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Protein

Probable ATP-dependent RNA helicase DDX60

Gene

DDX60

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

Functioni

Positively regulates DDX58/RIG-I- and IFIH1/MDA5-dependent type I interferon and interferon inducible gene expression in response to viral infection. Binds ssRNA, dsRNA and dsDNA and can promote the binding of DDX58/RIG-I to dsRNA. Exhibits antiviral activity against hepatitis C virus and vesicular stomatitis virus (VSV).2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi785 – 7928ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • double-stranded DNA binding Source: UniProtKB
  • double-stranded RNA binding Source: UniProtKB
  • helicase activity Source: UniProtKB-KW
  • single-stranded RNA binding Source: UniProtKB

GO - Biological processi

  • defense response to virus Source: UniProtKB-KW
  • innate immune response Source: UniProtKB-KW
  • positive regulation of MDA-5 signaling pathway Source: UniProtKB
  • positive regulation of RIG-I signaling pathway Source: UniProtKB
  • response to virus Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Antiviral defense, Immunity, Innate immunity

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX60 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 60
Gene namesi
Name:DDX60
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:25942. DDX60.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • intermediate filament cytoskeleton Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162383444.

Polymorphism and mutation databases

BioMutaiDDX60.
DMDMi296439377.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17121712Probable ATP-dependent RNA helicase DDX60PRO_0000318154Add
BLAST

Proteomic databases

EPDiQ8IY21.
MaxQBiQ8IY21.
PaxDbiQ8IY21.
PRIDEiQ8IY21.

PTM databases

iPTMnetiQ8IY21.
PhosphoSiteiQ8IY21.

Expressioni

Tissue specificityi

Brain, lymph node, prostate, stomach, thyroid, tongue, trachea, uterus, skeletal muscle, spleen, kidney, liver and small intestine.1 Publication

Inductioni

By interferon (IFN). Up-regulated during vesicular stomatitis virus (VSV), or poliovirus (PV) infection.2 Publications

Gene expression databases

BgeeiQ8IY21.
CleanExiHS_DDX60.
ExpressionAtlasiQ8IY21. baseline and differential.
GenevisibleiQ8IY21. HS.

Organism-specific databases

HPAiHPA046952.

Interactioni

Subunit structurei

Interacts with EXOSC1, EXOSC4, DDX58/RIG-I, IFIH1/MDA5 and DHX58/LGP2.1 Publication

Protein-protein interaction databases

BioGridi120742. 6 interactions.
IntActiQ8IY21. 6 interactions.
STRINGi9606.ENSP00000377344.

Structurei

3D structure databases

ProteinModelPortaliQ8IY21.
SMRiQ8IY21. Positions 748-931, 1185-1512.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini772 – 939168Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini1226 – 1370145Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi889 – 8924DEVH box

