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Q9NY93 (DDX56_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 21
DEAD box protein 56
Gene names
Name:DDX56
Synonyms:DDX21, NOH61
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length547 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

May form homooligomeric complexes.

Subcellular location

Nucleusnucleolus Ref.10.

Tissue specificity

Detected in heart, brain, liver, pancreas, placenta and lung.

Sequence similarities

Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processRibosome biogenesis
rRNA processing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processATP catabolic process

Traceable author statement Ref.1. Source: GOC

rRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleolus

Inferred from direct assay. Source: LIFEdb

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent RNA helicase activity

Traceable author statement Ref.1. Source: ProtInc

poly(A) RNA binding

Inferred from direct assay PubMed 22658674. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9NY93-1)

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.
Isoform 2 (identifier: Q9NY93-2)

The sequence of this isoform differs from the canonical sequence as follows:
     298-337: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 547547Probable ATP-dependent RNA helicase DDX56
PRO_0000055058

Regions

Domain38 – 218181Helicase ATP-binding
Domain230 – 424195Helicase C-terminal
Nucleotide binding51 – 588ATP By similarity
Motif7 – 3529Q motif
Motif166 – 1694DEAD box

Amino acid modifications

Modified residue1261Phosphoserine Ref.11

Natural variations

Alternative sequence298 – 33740Missing in isoform 2.
VSP_044869

Experimental info

Sequence conflict301P → S in CAG33494. Ref.5
Sequence conflict1451I → T in BAB14238. Ref.4
Sequence conflict4021E → D in AK315363. Ref.4
Sequence conflict5181C → Y in CAG33494. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 6D127CDAA73610D2

FASTA54761,590
        10         20         30         40         50         60 
MEDSEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR ARTGSGKTAA 

        70         80         90        100        110        120 
YAIPMLQLLL HRKATGPVVE QAVRGLVLVP TKELARQAQS MIQQLATYCA RDVRVANVSA 

       130        140        150        160        170        180 
AEDSVSQRAV LMEKPDVVVG TPSRILSHLQ QDSLKLRDSL ELLVVDEADL LFSFGFEEEL 

       190        200        210        220        230        240 
KSLLCHLPRI YQAFLMSATF NEDVQALKEL ILHNPVTLKL QESQLPGPDQ LQQFQVVCET 

       250        260        270        280        290        300 
EEDKFLLLYA LLKLSLIRGK SLLFVNTLER SYRLRLFLEQ FSIPTCVLNG ELPLRSRCHI 

       310        320        330        340        350        360 
ISQFNQGFYD CVIATDAEVL GAPVKGKRRG RGPKGDKASD PEAGVARGID FHHVSAVLNF 

       370        380        390        400        410        420 
DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI EELLSGENRG PILLPYQFRM 

       430        440        450        460        470        480 
EEIEGFRYRC RDAMRSVTKQ AIREARLKEI KEELLHSEKL KTYFEDNPRD LQLLRHDLPL 

       490        500        510        520        530        540 
HPAVVKPHLG HVPDYLVPPA LRGLVRPHKK RKKLSSSCRK AKRAKSQNPL RSFKHKGKKF 


RPTAKPS 

« Hide

Isoform 2 [UniParc].

Checksum: 0D65F55E75AAF73D
Show »

FASTA50757,275

References

« Hide 'large scale' references
[1]"A novel helicase-type protein in the nucleolus: protein NOH61."
Zirwes R.F., Eilbracht J., Kneissel S., Schmidt-Zachmann M.S.
Mol. Biol. Cell 11:1153-1167(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Keratinocyte.
[2]"Sequencing of a new human DEAD-box RNA helicase."
Camargo A.A., Nunes D.N., Samaia H.B., Simpson A.J.G., Dias-Neto E.
Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[3]"Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs."
Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S., Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J., Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W., Ottenwaelder B., Obermaier B. expand/collapse author list , Tampe J., Heubner D., Wambutt R., Korn B., Klein M., Poustka A.
Genome Res. 11:422-435(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Fetal brain.
[4]"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. expand/collapse author list , 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 1 AND 2).
Tissue: Glial tumor.
[5]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[6]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"Human chromosome 7: DNA sequence and biology."
Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S. expand/collapse author list , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[9]"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: Cervix.
[10]"Functional proteomic analysis of human nucleolus."
Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.-C., Greco A., Hochstrasser D.F., Diaz J.-J.
Mol. Biol. Cell 13:4100-4109(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage."
Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J.
Science 316:1160-1166(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-126, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic kidney.
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ131712 mRNA. Translation: CAB87992.1.
AF247666 mRNA. Translation: AAG36876.1.
AL136700 mRNA. Translation: CAB66635.1.
AK022774 mRNA. Translation: BAB14238.1.
AK315363 mRNA. No translation available.
CR457213 mRNA. Translation: CAG33494.1.
AC004938 Genomic DNA. No translation available.
CH236960 Genomic DNA. Translation: EAL23752.1.
CH471128 Genomic DNA. Translation: EAW61094.1.
BC001235 mRNA. Translation: AAH01235.1.
RefSeqNP_001244118.1. NM_001257189.1.
NP_061955.1. NM_019082.3.
UniGeneHs.654762.

3D structure databases

ProteinModelPortalQ9NY93.
SMRQ9NY93. Positions 3-434.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120075. 42 interactions.
IntActQ9NY93. 5 interactions.
MINTMINT-2819731.
STRING9606.ENSP00000258772.

PTM databases

PhosphoSiteQ9NY93.

Polymorphism databases

DMDM20139238.

2D gel databases

SWISS-2DPAGEQ9NY93.

Proteomic databases

PaxDbQ9NY93.
PRIDEQ9NY93.

Protocols and materials databases

DNASU54606.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000258772; ENSP00000258772; ENSG00000136271. [Q9NY93-1]
ENST00000431640; ENSP00000393488; ENSG00000136271. [Q9NY93-2]
GeneID54606.
KEGGhsa:54606.
UCSCuc003tlg.4. human. [Q9NY93-1]

Organism-specific databases

CTD54606.
GeneCardsGC07M044571.
HGNCHGNC:18193. DDX56.
HPAHPA019749.
MIM608023. gene.
neXtProtNX_Q9NY93.
PharmGKBPA134916346.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0513.
HOGENOMHOG000253015.
HOVERGENHBG051334.
InParanoidQ9NY93.
KOK14810.
OMARYRMEDA.
OrthoDBEOG70S750.
PhylomeDBQ9NY93.
TreeFamTF300620.

Gene expression databases

ArrayExpressQ9NY93.
BgeeQ9NY93.
CleanExHS_DDX21.
HS_DDX56.
GenevestigatorQ9NY93.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 2 hits.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 3 hits.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiDDX56.
GenomeRNAi54606.
NextBio57133.
PROQ9NY93.
SOURCESearch...

Entry information

Entry nameDDX56_HUMAN
AccessionPrimary (citable) accession number: Q9NY93
Secondary accession number(s): A4D2K9 expand/collapse secondary AC list , C9JV95, Q6IAE2, Q9H9I8
Entry history
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM