Q9NY93 (DDX56_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 21
DEAD box protein 56

Gene names

Name:	DDX56
Synonyms:	DDX21, NOH61

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	547 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nucleolus 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 process	Ribosome biogenesis rRNA processing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleolus Inferred from direct assay. Source: LIFEdb
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Traceable author statement Ref.1. Source: ProtInc RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 547	547	Probable ATP-dependent RNA helicase DDX56		PRO_0000055058
Regions
	Domain	38 – 218	181	Helicase ATP-binding
	Domain	230 – 424	195	Helicase C-terminal
	Nucleotide binding	51 – 58	8	ATP By similarity
	Motif	7 – 35	29	Q motif
	Motif	166 – 169	4	DEAD box
Amino acid modifications
	Modified residue	126	1	Phosphoserine Ref.11
Natural variations
	Alternative sequence	298 – 337	40	Missing in isoform 2.		VSP_044869
Experimental info
	Sequence conflict	30	1	P → S in CAG33494. Ref.5
	Sequence conflict	145	1	I → T in BAB14238. Ref.4
	Sequence conflict	402	1	E → D in AK315363. Ref.4
	Sequence conflict	518	1	C → Y in CAG33494. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 6D127CDAA73610D2	FASTA	547	61,590
	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
	Isoform 2 [UniParc]. Checksum: 0D65F55E75AAF73D	FASTA	507	57,275
	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 ELPLRSRASD 310 320 330 340 350 360 PEAGVARGID FHHVSAVLNF DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI 370 380 390 400 410 420 EELLSGENRG PILLPYQFRM EEIEGFRYRC RDAMRSVTKQ AIREARLKEI KEELLHSEKL 430 440 450 460 470 480 KTYFEDNPRD LQLLRHDLPL HPAVVKPHLG HVPDYLVPPA LRGLVRPHKK RKKLSSSCRK 490 500 AKRAKSQNPL RSFKHKGKKF RPTAKPS

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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. , 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. , 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], MASS SPECTROMETRY. 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, MASS SPECTROMETRY. 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.
IPI	IPI00302281. IPI00925037.
RefSeq	NP_001244118.1. NM_001257189.1. NP_061955.1. NM_019082.3.
UniGene	Hs.654762.
3D structure databases
ProteinModelPortal	Q9NY93.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9NY93. 5 interactions.
STRING	9606.ENSP00000258772.
PTM databases
PhosphoSite	Q9NY93.
Polymorphism databases
DMDM	20139238.
2D gel databases
SWISS-2DPAGE	Q9NY93.
Proteomic databases
PaxDb	Q9NY93.
PRIDE	Q9NY93.
Protocols and materials databases
DNASU	54606.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000258772; ENSP00000258772; ENSG00000136271. ENST00000431640; ENSP00000393488; ENSG00000136271.
GeneID	54606.
KEGG	hsa:54606.
UCSC	uc003tlg.3. human.
Organism-specific databases
CTD	54606.
GeneCards	GC07M044571.
HGNC	HGNC:18193. DDX56.
HPA	HPA019749.
MIM	608023. gene.
neXtProt	NX_Q9NY93.
PharmGKB	PA134916346.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG0513.
HOGENOM	HOG000253015.
HOVERGEN	HBG051334.
InParanoid	Q9NY93.
KO	K14810.
OMA	TFLMSAT.
OrthoDB	EOG47H5PT.
PhylomeDB	Q9NY93.
Gene expression databases
ArrayExpress	Q9NY93.
Bgee	Q9NY93.
CleanEx	HS_DDX21. HS_DDX56.
Genevestigator	Q9NY93.
GermOnline	ENSG00000136271. Homo sapiens.
Family and domain databases
InterPro	IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. [Graphical view]
Pfam	PF00270. DEAD. 1 hit. PF00271. Helicase_C. 2 hits. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51195. Q_MOTIF. 1 hit. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	54606.
NextBio	57133.
SOURCE	Search...

Entry information

Entry name

DDX56_HUMAN

Accession

Primary (citable) accession number: Q9NY93
Secondary accession number(s): A4D2K9 , C9JV95, Q6IAE2, Q9H9I8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 23, 2002
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 121 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.