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Protein

ATP-dependent RNA helicase DDX3Y

Gene

DDX3Y

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

Functioni

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi198 – 2058ATPPROSITE-ProRule annotation
Nucleotide bindingi222 – 2298ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BRENDAi3.6.4.13. 2681.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DDX3Y (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 3, Y-chromosomal
Gene namesi
Name:DDX3Y
Synonyms:DBY
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome Y

Organism-specific databases

HGNCiHGNC:2699. DDX3Y.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus 1 Publication

  • Note: Shuttles between the nucleus and the cytoplasm in an XPO1-dependent manner.

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytoplasmic ribonucleoprotein granule Source: GO_Central
  • membrane Source: UniProtKB
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

DDX3Y is located in the 'azoospermia factor a' (AZFa) region on chromosome Y which is deleted in Sertoli cell-only syndrome. This is an infertility disorder in which no germ cells are visible in seminiferous tubules leading to azoospermia.

Organism-specific databases

MalaCardsiDDX3Y.
Orphaneti1646. Partial chromosome Y deletion.
PharmGKBiPA27168.

Polymorphism and mutation databases

BioMutaiDDX3Y.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 660659ATP-dependent RNA helicase DDX3YPRO_0000055011Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei55 – 551N6-acetyllysineBy similarity
Modified residuei101 – 1011PhosphoserineBy similarity
Modified residuei103 – 1031PhosphotyrosineBy similarity
Modified residuei129 – 1291PhosphoserineBy similarity
Modified residuei181 – 1811PhosphoserineBy similarity
Cross-linki213 – 213Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei454 – 4541PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO15523.
MaxQBiO15523.
PaxDbiO15523.
PRIDEiO15523.

PTM databases

iPTMnetiO15523.
PhosphoSiteiO15523.
SwissPalmiO15523.

Expressioni

Tissue specificityi

Testis-specific. Expressed predominantly in spermatogonia.1 Publication

Gene expression databases

BgeeiO15523.
CleanExiHS_DDX3Y.
ExpressionAtlasiO15523. baseline and differential.
GenevisibleiO15523. HS.

Organism-specific databases

HPAiHPA005631.

Interactioni

Subunit structurei

May interact with TDRD3.

Protein-protein interaction databases

BioGridi114204. 18 interactions.
IntActiO15523. 16 interactions.
MINTiMINT-2999090.
STRINGi9606.ENSP00000336725.

Structurei

3D structure databases

ProteinModelPortaliO15523.
SMRiO15523. Positions 133-574.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini209 – 401193Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini412 – 573162Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi178 – 20629Q motifAdd
BLAST
Motifi345 – 3484DEAD box

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG0335. Eukaryota.
ENOG410XNTI. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000268804.
HOVERGENiHBG015893.
InParanoidiO15523.
KOiK17642.
OMAiPNPFANT.
OrthoDBiEOG7B5WV8.
PhylomeDBiO15523.
TreeFamiTF300364.

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 (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O15523-1) [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
MSHVVVKNDP ELDQQLANLD LNSEKQSGGA STASKGRYIP PHLRNREASK
60 70 80 90 100
GFHDKDSSGW SCSKDKDAYS SFGSRDSRGK PGYFSERGSG SRGRFDDRGR
110 120 130 140 150
SDYDGIGNRE RPGFGRFERS GHSRWCDKSV EDDWSKPLPP SERLEQELFS
160 170 180 190 200
GGNTGINFEK YDDIPVEATG SNCPPHIENF SDIDMGEIIM GNIELTRYTR
210 220 230 240 250
PTPVQKHAIP IIKGKRDLMA CAQTGSGKTA AFLLPILSQI YTDGPGEALK
260 270 280 290 300
AVKENGRYGR RKQYPISLVL APTRELAVQI YEEARKFSYR SRVRPCVVYG
310 320 330 340 350
GADIGQQIRD LERGCHLLVA TPGRLVDMME RGKIGLDFCK YLVLDEADRM
360 370 380 390 400
LDMGFEPQIR RIVEQDTMPP KGVRHTMMFS ATFPKEIQML ARDFLDEYIF
410 420 430 440 450
LAVGRVGSTS ENITQKVVWV EDLDKRSFLL DILGATGSDS LTLVFVETKK
460 470 480 490 500
GADSLEDFLY HEGYACTSIH GDRSQRDREE ALHQFRSGKS PILVATAVAA
510 520 530 540 550
RGLDISNVRH VINFDLPSDI EEYVHRIGRT GRVGNLGLAT SFFNEKNMNI
560 570 580 590 600
TKDLLDLLVE AKQEVPSWLE NMAYEHHYKG GSRGRSKSNR FSGGFGARDY
610 620 630 640 650
RQSSGSSSSG FGASRGSSSR SGGGGYGNSR GFGGGGYGGF YNSDGYGGNY
660
NSQGVDWWGN
Length:660
Mass (Da):73,154
Last modified:August 16, 2005 - v2
Checksum:i0C370E9367952AB6
GO
Isoform 2 (identifier: O15523-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-15: MSHVVVKNDPELDQQ → MEIGRPRKDTWK

Note: No experimental confirmation available.
Show »
Length:657
Mass (Da):72,931
Checksum:iD31DEC552AAF75DB
GO
Isoform 3 (identifier: O15523-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     287-291: FSYRS → VKYSF
     292-660: Missing.