Sequence similaritiesi

Belongs to the helicase family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0949. Eukaryota.
KOG0950. Eukaryota.
COG4581. LUCA.
GeneTreeiENSGT00820000127042.
HOGENOMiHOG000169263.
HOVERGENiHBG107797.
InParanoidiQ8IY21.
OMAiFAQNSVY.
OrthoDBiEOG75F4C8.
PhylomeDBiQ8IY21.
TreeFamiTF314846.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[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. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8IY21-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERNVLTTFS QEMSQLILNE MPKAEYSSLF NDFVESEFFL IDGDSLLITC
60 70 80 90 100
ICEISFKPGQ NLHFFYLVER YLVDLISKGG QFTIVFFKDA EYAYFNFPEL
110 120 130 140 150
LSLRTALILH LQKNTTIDVR TTFSRCLSKE WGSFLEESYP YFLIVADEGL
160 170 180 190 200
NDLQTQLFNF LIIHSWARKV NVVLSSGQES DVLCLYAYLL PSMYRHQIFS
210 220 230 240 250
WKNKQNIKDA YTTLLNQLER FKLSALAPLF GSLKWNNITE EAHKTVSLLT
260 270 280 290 300
QVWPEGSDIR RVFCVTSCSL SLRMYHRFLG NREPSSGQET EIQQVNSNCL
310 320 330 340 350
TLQEMEDLCK LHCLTVVFLL HLPLSQRACA RVITSHWAED MKPLLQMKKW
360 370 380 390 400
CEYFILRNIH TFEFWNLNLI HLSDLNDELL LKNIAFYYEN ENVKGLHLNL
410 420 430 440 450
GDTIMKDYEY LWNTVSKLVR DFEVGQPFPL RTTKVCFLEK KPSPIKDSSN
460 470 480 490 500
EMVPNLGFIP TSSFVVDKFA GDILKDLPFL KSDDPIVTSL VKQKEFDELV
510 520 530 540 550
HWHSHKPLSD DYDRSRCQFD EKSRDPRVLR SVQKYHVFQR FYGNSLETVS
560 570 580 590 600
SKIIVTQTIK SKKDFSGPKS KKAHETKAEI IARENKKRLF AREEQKEEQK
610 620 630 640 650
WNALSFSIEE QLKENLHSGI KSLEDFLKSC KSSCVKLQVE MVGLTACLKA
660 670 680 690 700
WKEHCRSEEG KTTKDLSIAV QVMKRIHSLM EKYSELLQED DRQLIARCLK
710 720 730 740 750
YLGFDELASS LHPAQDAEND VKVKKRNKYS VGIGPARFQL QYMGHYLIRD
760 770 780 790 800
ERKDPDPRVQ DFIPDTWQRE LLDVVDKNES AVIVAPTSSG KTYASYYCME
810 820 830 840 850
KVLKESDDGV VVYVAPTKAL VNQVAATVQN RFTKNLPSGE VLCGVFTREY
860 870 880 890 900
RHDALNCQVL ITVPACFEIL LLAPHRQNWV KKIRYVIFDE VHCLGGEIGA
910 920 930 940 950
EIWEHLLVMI RCPFLALSAT ISNPEHLTEW LQSVKWYWKQ EDKIIENNTA
960 970 980 990 1000
SKRHVGRQAG FPKDYLQVKQ SYKVRLVLYG ERYNDLEKHV CSIKHGDIHF
1010 1020 1030 1040 1050
DHFHPCAALT TDHIERYGFP PDLTLSPRES IQLYDAMFQI WKSWPRAQEL
1060 1070 1080 1090 1100
CPENFIHFNN KLVIKKMDAR KYEESLKAEL TSWIKNGNVE QARMVLQNLS
1110 1120 1130 1140 1150
PEADLSPENM ITMFPLLVEK LRKMEKLPAL FFLFKLGAVE NAAESVSTFL
1160 1170 1180 1190 1200
KKKQETKRPP KADKEAHVMA NKLRKVKKSI EKQKIIDEKS QKKTRNVDQS
1210 1220 1230 1240 1250
LIHEAEHDNL VKCLEKNLEI PQDCTYADQK AVDTETLQKV FGRVKFERKG
1260 1270 1280 1290 1300
EELKALAERG IGYHHSAMSF KEKQLVEILF RKGYLRVVTA TGTLALGVNM
1310 1320 1330 1340 1350
PCKSVVFAQN SVYLDALNYR QMSGRAGRRG QDLMGDVYFF DIPFPKIGKL
1360 1370 1380 1390 1400
IKSNVPELRG HFPLSITLVL RLMLLASKGD DPEDAKAKVL SVLKHSLLSF
1410 1420 1430 1440 1450
KQPRVMDMLK LYFLFSLQFL VKEGYLDQEG NPMGFAGLVS HLHYHEPSNL
1460 1470 1480 1490 1500
VFVSFLVNGL FHDLCQPTRK GSKHFSQDVM EKLVLVLAHL FGRRYFPPKF
1510 1520 1530 1540 1550
QDAHFEFYQS KVFLDDLPED FSDALDEYNM KIMEDFTTFL RIVSKLADMN
1560 1570 1580 1590 1600
QEYQLPLSKI KFTGKECEDS QLVSHLMSCK EGRVAISPFV CLSGNFDDDL
1610 1620 1630 1640 1650
LRLETPNHVT LGTIGVNRSQ APVLLSQKFD NRGRKMSLNA YALDFYKHGS
1660 1670 1680 1690 1700
LIGLVQDNRM NEGDAYYLLK DFALTIKSIS VSLRELCENE DDNVVLAFEQ
1710
LSTTFWEKLN KV
Length:1,712
Mass (Da):197,853
Last modified:May 18, 2010 - v3
Checksum:i4F71D8E5A06D3EB9
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti415 – 4151V → I in BAA91809 (PubMed:14702039).Curated
Sequence conflicti439 – 4391E → G in AAH38115 (PubMed:15489334).Curated
Sequence conflicti731 – 7311V → I in AAH38115 (PubMed:15489334).Curated
Sequence conflicti1385 – 13851A → T in AAH38115 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti672 – 6721V → M.
Corresponds to variant rs550625 [ dbSNP | Ensembl ].
VAR_055895
Natural varianti998 – 9981I → V.
Corresponds to variant rs576619 [ dbSNP | Ensembl ].
VAR_055896

