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Protein

Probable ATP-dependent RNA helicase DDX56

Gene

Ddx56

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi51 – 588ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX56 (EC:3.6.4.13)
Alternative name(s):
ATP-dependent 61 kDa nucleolar RNA helicase
DEAD box protein 56
Gene namesi
Name:Ddx56
Synonyms:D11Ertd619e, Noh61
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1277172. Ddx56.

Subcellular locationi

GO - Cellular componenti

  • membrane Source: MGI
  • nucleolus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 546546Probable ATP-dependent RNA helicase DDX56PRO_0000055059Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei126 – 1261PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9D0R4.
MaxQBiQ9D0R4.
PaxDbiQ9D0R4.
PRIDEiQ9D0R4.

PTM databases

iPTMnetiQ9D0R4.
PhosphoSiteiQ9D0R4.

Expressioni

Gene expression databases

BgeeiQ9D0R4.
CleanExiMM_DDX56.
ExpressionAtlasiQ9D0R4. baseline and differential.
GenevisibleiQ9D0R4. MM.

Interactioni

Subunit structurei

May form homooligomeric complexes.

Protein-protein interaction databases

BioGridi206632. 2 interactions.
IntActiQ9D0R4. 1 interaction.
STRINGi10090.ENSMUSP00000004507.

Structurei

3D structure databases

ProteinModelPortaliQ9D0R4.
SMRiQ9D0R4. Positions 1-407.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 218181Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini230 – 424195Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi7 – 3529Q motifAdd
BLAST
Motifi166 – 1694DEAD box

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG0346. Eukaryota.
ENOG410XR15. LUCA.
GeneTreeiENSGT00550000074946.
HOGENOMiHOG000253015.
HOVERGENiHBG051334.
InParanoidiQ9D0R4.
KOiK14810.
OMAiKHIDKES.
OrthoDBiEOG70S750.
PhylomeDBiQ9D0R4.
TreeFamiTF300620.

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.
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. 3 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9D0R4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDQEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR
60 70 80 90 100
ARTGSGKTAA YAIPMLQSLL HKKATGPVME QAVRGLVLVP TKELARQAQA
110 120 130 140 150
MIQQLAAYCA RDVRVANVSA AEDSASQRAV LMEKPDVVVG TPSRVLSHLQ
160 170 180 190 200
QNTLKLRDSL ELLVVDEADL LFSFGFEDEL KSLLCHLPRI YQAFLMSATF
210 220 230 240 250
NEDVQTLKEL VLHNPVTLKL QESQLPGPDQ LQQFQVVCET EEDKFLLLYA
260 270 280 290 300
LLKLSLIRGK ALLFVNTLER GYRLRLFLEQ FSIPSCVLNG ELPLRSRCHI
310 320 330 340 350
ISQFNQGLYD CVIATDAEIL GPQVKGKRRG RGSKGNKASD PESGVARGID
360 370 380 390 400
FHHVSAVLNF DLPPTAEAYV HRAGRTARAN NPGIVLTFVL PAEQPFLGKI
410 420 430 440 450
EDLLSGEGEA PILLPYQFQM EEIESFRYRC RDAMRSVTKQ AIREARLKEI
460 470 480 490 500
KEELLHSEKL KTYFEDNPRD LQLLRHDLPL HPAVVKPHLG HVPDYLVPAA
510 520 530 540
LRGLVHPRKK RRKVPFSRKA KKVKAQNPLR DFKHRGKKPK PAAKPS
Length:546
Mass (Da):61,212
Last modified:June 1, 2001 - v1
Checksum:i3C19F7354C29F9A1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK011136 mRNA. Translation: BAB27426.1.
AK077514 mRNA. Translation: BAC36839.1.
BC018291 mRNA. Translation: AAH18291.1.
CCDSiCCDS24414.1.
RefSeqiNP_080814.1. NM_026538.3.
UniGeneiMm.29810.

Genome annotation databases

EnsembliENSMUST00000004507; ENSMUSP00000004507; ENSMUSG00000004393.
GeneIDi52513.
KEGGimmu:52513.
UCSCiuc007hyc.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK011136 mRNA. Translation: BAB27426.1.
AK077514 mRNA. Translation: BAC36839.1.
BC018291 mRNA. Translation: AAH18291.1.
CCDSiCCDS24414.1.
RefSeqiNP_080814.1. NM_026538.3.
UniGeneiMm.29810.

3D structure databases

ProteinModelPortaliQ9D0R4.
SMRiQ9D0R4. Positions 1-407.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi206632. 2 interactions.
IntActiQ9D0R4. 1 interaction.
STRINGi10090.ENSMUSP00000004507.

PTM databases

iPTMnetiQ9D0R4.
PhosphoSiteiQ9D0R4.

Proteomic databases

EPDiQ9D0R4.
MaxQBiQ9D0R4.
PaxDbiQ9D0R4.
PRIDEiQ9D0R4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000004507; ENSMUSP00000004507; ENSMUSG00000004393.
GeneIDi52513.
KEGGimmu:52513.
UCSCiuc007hyc.1. mouse.

Organism-specific databases

CTDi54606.
MGIiMGI:1277172. Ddx56.

Phylogenomic databases

eggNOGiKOG0346. Eukaryota.
ENOG410XR15. LUCA.
GeneTreeiENSGT00550000074946.
HOGENOMiHOG000253015.
HOVERGENiHBG051334.
InParanoidiQ9D0R4.
KOiK14810.
OMAiKHIDKES.
OrthoDBiEOG70S750.
PhylomeDBiQ9D0R4.
TreeFamiTF300620.

Miscellaneous databases

ChiTaRSiDdx56. mouse.
NextBioi309069.
PROiQ9D0R4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D0R4.
CleanExiMM_DDX56.
ExpressionAtlasiQ9D0R4. baseline and differential.
GenevisibleiQ9D0R4. MM.

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.
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. 3 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Embryo.
  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].
    Strain: FVB/N.
    Tissue: Salivary gland.

Entry informationi

Entry nameiDDX56_MOUSE
AccessioniPrimary (citable) accession number: Q9D0R4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: June 1, 2001
Last modified: May 11, 2016
This is version 124 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.