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Protein

Probable ATP-dependent RNA helicase DDX20

Gene

DDX20

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also play a role in the metabolism of small nucleolar ribonucleoprotein (snoRNPs).1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei84ATP; via carbonyl oxygen1
Binding sitei89ATP1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi109 – 114ATP6

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: ProtInc
  • DNA binding Source: UniProtKB-KW
  • repressing transcription factor binding Source: BHF-UCL

GO - Biological processi

  • negative regulation of cell proliferation Source: Ensembl
  • negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • nuclear import Source: Reactome
  • oogenesis Source: Ensembl
  • positive regulation of apoptotic process Source: UniProtKB
  • regulation of steroid biosynthetic process Source: Ensembl
  • RNA processing Source: ProtInc
  • RNA secondary structure unwinding Source: GO_Central
  • spliceosomal snRNP assembly Source: UniProtKB
  • spliceosomal tri-snRNP complex assembly Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000064703-MONOMER.
ReactomeiR-HSA-191859. snRNP Assembly.
SIGNORiQ9UHI6.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX20 (EC:3.6.4.13)
Alternative name(s):
Component of gems 3
DEAD box protein 20
DEAD box protein DP 103
Gemin-3
Gene namesi
Name:DDX20
Synonyms:DP103, GEMIN3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:2743. DDX20.

Subcellular locationi

  • Cytoplasm
  • Nucleusgem

  • Note: Localized in subnuclear structures next to coiled bodies, called Gemini of Cajal bodies (Gems).

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytoskeleton Source: ProtInc
  • cytosol Source: UniProtKB
  • Gemini of coiled bodies Source: UniProtKB-SubCell
  • membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • RNA polymerase II transcription repressor complex Source: Ensembl
  • SMN complex Source: UniProtKB
  • SMN-Sm protein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi11218.
OpenTargetsiENSG00000064703.
PharmGKBiPA27209.

Polymorphism and mutation databases

BioMutaiDDX20.
DMDMi12643886.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550251 – 824Probable ATP-dependent RNA helicase DDX20Add BLAST824

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei48PhosphoserineCombined sources1
Modified residuei187PhosphoserineCombined sources1
Modified residuei268PhosphoserineCombined sources1
Modified residuei269PhosphoserineCombined sources1
Modified residuei500PhosphoserineCombined sources1
Modified residuei505PhosphoserineCombined sources1
Modified residuei532PhosphoserineCombined sources1
Modified residuei552PhosphothreonineCombined sources1
Modified residuei560PhosphoserineCombined sources1
Modified residuei652PhosphoserineCombined sources1
Modified residuei654PhosphoserineCombined sources1
Modified residuei656PhosphoserineCombined sources1
Modified residuei672PhosphoserineCombined sources1
Modified residuei677PhosphoserineCombined sources1
Modified residuei678PhosphoserineCombined sources1
Modified residuei688PhosphothreonineCombined sources1
Modified residuei703PhosphoserineCombined sources1
Modified residuei705PhosphothreonineCombined sources1
Modified residuei714PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9UHI6.
PaxDbiQ9UHI6.
PeptideAtlasiQ9UHI6.
PRIDEiQ9UHI6.

PTM databases

iPTMnetiQ9UHI6.
PhosphoSitePlusiQ9UHI6.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000064703.
CleanExiHS_DDX20.
ExpressionAtlasiQ9UHI6. baseline and differential.
GenevisibleiQ9UHI6. HS.

Organism-specific databases

HPAiCAB015427.
HPA005516.
HPA023541.

Interactioni

Subunit structurei

Part of the core SMN complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG. Interacts directly with GEMIN5. Interacts directly with SNUPN. Interacts with PPP4R2. Interacts with FOXL2. Interacts with EBV EBNA2 and EBNA3C. Interacts with NANOS1 and PUM2.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GEMIN4P576785EBI-347658,EBI-356700

GO - Molecular functioni

  • repressing transcription factor binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi116387. 75 interactors.
DIPiDIP-32606N.
IntActiQ9UHI6. 24 interactors.
MINTiMINT-96973.
STRINGi9606.ENSP00000358716.

