UniProtKB - Q9NR30 (DDX21_HUMAN)
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Protein
Nucleolar RNA helicase 2
Gene
DDX21
Organism
Homo sapiens (Human)
Status
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).8 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 230 – 237 | ATPPROSITE-ProRule annotation | 8 |
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
- miRNA binding Source: UniProtKB
- RNA binding Source: UniProtKB
- rRNA binding Source: UniProtKB
- snoRNA binding Source: UniProtKB
GO - Biological processi
- osteoblast differentiation Source: UniProtKB
- positive regulation of gene expression, epigenetic Source: Reactome
- response to exogenous dsRNA Source: Ensembl
- response to virus Source: Ensembl
- RNA secondary structure unwinding Source: GO_Central
- rRNA processing Source: UniProtKB-KW
- transcription by RNA polymerase II Source: UniProtKB
Keywordsi
Molecular function | Helicase, Hydrolase, RNA-binding |
Biological process | rRNA processing, Transcription |
Ligand | ATP-binding, Nucleotide-binding |
Enzyme and pathway databases
Reactomei | R-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 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000165732.12. |
HGNCi | HGNC:2744. DDX21. |
MIMi | 606357. gene. |
neXtProti | NX_Q9NR30. |
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 339 – 340 | DE → HG in mutant DEV; loss of helicase activity. Defects in release of P-TEFb from inhibitory 7SK snRNP. 2 Publications | 2 | |
Mutagenesisi | 375 – 376 | SA → LE in mutant SAT; ATPase defective. Defects in release of P-TEFb from inhibitory 7SK snRNP. 2 Publications | 2 |
Organism-specific databases
DisGeNETi | 9188. |
OpenTargetsi | ENSG00000165732. |
PharmGKBi | PA27210. |
Polymorphism and mutation databases
BioMutai | DDX21. |
DMDMi | 76803555. |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000055027 | 1 – 783 | Nucleolar RNA helicase 2Add BLAST | 783 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length | |
---|---|---|---|---|---|
Modified residuei | 7 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 13 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 71 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 89 | PhosphoserineCombined sources | 1 | ||
Cross-linki | 116 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources | |||
Cross-linki | 116 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources | |||
Modified residuei | 121 | PhosphoserineCombined sources1 Publication | 1 | ||
Modified residuei | 147 | PhosphoserineBy similarity | 1 | ||
Modified residuei | 164 | PhosphoserineBy similarity | 1 | ||
Modified residuei | 171 | PhosphoserineBy similarity | 1 | ||
Modified residuei | 173 | PhosphoserineBy similarity | 1 | ||
Modified residuei | 296 | PhosphothreonineCombined sources | 1 | ||
Modified residuei | 567 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 779 | N6-acetyllysineCombined sources | 1 | ||
Isoform 2 (identifier: Q9NR30-2) | |||||
Modified residuei | 1 | N-acetylmethionineCombined sources | 1 |
Keywords - PTMi
Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q9NR30. |
MaxQBi | Q9NR30. |
PaxDbi | Q9NR30. |
PeptideAtlasi | Q9NR30. |
PRIDEi | Q9NR30. |
TopDownProteomicsi | Q9NR30-1. [Q9NR30-1] |
2D gel databases
SWISS-2DPAGEi | Q9NR30. |
PTM databases
iPTMneti | Q9NR30. |
PhosphoSitePlusi | Q9NR30. |
SwissPalmi | Q9NR30. |
Expressioni
Gene expression databases
Bgeei | ENSG00000165732. |
CleanExi | HS_DDX21. |
Genevisiblei | Q9NR30. HS. |
Organism-specific databases
HPAi | HPA036592. 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
Protein-protein interaction databases
BioGridi | 114625. 155 interactors. |
CORUMi | Q9NR30. |
DIPi | DIP-32941N. |
IntActi | Q9NR30. 78 interactors. |
MINTi | Q9NR30. |
