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Q9NY93

- DDX56_HUMAN

UniProt

Q9NY93 - DDX56_HUMAN

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Protein

Probable ATP-dependent RNA helicase DDX56

Gene
DDX56, DDX21, NOH61
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein 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.

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi51 – 588ATP By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent RNA helicase activity Source: ProtInc
  3. poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. rRNA processing Source: UniProtKB-KW
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 21
DEAD box protein 56
Gene namesi
Name:DDX56
Synonyms:DDX21, NOH61
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 7

Organism-specific databases

HGNCiHGNC:18193. DDX56.

Subcellular locationi

Nucleusnucleolus 1 Publication

GO - Cellular componenti

  1. nucleolus Source: LIFEdb
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134916346.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 547547Probable ATP-dependent RNA helicase DDX56PRO_0000055058Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei126 – 1261Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9NY93.
PaxDbiQ9NY93.
PRIDEiQ9NY93.

2D gel databases

SWISS-2DPAGEQ9NY93.

PTM databases

PhosphoSiteiQ9NY93.

Expressioni

Tissue specificityi

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

Gene expression databases

ArrayExpressiQ9NY93.
BgeeiQ9NY93.
CleanExiHS_DDX21.
HS_DDX56.
GenevestigatoriQ9NY93.

Organism-specific databases

HPAiHPA019749.

Interactioni

Subunit structurei

May form homooligomeric complexes.

Protein-protein interaction databases

BioGridi120075. 44 interactions.
IntActiQ9NY93. 5 interactions.
MINTiMINT-2819731.
STRINGi9606.ENSP00000258772.

Structurei

3D structure databases

ProteinModelPortaliQ9NY93.
SMRiQ9NY93. Positions 9-434.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 218181Helicase ATP-bindingAdd
BLAST
Domaini230 – 424195Helicase C-terminalAdd
BLAST

Motif

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0513.
HOGENOMiHOG000253015.
HOVERGENiHBG051334.
InParanoidiQ9NY93.
KOiK14810.
OMAiRYRMEDA.
OrthoDBiEOG70S750.
PhylomeDBiQ9NY93.
TreeFamiTF300620.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. 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]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 2 hits.
[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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9NY93-1) [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

MEDSEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR    50
ARTGSGKTAA YAIPMLQLLL HRKATGPVVE QAVRGLVLVP TKELARQAQS 100
MIQQLATYCA RDVRVANVSA AEDSVSQRAV LMEKPDVVVG TPSRILSHLQ 150
QDSLKLRDSL ELLVVDEADL LFSFGFEEEL KSLLCHLPRI YQAFLMSATF 200
NEDVQALKEL ILHNPVTLKL QESQLPGPDQ LQQFQVVCET EEDKFLLLYA 250
LLKLSLIRGK SLLFVNTLER SYRLRLFLEQ FSIPTCVLNG ELPLRSRCHI 300
ISQFNQGFYD CVIATDAEVL GAPVKGKRRG RGPKGDKASD PEAGVARGID 350
FHHVSAVLNF DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI 400
EELLSGENRG PILLPYQFRM EEIEGFRYRC RDAMRSVTKQ AIREARLKEI 450
KEELLHSEKL KTYFEDNPRD LQLLRHDLPL HPAVVKPHLG HVPDYLVPPA 500
LRGLVRPHKK RKKLSSSCRK AKRAKSQNPL RSFKHKGKKF RPTAKPS 547
Length:547
Mass (Da):61,590
Last modified:October 1, 2000 - v1
Checksum:i6D127CDAA73610D2
GO
Isoform 2 (identifier: Q9NY93-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     298-337: Missing.

Note: No experimental confirmation available.

Show »
Length:507
Mass (Da):57,275
Checksum:i0D65F55E75AAF73D
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei298 – 33740Missing in isoform 2. VSP_044869Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti30 – 301P → S in CAG33494. 1 Publication
Sequence conflicti145 – 1451I → T in BAB14238. 1 Publication
Sequence conflicti402 – 4021E → D in AK315363. 1 Publication
Sequence conflicti518 – 5181C → Y in CAG33494. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS5492.1. [Q9NY93-1]
CCDS59053.1. [Q9NY93-2]
RefSeqiNP_001244118.1. NM_001257189.1. [Q9NY93-2]
NP_061955.1. NM_019082.3. [Q9NY93-1]
UniGeneiHs.654762.

Genome annotation databases

EnsembliENST00000258772; ENSP00000258772; ENSG00000136271. [Q9NY93-1]
ENST00000431640; ENSP00000393488; ENSG00000136271. [Q9NY93-2]
GeneIDi54606.
KEGGihsa:54606.
UCSCiuc003tlg.4. human. [Q9NY93-1]

Polymorphism databases

DMDMi20139238.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS5492.1. [Q9NY93-1 ]
CCDS59053.1. [Q9NY93-2 ]
RefSeqi NP_001244118.1. NM_001257189.1. [Q9NY93-2 ]
NP_061955.1. NM_019082.3. [Q9NY93-1 ]
UniGenei Hs.654762.

3D structure databases

ProteinModelPortali Q9NY93.
SMRi Q9NY93. Positions 9-434.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 120075. 44 interactions.
IntActi Q9NY93. 5 interactions.
MINTi MINT-2819731.
STRINGi 9606.ENSP00000258772.

PTM databases

PhosphoSitei Q9NY93.

Polymorphism databases

DMDMi 20139238.

2D gel databases

SWISS-2DPAGE Q9NY93.

Proteomic databases

MaxQBi Q9NY93.
PaxDbi Q9NY93.
PRIDEi Q9NY93.

Protocols and materials databases

DNASUi 54606.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000258772 ; ENSP00000258772 ; ENSG00000136271 . [Q9NY93-1 ]
ENST00000431640 ; ENSP00000393488 ; ENSG00000136271 . [Q9NY93-2 ]
GeneIDi 54606.
KEGGi hsa:54606.
UCSCi uc003tlg.4. human. [Q9NY93-1 ]

Organism-specific databases

CTDi 54606.
GeneCardsi GC07M044571.
HGNCi HGNC:18193. DDX56.
HPAi HPA019749.
MIMi 608023. gene.
neXtProti NX_Q9NY93.
PharmGKBi PA134916346.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0513.
HOGENOMi HOG000253015.
HOVERGENi HBG051334.
InParanoidi Q9NY93.
KOi K14810.
OMAi RYRMEDA.
OrthoDBi EOG70S750.
PhylomeDBi Q9NY93.
TreeFami TF300620.

Miscellaneous databases

GeneWikii DDX56.
GenomeRNAii 54606.
NextBioi 57133.
PROi Q9NY93.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q9NY93.
Bgeei Q9NY93.
CleanExi HS_DDX21.
HS_DDX56.
Genevestigatori Q9NY93.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. 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 ]
Pfami PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 2 hits.
[Graphical view ]
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 3 hits.
PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-126, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic kidney.
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDDX56_HUMAN
AccessioniPrimary (citable) accession number: Q9NY93
Secondary accession number(s): A4D2K9
, C9JV95, Q6IAE2, Q9H9I8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: October 1, 2000
Last modified: July 9, 2014
This is version 133 of the entry and version 1 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 7
    Human chromosome 7: 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

External Data

Dasty 3

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