Structurei

Secondary structure

1824
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi64 – 67Combined sources4
Helixi71 – 79Combined sources9
Helixi87 – 97Combined sources11
Beta strandi102 – 105Combined sources4
Helixi112 – 123Combined sources12
Beta strandi133 – 136Combined sources4
Helixi140 – 153Combined sources14
Turni154 – 156Combined sources3
Beta strandi162 – 165Combined sources4
Helixi171 – 177Combined sources7
Beta strandi182 – 186Combined sources5
Helixi188 – 196Combined sources9
Helixi202 – 204Combined sources3
Beta strandi207 – 212Combined sources6
Helixi213 – 217Combined sources5
Helixi223 – 232Combined sources10
Beta strandi238 – 244Combined sources7
Helixi248 – 254Combined sources7
Turni255 – 257Combined sources3
Beta strandi262 – 264Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OXCX-ray1.30A/B41-268[»]
3B7GX-ray1.90A/B41-268[»]
ProteinModelPortaliQ9UHI6.
SMRiQ9UHI6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UHI6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 264Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST172
Domaini299 – 448Helicase C-terminalPROSITE-ProRule annotationAdd BLAST150

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni456 – 548SMN interactingAdd BLAST93

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi62 – 90Q motifAdd BLAST29
Motifi211 – 214DEAD box4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG4284. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00860000133781.
HOGENOMiHOG000112184.
HOVERGENiHBG051330.
InParanoidiQ9UHI6.
KOiK13131.
OMAiKSHSECG.
OrthoDBiEOG091G0461.
PhylomeDBiQ9UHI6.
TreeFamiTF352222.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. 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: Q9UHI6-1) [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
MAAAFEASGA LAAVATAMPA EHVAVQVPAP EPTPGPVRIL RTAQDLSSPR
60 70 80 90 100
TRTGDVLLAE PADFESLLLS RPVLEGLRAA GFERPSPVQL KAIPLGRCGL
110 120 130 140 150
DLIVQAKSGT GKTCVFSTIA LDSLVLENLS TQILILAPTR EIAVQIHSVI
160 170 180 190 200
TAIGIKMEGL ECHVFIGGTP LSQDKTRLKK CHIAVGSPGR IKQLIELDYL
210 220 230 240 250
NPGSIRLFIL DEADKLLEEG SFQEQINWIY SSLPASKQML AVSATYPEFL
260 270 280 290 300
ANALTKYMRD PTFVRLNSSD PSLIGLKQYY KVVNSYPLAH KVFEEKTQHL
310 320 330 340 350
QELFSRIPFN QALVFSNLHS RAQHLADILS SKGFPAECIS GNMNQNQRLD
360 370 380 390 400
AMAKLKHFHC RVLISTDLTS RGIDAEKVNL VVNLDVPLDW ETYMHRIGRA
410 420 430 440 450
GRFGTLGLTV TYCCRGEEEN MMMRIAQKCN INLLPLPDPI PSGLMEECVD
460 470 480 490 500
WDVEVKAAVH TYGIASVPNQ PLKKQIQKIE RTLQIQKAHG DHMASSRNNS
510 520 530 540 550
VSGLSVKSKN NTKQKLPVKS HSECGIIEKA TSPKELGCDR QSEEQMKNSV
560 570 580 590 600
QTPVENSTNS QHQVKEALPV SLPQIPCLSS FKIHQPYTLT FAELVEDYEH
610 620 630 640 650
YIKEGLEKPV EIIRHYTGPG DQTVNPQNGF VRNKVIEQRV PVLASSSQSG
660 670 680 690 700
DSESDSDSYS SRTSSQSKGN KSYLEGSSDN QLKDSESTPV DDRISLEQPP
710 720 730 740 750
NGSDTPNPEK YQESPGIQMK TRLKEGASQR AKQSRRNLPR RSSFRLQTEA
760 770 780 790 800
QEDDWYDCHR EIRLSFSDTY QDYEEYWRAY YRAWQEYYAA ASHSYYWNAQ
810 820
RHPSWMAAYH MNTIYLQEMM HSNQ
Length:824
Mass (Da):92,241
Last modified:December 1, 2000 - v2
Checksum:i76712F014B2A0CF2
GO
Isoform 2 (identifier: Q9UHI6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     133-138: ILILAP → AELSNS
     139-824: Missing.

