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Protein

Nucleolar RNA helicase 2

Gene

Ddx21

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi226 – 2338ATPPROSITE-ProRule annotation

GO - Molecular functioni

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

ReactomeiR-RNO-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
Synonyms:Ddx21a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 20

Organism-specific databases

RGDi1307306. 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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 782782Nucleolar RNA helicase 2PRO_0000282712Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei13 – 131PhosphoserineBy similarity
Modified residuei39 – 391N6-acetyllysineBy similarity
Modified residuei119 – 1191PhosphoserineBy similarity
Modified residuei145 – 1451PhosphoserineBy similarity
Modified residuei169 – 1691PhosphoserineBy similarity
Modified residuei292 – 2921PhosphothreonineBy similarity
Modified residuei563 – 5631PhosphoserineBy similarity
Modified residuei778 – 7781N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ3B8Q1.
PRIDEiQ3B8Q1.

PTM databases

iPTMnetiQ3B8Q1.
PhosphoSiteiQ3B8Q1.

Expressioni

Gene expression databases

GenevisibleiQ3B8Q1. RN.

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

STRINGi10116.ENSRNOP00000063494.

Structurei

3D structure databases

ProteinModelPortaliQ3B8Q1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini213 – 392180Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini425 – 569145Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST
Repeati720 – 72451
Repeati731 – 73552
Repeati741 – 74773

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni720 – 747283 X 5 AA repeatsAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi182 – 21029Q motifPROSITE-ProRule annotationAdd
BLAST
Motifi335 – 3384DEAD boxPROSITE-ProRule annotation

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.
GeneTreeiENSGT00840000129877.
HOGENOMiHOG000268805.
HOVERGENiHBG051331.
InParanoidiQ3B8Q1.
KOiK16911.
OMAiEHLAINC.
OrthoDBiEOG77HDD6.
PhylomeDBiQ3B8Q1.
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.

Q3B8Q1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPGKLRSASK SESEGTEESM ETLQKPSEKK TRKEKPKSKT DEATEGVEEA
60 70 80 90 100
ASSKVKAVKK KGPSEDDVGP PKSKKAKKQE EEPQDDPASK SKTSKKKKEP
110 120 130 140 150
LEKKAPSAKT KEMKAEEPSE EEADAPKPKK TKKGKEANGD VGEKSPGLKN
160 170 180 190 200
GLSHPKPDSS STQAPGEESE TEKEIPVEQK EGAFSNFPIS EETVKLLKAR
210 220 230 240 250
GVNFLFPIQA KTFHHVYSGK DLIAQARTGT GKTFSFAIPL IEKLQGGLQE
260 270 280 290 300
RKRGRAPQVL VLAPTRELAN QVSKDFSDIT KKLSVACFYG GTPYGGQIER
310 320 330 340 350
MRSGIDILVG TPGRIKDHLQ NGKLDLTKLK HVVLDEVDQM LDMGFADQVE
360 370 380 390 400
EILCVAYKKD SEDNPQTLLF SATCPHWVFN VAKKYMKSTY EQVDLIGKKT
410 420 430 440 450
QKAAITVEHL AIKCHWTERA AVIGDVIRVY SGHQGRTIIF CETKKDAQEL
460 470 480 490 500
SQNTCIKQDA QSLHGDIPQK QREITLKGFR NGNFGVLVAT NVAARGLDIP
510 520 530 540 550
EVDLVVQSCP PKDVESYIHR SGRTGRAGRT GVCICFYQHK EEYQLAQVEQ
560 570 580 590 600
KAGIKFKRIG VPSATEIIKA SSKDAIRLLD SVPPTAIGHF KQSAEKLIEE
610 620 630 640 650
KGAVEALAAA LAHISGATSV DQRSLINSQA GFVTMILRCS VEMPNISYAW
660 670 680 690 700
KELKEQLGES IDAKVKGMVF LKGKLGVCFD VRTEAVTEIK EKWHDSRRWQ
710 720 730 740 750
LTVATEQPEL EGPPEGYRGG RGQRDGSRGS FRGQRGGSRN FRGQGQRGGS
760 770 780
RNFRGQRPGG GNKSNRSPNK GQKRSFSKAF GQ
Length:782
Mass (Da):85,966
Last modified:November 22, 2005 - v1
Checksum:iFD8074E373921621
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC105878 mRNA. Translation: AAI05879.1.
RefSeqiNP_001032278.1. NM_001037201.1.
UniGeneiRn.162310.
Rn.201790.

Genome annotation databases

EnsembliENSRNOT00000068184; ENSRNOP00000063494; ENSRNOG00000043099.
GeneIDi317399.
KEGGirno:317399.
UCSCiRGD:1307306. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC105878 mRNA. Translation: AAI05879.1.
RefSeqiNP_001032278.1. NM_001037201.1.
UniGeneiRn.162310.
Rn.201790.

3D structure databases

ProteinModelPortaliQ3B8Q1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000063494.

PTM databases

iPTMnetiQ3B8Q1.
PhosphoSiteiQ3B8Q1.

Proteomic databases

PaxDbiQ3B8Q1.
PRIDEiQ3B8Q1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000068184; ENSRNOP00000063494; ENSRNOG00000043099.
GeneIDi317399.
KEGGirno:317399.
UCSCiRGD:1307306. rat.

Organism-specific databases

CTDi9188.
RGDi1307306. Ddx21.

Phylogenomic databases

eggNOGiKOG0331. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00840000129877.
HOGENOMiHOG000268805.
HOVERGENiHBG051331.
InParanoidiQ3B8Q1.
KOiK16911.
OMAiEHLAINC.
OrthoDBiEOG77HDD6.
PhylomeDBiQ3B8Q1.
TreeFamiTF328622.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ3B8Q1.

Gene expression databases

GenevisibleiQ3B8Q1. RN.

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...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.

Entry informationi

Entry nameiDDX21_RAT
AccessioniPrimary (citable) accession number: Q3B8Q1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: November 22, 2005
Last modified: June 8, 2016
This is version 95 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.