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Protein

ATP-dependent RNA helicase ddx6

Gene

ddx6

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent RNA helicase that is an integral component of messenger ribonucleoprotein complexes (mRNPs), storage particles that mask maternal mRNAs from the translational apparatus during oocyte maturation.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi139 – 1468ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: UniProtKB
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Helicase, Hydrolase, Ribonucleoprotein

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase ddx6 (EC:3.6.4.13)
Alternative name(s):
ATP-dependent RNA helicase p54
Short name:
P54H
Short name:
Xp54
DEAD box protein 6
Gene namesi
Name:ddx6
Synonyms:p54h
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-922237. ddx6.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus 1 Publication

  • Note: Mostly cytoplasmic.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 481481ATP-dependent RNA helicase ddx6PRO_0000054985Add
BLAST

Proteomic databases

PRIDEiP54824.

Expressioni

Tissue specificityi

In adults, expression is restricted to the germline cells of the ovary.1 Publication

Developmental stagei

Expressed maternally. Expression peaks at stage I of oogenesis and remains fairly constant through to the end of oogenesis and, after fertilization, up to blastula. From blastula, through gastrula and neurula, expression declines significantly. May also be expressed zygotically since a low level of expression is detected up to the free-feeding tadpole stage (embryonic stage 42) (at protein level).2 Publications

Interactioni

Subunit structurei

Component of a ribonucleoprotein (RNP) complex, composed at least of cpeb1, lsm14b/rap55b, ddx6/Xp54, ybx2/frgy2, pat1/P100, eif4enif1/4E-T and eif4e1b. Component of a ribonucleoprotein (RNP) complex, composed at least of elavl1/elrA and/or elavl2/elrB, igf2bp3/vg1RBP, ddx6/Xp54, ybx2/frgy2, lsm14b/rap55b and, in a subset of RNP complexes, stau1/staufen. Component of a ribonucleoprotein (RNP) complex, composed at least of lsm14a/rap55a, ybx2/frgy2, ddx6/Xp54 and eif4enif1/4E-T. Interacts with lsm14a/rap55a.4 Publications

Protein-protein interaction databases

BioGridi100406. 1 interaction.
IntActiP54824. 2 interactions.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini126 – 297172Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini307 – 467161Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi95 – 12329Q motifAdd
BLAST
Motifi245 – 2484DEAD box

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG106685.
KOiK12614.

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]

Sequencei

Sequence statusi: Complete.

P54824-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTARTENPV LMGMSSQNGQ LRGPLKPSAG PGGGGTQTQQ INQLKNASTI
60 70 80 90 100
NSGSQQQAQS MSSIIKPGDD WKKTLKLPPK DLRIKTSDVT STKGNEFEDY
110 120 130 140 150
CLKRELLMGI FEMGWEKPSP IQEESIPIAL SGRDILARAK NGTGKSGAYL
160 170 180 190 200
IPLLERLDLK KDCIQAMVIV PTRELALQVS QICIQVSKHM GGAKVMATTG
210 220 230 240 250
GTNLRDDIMR LDDTVHVVIA TPGRILDLIK KGVAKVDHIQ MIVLDEADKL
260 270 280 290 300
LSQDFMQIME DIIMTLPKNR QILLYSATFP LSVQKFMTLH LQKPYEINLM
310 320 330 340 350
EELTLKGVTQ YYAYVTERQK VHCLNTLFSR LQINQSIIFC NSSQRVELLA
360 370 380 390 400
KKISQLGYSC FYIHAKMRQE HRNRVFHDFR NGLCRNLVCT DLFTRGIDIQ
410 420 430 440 450
AVNVVINFDF PKLAETYLHR IGRSGRFGHL GLAINLITYD DRFNLKSIEE
460 470 480
QLGTEIKPIP SSIDKNLYVA EYHSESGEDK P
Length:481
Mass (Da):54,074
Last modified:February 9, 2010 - v2
Checksum:i3CB5516F707C7C3D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti146 – 1461S → T in CAA63149 (PubMed:9023105).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92421 mRNA. Translation: CAA63149.1.
BC170228 mRNA. Translation: AAI70228.1.
BC170230 mRNA. Translation: AAI70230.1.
RefSeqiNP_001083721.1. NM_001090252.1.
UniGeneiXl.157.

Genome annotation databases

GeneIDi399080.
KEGGixla:399080.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92421 mRNA. Translation: CAA63149.1.
BC170228 mRNA. Translation: AAI70228.1.
BC170230 mRNA. Translation: AAI70230.1.
RefSeqiNP_001083721.1. NM_001090252.1.
UniGeneiXl.157.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi100406. 1 interaction.
IntActiP54824. 2 interactions.

Proteomic databases

PRIDEiP54824.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi399080.
KEGGixla:399080.

Organism-specific databases

CTDi1656.
XenbaseiXB-GENE-922237. ddx6.

Phylogenomic databases

HOVERGENiHBG106685.
KOiK12614.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes."
    Ladomery M.R., Wade E., Sommerville J.
    Nucleic Acids Res. 25:965-973(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 114-122 AND 368-377, FUNCTION, SUBCELLULAR LOCATION, IDENTIFICATION IN A RIBONUCLEOPROTEIN COMPLEX WITH YBX2, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Tissue: Oocyte.
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (NOV-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes."
    Tanaka K.J., Ogawa K., Takagi M., Imamoto N., Matsumoto K., Tsujimoto M.
    J. Biol. Chem. 281:40096-40106(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A RIBONUCLEOPROTEIN COMPLEX WITH LSM14A; YBX2 AND EIF4ENIF1, INTERACTION WITH LSM14A.
  4. "CPEB interacts with an ovary-specific eIF4E and 4E-T in early Xenopus oocytes."
    Minshall N., Reiter M.H., Weil D., Standart N.
    J. Biol. Chem. 282:37389-37401(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A RIBONUCLEOPROTEIN COMPLEX WITH CPEB1; PAT1; LSM14B; EIF4ENIF1; EIF4E1B AND YBX2, DEVELOPMENTAL STAGE.
  5. "Participation of Xenopus Elr-type proteins in vegetal mRNA localization during oogenesis."
    Arthur P.K., Claussen M., Koch S., Tarbashevich K., Jahn O., Pieler T.
    J. Biol. Chem. 284:19982-19992(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A RIBONUCLEOPROTEIN COMPLEX WITH ELAVL1; ELAVL2; IGF2BP3; STAU1; LSM14B AND YBX2.

Entry informationi

Entry nameiDDX6_XENLA
AccessioniPrimary (citable) accession number: P54824
Secondary accession number(s): B7ZRN4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: February 9, 2010
Last modified: May 11, 2016
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Direct protein sequencing

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.