressed in 234 organ(s), highest expression level in layer of synovial tissue
CleanExiHS_DDX21
GenevisibleiQ9NR30 HS

Organism-specific databases

HPAiHPA036592
HPA036593

Interactioni

Subunit structurei

Homodimer; homodimerizes via its N-terminus. Found in a multi-helicase-TICAM1 complex at least composed of DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells with or without poly(I:C) RNA ligand stimulation. Interacts (via C-terminus) with TICAM1 (via TIR domain). Interacts with DHX36 (via C-terminus); this interaction serves as bridges to TICAM1. Interacts (via C-terminus) with DDX1 (via B30.2/SPRY domain); this interaction serves as bridges to TICAM1. 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). 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 (PubMed:11823437, PubMed:18180292). Interacts with WDR46 (PubMed:23848194).By similarity5 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114625, 233 interactors
ComplexPortaliCPX-1099 B-WICH chromatin remodelling complex
CORUMiQ9NR30
DIPiDIP-32941N
IntActiQ9NR30, 69 interactors
MINTiQ9NR30
STRINGi9606.ENSP00000346120

Structurei

Secondary structure

1783
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9NR30
SMRiQ9NR30
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini217 – 396Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST180
Domaini429 – 573Helicase C-terminalPROSITE-ProRule annotationAdd BLAST145
Repeati724 – 72815
Repeati734 – 73825
Repeati744 – 74835

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni724 – 7483 X 5 AA repeatsAdd BLAST25

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi186 – 214Q motifPROSITE-ProRule annotationAdd BLAST29
Motifi339 – 342DEAD boxPROSITE-ProRule annotation4

Domaini

The helicase and foldase activities reside in two separate domains, the helicase in the N-terminus and the foldase in the C-terminus.1 Publication
The 3 X 5 AA repeats seem to be critical for the RNA folding activity.By similarity

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0331 Eukaryota
COG0513 LUCA
GeneTreeiENSGT00930000150858
HOGENOMiHOG000268805
HOVERGENiHBG051331
InParanoidiQ9NR30
KOiK16911
OMAiLPCNRAA
OrthoDBiEOG091G04F8
PhylomeDBiQ9NR30
TreeFamiTF328622

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR012562 GUCT
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR035979 RBD_domain_sf
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF08152 GUCT, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
SSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q9NR30-1) [UniParc]FASTAAdd to basket

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.

« Hide
        10         20         30         40         50
MPGKLRSDAG LESDTAMKKG ETLRKQTEEK EKKEKPKSDK TEEIAEEEET
60 70 80 90 100
VFPKAKQVKK KAEPSEVDMN SPKSKKAKKK EEPSQNDISP KTKSLRKKKE
110 120 130 140 150
PIEKKVVSSK TKKVTKNEEP SEEEIDAPKP KKMKKEKEMN GETREKSPKL
160 170 180 190 200
KNGFPHPEPD CNPSEAASEE SNSEIEQEIP VEQKEGAFSN FPISEETIKL
210 220 230 240 250
LKGRGVTFLF PIQAKTFHHV YSGKDLIAQA RTGTGKTFSF AIPLIEKLHG
260 270 280 290 300
ELQDRKRGRA PQVLVLAPTR ELANQVSKDF SDITKKLSVA CFYGGTPYGG
310 320 330 340 350
QFERMRNGID ILVGTPGRIK DHIQNGKLDL TKLKHVVLDE VDQMLDMGFA
360 370 380 390 400
DQVEEILSVA YKKDSEDNPQ TLLFSATCPH WVFNVAKKYM KSTYEQVDLI
410 420 430 440 450
GKKTQKTAIT VEHLAIKCHW TQRAAVIGDV IRVYSGHQGR TIIFCETKKE
460 470 480 490 500
AQELSQNSAI KQDAQSLHGD IPQKQREITL KGFRNGSFGV LVATNVAARG
510 520 530 540 550
LDIPEVDLVI QSSPPKDVES YIHRSGRTGR AGRTGVCICF YQHKEEYQLV
560 570 580 590 600
QVEQKAGIKF KRIGVPSATE IIKASSKDAI RLLDSVPPTA ISHFKQSAEK
610 620 630 640 650
LIEEKGAVEA LAAALAHISG ATSVDQRSLI NSNVGFVTMI LQCSIEMPNI
660 670 680 690 700
SYAWKELKEQ LGEEIDSKVK GMVFLKGKLG VCFDVPTASV TEIQEKWHDS
710 720 730 740 750
RRWQLSVATE QPELEGPREG YGGFRGQREG SRGFRGQRDG NRRFRGQREG
760 770 780
SRGPRGQRSG GGNKSNRSQN KGQKRSFSKA FGQ
Length:783
Mass (Da):87,344
Last modified:September 27, 2005 - v5
Checksum:i4F6673E38686644F
GO
Isoform 2 (identifier: Q9NR30-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-68: Missing.