Note: No experimental confirmation available.
Show »
Length:138
Mass (Da):14,272
Checksum:iA3075B1CEE1AF15C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti5F → V in AAD42744 (PubMed:10383418).Curated1
Sequence conflicti279Y → C in BAA91727 (PubMed:14702039).Curated1
Sequence conflicti639R → K in AAF14544 (PubMed:10601333).Curated1
Sequence conflicti659Y → H in AAD42744 (PubMed:10383418).Curated1
Sequence conflicti676G → S in AAF14544 (PubMed:10601333).Curated1
Sequence conflicti703S → T in AAF14544 (PubMed:10601333).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_057231636I → T.1 PublicationCorresponds to variant rs197412dbSNPEnsembl.1
Natural variantiVAR_057232693R → S.Corresponds to variant rs197414dbSNPEnsembl.1
Natural variantiVAR_057233762I → T.Corresponds to variant rs85276dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_056505133 – 138ILILAP → AELSNS in isoform 2. 1 Publication6
Alternative sequenceiVSP_056506139 – 824Missing in isoform 2. 1 PublicationAdd BLAST686

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171063 mRNA. Translation: AAF14544.1.
AF106019 mRNA. Translation: AAD42744.1.
AK001506 mRNA. Translation: BAA91727.1.
AK301697 mRNA. Translation: BAG63169.1.
AL049557 Genomic DNA. Translation: CAB55686.2.
BC011556 mRNA. Translation: AAH11556.1.
AL133598 mRNA. Translation: CAB63734.2.
CCDSiCCDS842.1. [Q9UHI6-1]
PIRiT43476.
RefSeqiNP_009135.4. NM_007204.4. [Q9UHI6-1]
UniGeneiHs.591405.

Genome annotation databases

EnsembliENST00000369702; ENSP00000358716; ENSG00000064703. [Q9UHI6-1]
ENST00000533164; ENSP00000434085; ENSG00000064703. [Q9UHI6-2]
GeneIDi11218.
KEGGihsa:11218.
UCSCiuc001ebs.4. human. [Q9UHI6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171063 mRNA. Translation: AAF14544.1.
AF106019 mRNA. Translation: AAD42744.1.
AK001506 mRNA. Translation: BAA91727.1.
AK301697 mRNA. Translation: BAG63169.1.
AL049557 Genomic DNA. Translation: CAB55686.2.
BC011556 mRNA. Translation: AAH11556.1.
AL133598 mRNA. Translation: CAB63734.2.
CCDSiCCDS842.1. [Q9UHI6-1]
PIRiT43476.
RefSeqiNP_009135.4. NM_007204.4. [Q9UHI6-1]
UniGeneiHs.591405.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OXCX-ray1.30A/B41-268[»]
3B7GX-ray1.90A/B41-268[»]
ProteinModelPortaliQ9UHI6.
SMRiQ9UHI6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116387. 75 interactors.
DIPiDIP-32606N.
IntActiQ9UHI6. 24 interactors.
MINTiMINT-96973.
STRINGi9606.ENSP00000358716.

PTM databases

iPTMnetiQ9UHI6.
PhosphoSitePlusiQ9UHI6.

Polymorphism and mutation databases

BioMutaiDDX20.
DMDMi12643886.

Proteomic databases

EPDiQ9UHI6.
PaxDbiQ9UHI6.
PeptideAtlasiQ9UHI6.
PRIDEiQ9UHI6.

Protocols and materials databases

DNASUi11218.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369702; ENSP00000358716; ENSG00000064703. [Q9UHI6-1]
ENST00000533164; ENSP00000434085; ENSG00000064703. [Q9UHI6-2]
GeneIDi11218.
KEGGihsa:11218.
UCSCiuc001ebs.4. human. [Q9UHI6-1]

Organism-specific databases

CTDi11218.
DisGeNETi11218.
GeneCardsiDDX20.
HGNCiHGNC:2743. DDX20.
HPAiCAB015427.
HPA005516.
HPA023541.
MIMi606168. gene.
neXtProtiNX_Q9UHI6.
OpenTargetsiENSG00000064703.
PharmGKBiPA27209.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4284. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00860000133781.
HOGENOMiHOG000112184.
HOVERGENiHBG051330.
InParanoidiQ9UHI6.
KOiK13131.
OMAiKSHSECG.
OrthoDBiEOG091G0461.
PhylomeDBiQ9UHI6.
TreeFamiTF352222.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000064703-MONOMER.
ReactomeiR-HSA-191859. snRNP Assembly.
SIGNORiQ9UHI6.

Miscellaneous databases

EvolutionaryTraceiQ9UHI6.
GeneWikiiDDX20.
GenomeRNAii11218.
PROiQ9UHI6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000064703.
CleanExiHS_DDX20.
ExpressionAtlasiQ9UHI6. baseline and differential.
GenevisibleiQ9UHI6. HS.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDX20_HUMAN
AccessioniPrimary (citable) accession number: Q9UHI6
Secondary accession number(s): B4DWV7
, Q96F72, Q9NVM3, Q9UF59, Q9UIY0, Q9Y659
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: November 30, 2016
This is version 183 of the entry and version 2 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: 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.