STRINGi | 9606.ENSP00000346120. |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more detailsFeature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Beta strandi | 631 – 642 | Combined sources | 12 | |
Helixi | 651 – 660 | Combined sources | 10 | |
Turni | 664 – 667 | Combined sources | 4 | |
Helixi | 676 – 678 | Combined sources | 3 | |
Beta strandi | 679 – 686 | Combined sources | 8 | |
Helixi | 687 – 693 | Combined sources | 7 | |
Beta strandi | 704 – 707 | Combined sources | 4 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2M3D | NMR | - | A | 617-710 | [»] | |
ProteinModelPortali | Q9NR30. | |||||
SMRi | Q9NR30. | |||||
ModBasei | Search... | |||||
MobiDBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 217 – 396 | Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST | 180 | |
Domaini | 429 – 573 | Helicase C-terminalPROSITE-ProRule annotationAdd BLAST | 145 | |
Repeati | 724 – 728 | 1 | 5 | |
Repeati | 734 – 738 | 2 | 5 | |
Repeati | 744 – 748 | 3 | 5 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 724 – 748 | 3 X 5 AA repeatsAdd BLAST | 25 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 186 – 214 | Q motifPROSITE-ProRule annotationAdd BLAST | 29 | |
Motifi | 339 – 342 | DEAD boxPROSITE-ProRule annotation | 4 |
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
RepeatPhylogenomic databases
eggNOGi | KOG0331. Eukaryota. COG0513. LUCA. |
GeneTreei | ENSGT00900000140856. |
HOGENOMi | HOG000268805. |
HOVERGENi | HBG051331. |
InParanoidi | Q9NR30. |
KOi | K16911. |
OMAi | RFRGQRE. |
OrthoDBi | EOG091G04F8. |
PhylomeDBi | Q9NR30. |
TreeFami | TF328622. |
Family and domain databases
CDDi | cd00079. HELICc. 1 hit. |
InterProi | View 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. |
Pfami | View protein in Pfam PF00270. DEAD. 1 hit. PF08152. GUCT. 1 hit. PF00271. Helicase_C. 1 hit. |
SMARTi | View protein in SMART SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. |
SUPFAMi | SSF52540. SSF52540. 3 hits. SSF54928. SSF54928. 1 hit. |
PROSITEi | View protein in PROSITE PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51195. Q_MOTIF. 1 hit. |
s (2)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative 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.
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
Sequence cautioni
The sequence AAB02546 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 273 | A → C in AAF78930 (PubMed:11237763).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_052161 | 27 | T → I2 PublicationsCorresponds to variant dbSNP:rs17556220Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_015716 | 1 – 68 | Missing in isoform 2. 2 PublicationsAdd BLAST | 68 |
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 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. |
CCDSi | CCDS31211.1. [Q9NR30-1] CCDS73144.1. [Q9NR30-2] |
PIRi | PC6010. |
RefSeqi | NP_001243839.1. NM_001256910.1. [Q9NR30-2] NP_004719.2. NM_004728.3. [Q9NR30-1] |
UniGenei | Hs.223141. |
Genome annotation databases
Ensembli | ENST00000354185; ENSP00000346120; ENSG00000165732. [Q9NR30-1] ENST00000620315; ENSP00000480334; ENSG00000165732. [Q9NR30-2] |
GeneIDi | 9188. |
KEGGi | hsa:9188. |
UCSCi | uc001jov.3. human. [Q9NR30-1] |
Keywords - Coding sequence diversityi
Alternative splicing, PolymorphismSimilar proteinsi
Entry informationi
Entry namei | DDX21_HUMAN | |
Accessioni | Q9NR30Primary (citable) accession number: Q9NR30 Secondary accession number(s): B2RDL0 Q68D35 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 27, 2001 |
Last sequence update: | September 27, 2005 | |
Last modified: | March 28, 2018 | |
This is version 193 of the entry and version 5 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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. |