Show »
Length:715
Mass (Da):79,657
Checksum:i8CB8E8BE914EA9DB
GO

Sequence cautioni

The sequence AAB02546 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti273A → C in AAF78930 (PubMed:11237763).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05216127T → I2 PublicationsCorresponds to variant dbSNP:rs17556220Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0157161 – 68Missing in isoform 2. 2 PublicationsAdd BLAST68

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41387 mRNA Translation: AAB02546.1 Different initiation.
AF261903 Genomic DNA No translation available.
AF261917
, AF261904, AF261905, AF261906, AF261907, AF261908, AF261909, AF261910, AF261911, AF261912, AF261913, AF261914, AF261915, AF261916 Genomic DNA Translation: AAF78930.2
AK315585 mRNA Translation: BAG37957.1
CR749598 mRNA Translation: CAH18395.1
AL359844 Genomic DNA No translation available.
CH471083 Genomic DNA Translation: EAW54307.1
BC008071 mRNA Translation: AAH08071.2
CCDSiCCDS31211.1 [Q9NR30-1]
CCDS73144.1 [Q9NR30-2]
PIRiPC6010
RefSeqiNP_001243839.1, NM_001256910.1 [Q9NR30-2]
NP_004719.2, NM_004728.3 [Q9NR30-1]
UniGeneiHs.223141

Genome annotation databases

EnsembliENST00000354185; ENSP00000346120; ENSG00000165732 [Q9NR30-1]
ENST00000620315; ENSP00000480334; ENSG00000165732 [Q9NR30-2]
GeneIDi9188
KEGGihsa:9188
UCSCiuc001jov.3 human [Q9NR30-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41387 mRNA Translation: AAB02546.1 Different initiation.
AF261903 Genomic DNA No translation available.
AF261917
, AF261904, AF261905, AF261906, AF261907, AF261908, AF261909, AF261910, AF261911, AF261912, AF261913, AF261914, AF261915, AF261916 Genomic DNA Translation: AAF78930.2
AK315585 mRNA Translation: BAG37957.1
CR749598 mRNA Translation: CAH18395.1
AL359844 Genomic DNA No translation available.
CH471083 Genomic DNA Translation: EAW54307.1
BC008071 mRNA Translation: AAH08071.2
CCDSiCCDS31211.1 [Q9NR30-1]
CCDS73144.1 [Q9NR30-2]
PIRiPC6010
RefSeqiNP_001243839.1, NM_001256910.1 [Q9NR30-2]
NP_004719.2, NM_004728.3 [Q9NR30-1]
UniGeneiHs.223141

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M3DNMR-A617-710[»]
ProteinModelPortaliQ9NR30
SMRiQ9NR30
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114625, 233 interactors
ComplexPortaliCPX-1099 B-WICH chromatin remodelling complex
CORUMiQ9NR30
DIPiDIP-32941N
IntActiQ9NR30, 69 interactors
MINTiQ9NR30
STRINGi9606.ENSP00000346120

PTM databases

iPTMnetiQ9NR30
PhosphoSitePlusiQ9NR30
SwissPalmiQ9NR30

Polymorphism and mutation databases

BioMutaiDDX21
DMDMi76803555

2D gel databases

SWISS-2DPAGEiQ9NR30

Proteomic databases

EPDiQ9NR30
MaxQBiQ9NR30
PaxDbiQ9NR30
PeptideAtlasiQ9NR30
PRIDEiQ9NR30
ProteomicsDBi82265
82266 [Q9NR30-2]
TopDownProteomicsiQ9NR30-1 [Q9NR30-1]

Protocols and materials databases

DNASUi9188
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000354185; ENSP00000346120; ENSG00000165732 [Q9NR30-1]
ENST00000620315; ENSP00000480334; ENSG00000165732 [Q9NR30-2]
GeneIDi9188
KEGGihsa:9188
UCSCiuc001jov.3 human [Q9NR30-1]

Organism-specific databases

CTDi9188
DisGeNETi9188
EuPathDBiHostDB:ENSG00000165732.12
GeneCardsiDDX21
H-InvDBiHIX0008880
HGNCiHGNC:2744 DDX21
HPAiHPA036592
HPA036593
MIMi606357 gene
neXtProtiNX_Q9NR30
OpenTargetsiENSG00000165732
PharmGKBiPA27210
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0331 Eukaryota
COG0513 LUCA
GeneTreeiENSGT00930000150858
HOGENOMiHOG000268805
HOVERGENiHBG051331
InParanoidiQ9NR30
KOiK16911
OMAiLPCNRAA
OrthoDBiEOG091G04F8
PhylomeDBiQ9NR30
TreeFamiTF328622

Enzyme and pathway databases

ReactomeiR-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Miscellaneous databases

ChiTaRSiDDX21 human
GeneWikiiDDX21
GenomeRNAii9188
PROiPR:Q9NR30
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165732 Expressed in 234 organ(s), highest expression level in layer of synovial tissue
CleanExiHS_DDX21
GenevisibleiQ9NR30 HS

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR012562 GUCT
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR035979 RBD_domain_sf
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF08152 GUCT, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
SSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDDX21_HUMAN
AccessioniPrimary (citable) accession number: Q9NR30
Secondary accession number(s): B2RDL0
, Q13436, Q5VX41, Q68D35
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: September 27, 2005
Last modified: November 7, 2018
This is version 200 of the entry and version 5 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
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