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
Homo sapiens (Human)
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) (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).7 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi230 – 237ATPPROSITE-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: Ensembl
  • poly(A) RNA binding Source: UniProtKB
  • rRNA binding Source: UniProtKB
  • snoRNA binding Source: UniProtKB

GO - Biological processi

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

BioCyciZFISH:ENSG00000165732-MONOMER.
ReactomeiR-HSA-5250924. B-WICH complex positively regulates rRNA expression.

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

HGNCiHGNC:2744. DDX21.

Subcellular locationi

GO - Cellular componenti

  • membrane Source: UniProtKB
  • nucleolus Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

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)Combined 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.
TopDownProteomicsiQ9NR30-1. [Q9NR30-1]

2D gel databases

SWISS-2DPAGEQ9NR30.

PTM databases

iPTMnetiQ9NR30.
PhosphoSitePlusiQ9NR30.
SwissPalmiQ9NR30.

Expressioni

Gene expression databases

BgeeiENSG00000165732.
CleanExiHS_DDX21.
GenevisibleiQ9NR30. HS.

Organism-specific databases

HPAiHPA036592.
HPA036593.

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 (PubMed:11823437, PubMed:18180292). Interacts with WDR46 (PubMed:23848194).5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
KPNA3Q8IYQ93EBI-357942,EBI-742146
TERF2Q155542EBI-357942,EBI-706637

Protein-protein interaction databases

BioGridi114625. 140 interactors.
DIPiDIP-32941N.
IntActiQ9NR30. 52 interactors.
MINTiMINT-231639.
STRINGi9606.ENSP00000346120.

Structurei

Secondary structure

1783
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi631 – 642Combined sources12
Helixi651 – 660Combined sources10
Turni664 – 667Combined sources4
Helixi676 – 678Combined sources3
Beta strandi679 – 686Combined sources8
Helixi687 – 693Combined sources7
Beta strandi704 – 707Combined sources4

3D structure databases

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

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.
InParanoidiQ9NR30.
KOiK16911.
OMAiRFRGQRE.
OrthoDBiEOG091G04F8.
PhylomeDBiQ9NR30.
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. 3 hits.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

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.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 → I.2 PublicationsCorresponds to variant rs17556220dbSNPEnsembl.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. Translation: CAH72377.1.
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

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. Translation: CAH72377.1.
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. 140 interactors.
DIPiDIP-32941N.
IntActiQ9NR30. 52 interactors.
MINTiMINT-231639.
STRINGi9606.ENSP00000346120.

PTM databases

iPTMnetiQ9NR30.
PhosphoSitePlusiQ9NR30.
SwissPalmiQ9NR30.

Polymorphism and mutation databases

BioMutaiDDX21.
DMDMi76803555.

2D gel databases

SWISS-2DPAGEQ9NR30.

Proteomic databases

EPDiQ9NR30.
MaxQBiQ9NR30.
PaxDbiQ9NR30.
PeptideAtlasiQ9NR30.
PRIDEiQ9NR30.
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.
GeneCardsiDDX21.
H-InvDBHIX0008880.
HGNCiHGNC:2744. DDX21.
HPAiHPA036592.
HPA036593.
MIMi606357. gene.
neXtProtiNX_Q9NR30.
OpenTargetsiENSG00000165732.
PharmGKBiPA27210.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0331. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268805.
HOVERGENiHBG051331.
InParanoidiQ9NR30.
KOiK16911.
OMAiRFRGQRE.
OrthoDBiEOG091G04F8.
PhylomeDBiQ9NR30.
TreeFamiTF328622.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000165732-MONOMER.
ReactomeiR-HSA-5250924. B-WICH complex positively regulates rRNA expression.

Miscellaneous databases

ChiTaRSiDDX21. human.
GeneWikiiDDX21.
GenomeRNAii9188.
PROiQ9NR30.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165732.
CleanExiHS_DDX21.
GenevisibleiQ9NR30. HS.

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. 3 hits.
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_HUMAN
AccessioniPrimary (citable) accession number: Q9NR30
Secondary accession number(s): B2RDL0
, Q13436, Q5VX41, Q68D35
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: September 27, 2005
Last modified: November 30, 2016
This is version 181 of the entry and version 5 of the sequence. [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

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

Keywords - Technical termi

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

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  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. 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.