Note: No experimental confirmation available.
Show »
Length:291
Mass (Da):32,416
Checksum:iB8B67E2C8E5C208B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti46 – 461R → K in AAC51832 (PubMed:9381176).Curated
Sequence conflicti46 – 461R → K in AAC51831 (PubMed:9381176).Curated
Sequence conflicti219 – 2191M → V in AAC51832 (PubMed:9381176).Curated
Sequence conflicti219 – 2191M → V in AAC51831 (PubMed:9381176).Curated
Sequence conflicti628 – 6281N → D in AAC51832 (PubMed:9381176).Curated
Sequence conflicti628 – 6281N → D in AAC51831 (PubMed:9381176).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1515MSHVV…ELDQQ → MEIGRPRKDTWK in isoform 2. 1 PublicationVSP_055456Add
BLAST
Alternative sequencei287 – 2915FSYRS → VKYSF in isoform 3. 1 PublicationVSP_055457
Alternative sequencei292 – 660369Missing in isoform 3. 1 PublicationVSP_055458Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000985 mRNA. Translation: AAC51832.1.
AF000984 mRNA. Translation: AAC51831.1.
AK296366 mRNA. Translation: BAG59041.1.
AK302172 mRNA. Translation: BAG63539.1.
AC004474 Genomic DNA. No translation available.
BC034942 mRNA. Translation: AAH34942.1.
CCDSiCCDS14782.1. [O15523-1]
RefSeqiNP_001116137.1. NM_001122665.2. [O15523-1]
NP_001289481.1. NM_001302552.1. [O15523-2]
NP_004651.2. NM_004660.4. [O15523-1]
UniGeneiHs.99120.

Genome annotation databases

EnsembliENST00000336079; ENSP00000336725; ENSG00000067048. [O15523-1]
ENST00000360160; ENSP00000353284; ENSG00000067048. [O15523-1]
GeneIDi8653.
KEGGihsa:8653.
UCSCiuc004fsu.2. human. [O15523-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000985 mRNA. Translation: AAC51832.1.
AF000984 mRNA. Translation: AAC51831.1.
AK296366 mRNA. Translation: BAG59041.1.
AK302172 mRNA. Translation: BAG63539.1.
AC004474 Genomic DNA. No translation available.
BC034942 mRNA. Translation: AAH34942.1.
CCDSiCCDS14782.1. [O15523-1]
RefSeqiNP_001116137.1. NM_001122665.2. [O15523-1]
NP_001289481.1. NM_001302552.1. [O15523-2]
NP_004651.2. NM_004660.4. [O15523-1]
UniGeneiHs.99120.

3D structure databases

ProteinModelPortaliO15523.
SMRiO15523. Positions 133-574.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114204. 18 interactions.
IntActiO15523. 16 interactions.
MINTiMINT-2999090.
STRINGi9606.ENSP00000336725.

PTM databases

iPTMnetiO15523.
PhosphoSiteiO15523.
SwissPalmiO15523.

Polymorphism and mutation databases

BioMutaiDDX3Y.

Proteomic databases

EPDiO15523.
MaxQBiO15523.
PaxDbiO15523.
PRIDEiO15523.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000336079; ENSP00000336725; ENSG00000067048. [O15523-1]
ENST00000360160; ENSP00000353284; ENSG00000067048. [O15523-1]
GeneIDi8653.
KEGGihsa:8653.
UCSCiuc004fsu.2. human. [O15523-1]

Organism-specific databases

CTDi8653.
GeneCardsiDDX3Y.
GeneReviewsiDDX3Y.
HGNCiHGNC:2699. DDX3Y.
HPAiHPA005631.
MalaCardsiDDX3Y.
MIMi400010. gene.
neXtProtiNX_O15523.
Orphaneti1646. Partial chromosome Y deletion.
PharmGKBiPA27168.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0335. Eukaryota.
ENOG410XNTI. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000268804.
HOVERGENiHBG015893.
InParanoidiO15523.
KOiK17642.
OMAiPNPFANT.
OrthoDBiEOG7B5WV8.
PhylomeDBiO15523.
TreeFamiTF300364.

Enzyme and pathway databases

BRENDAi3.6.4.13. 2681.

Miscellaneous databases

ChiTaRSiDDX3Y. human.
GeneWikiiDDX3Y.
GenomeRNAii8653.
PROiO15523.
SOURCEiSearch...

Gene expression databases

BgeeiO15523.
CleanExiHS_DDX3Y.
ExpressionAtlasiO15523. baseline and differential.
GenevisibleiO15523. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Functional coherence of the human Y chromosome."
    Lahn B.T., Page D.C.
    Science 278:675-680(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
    Tissue: Testis and Thalamus.
  4. "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] (ISOFORM 1).
    Tissue: Testis.
  5. "Human DDX3Y, the Y-encoded isoform of RNA helicase DDX3, rescues a hamster temperature-sensitive ET24 mutant cell line with a DDX3X mutation."
    Sekiguchi T., Iida H., Fukumura J., Nishimoto T.
    Exp. Cell Res. 300:213-222(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  6. "The AZFa gene DBY (DDX3Y) is widely transcribed but the protein is limited to the male germ cells by translation control."
    Ditton H.J., Zimmer J., Kamp C., Rajpert-De Meyts E., Vogt P.H.
    Hum. Mol. Genet. 13:2333-2341(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  7. "TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules."
    Goulet I., Boisvenue S., Mokas S., Mazroui R., Cote J.
    Hum. Mol. Genet. 17:3055-3074(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TDRD3.
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDDX3Y_HUMAN
AccessioniPrimary (citable) accession number: O15523
Secondary accession number(s): B4DK29, B4DXX7, Q8IYV7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: August 16, 2005
Last modified: June 8, 2016
This is version 158 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome Y
    Human chromosome Y: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. 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.