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC068989 Genomic DNA. No translation available.
BC007820 mRNA. Translation: AAH07820.1.
BC038115 mRNA. Translation: AAH38115.1.
AK001649 mRNA. Translation: BAA91809.1.
CCDSiCCDS34097.1.
RefSeqiNP_060101.3. NM_017631.5.
UniGeneiHs.591710.

Genome annotation databases

EnsembliENST00000393743; ENSP00000377344; ENSG00000137628.
GeneIDi55601.
KEGGihsa:55601.
UCSCiuc003irp.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC068989 Genomic DNA. No translation available.
BC007820 mRNA. Translation: AAH07820.1.
BC038115 mRNA. Translation: AAH38115.1.
AK001649 mRNA. Translation: BAA91809.1.
CCDSiCCDS34097.1.
RefSeqiNP_060101.3. NM_017631.5.
UniGeneiHs.591710.

3D structure databases

ProteinModelPortaliQ8IY21.
SMRiQ8IY21. Positions 748-931, 1185-1512.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120742. 6 interactions.
IntActiQ8IY21. 6 interactions.
STRINGi9606.ENSP00000377344.

PTM databases

iPTMnetiQ8IY21.
PhosphoSiteiQ8IY21.

Polymorphism and mutation databases

BioMutaiDDX60.
DMDMi296439377.

Proteomic databases

EPDiQ8IY21.
MaxQBiQ8IY21.
PaxDbiQ8IY21.
PRIDEiQ8IY21.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000393743; ENSP00000377344; ENSG00000137628.
GeneIDi55601.
KEGGihsa:55601.
UCSCiuc003irp.4. human.

Organism-specific databases

CTDi55601.
GeneCardsiDDX60.
HGNCiHGNC:25942. DDX60.
HPAiHPA046952.
MIMi613974. gene.
neXtProtiNX_Q8IY21.
PharmGKBiPA162383444.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0949. Eukaryota.
KOG0950. Eukaryota.
COG4581. LUCA.
GeneTreeiENSGT00820000127042.
HOGENOMiHOG000169263.
HOVERGENiHBG107797.
InParanoidiQ8IY21.
OMAiFAQNSVY.
OrthoDBiEOG75F4C8.
PhylomeDBiQ8IY21.
TreeFamiTF314846.

Miscellaneous databases

GenomeRNAii55601.
NextBioi60142.
PROiQ8IY21.
SOURCEiSearch...

Gene expression databases

BgeeiQ8IY21.
CleanExiHS_DDX60.
ExpressionAtlasiQ8IY21. baseline and differential.
GenevisibleiQ8IY21. HS.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[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. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "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: Brain and Uterus.
  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] OF 1-1174.
  4. "DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling."
    Miyashita M., Oshiumi H., Matsumoto M., Seya T.
    Mol. Cell. Biol. 31:3802-3819(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION, TISSUE SPECIFICITY, INTERACTION WITH EXOSC1; EXOSC4; DDX58/RIG-I; IFIH1/MDA5; DHX58/LGP2.
  5. "A diverse range of gene products are effectors of the type I interferon antiviral response."
    Schoggins J.W., Wilson S.J., Panis M., Murphy M.Y., Jones C.T., Bieniasz P., Rice C.M.
    Nature 472:481-485(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.

Entry informationi

Entry nameiDDX60_HUMAN
AccessioniPrimary (citable) accession number: Q8IY21
Secondary accession number(s): Q6PK35, Q9NVE3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: May 18, 2010
Last modified: April 13, 2016
This is version 115 of the entry and version 3 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 4
    Human chromosome 4: 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. 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.