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Protein

Probable ATP-dependent RNA helicase DDX56

Gene

DDX56

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Nucleotide bindingi51 – 58ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: ProtInc
  • RNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processRibosome biogenesis, rRNA processing
LigandATP-binding, Nucleotide-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
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000136271.10
HGNCiHGNC:18193 DDX56
MIMi608023 gene
neXtProtiNX_Q9NY93

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi54606
OpenTargetsiENSG00000136271
PharmGKBiPA134916346

Polymorphism and mutation databases

BioMutaiDDX56
DMDMi20139238

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550581 – 547Probable ATP-dependent RNA helicase DDX56Add BLAST547

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei126PhosphoserineCombined sources1
Modified residuei141PhosphothreonineCombined sources1
Modified residuei532PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9NY93
MaxQBiQ9NY93
PaxDbiQ9NY93
PeptideAtlasiQ9NY93
PRIDEiQ9NY93
ProteomicsDBi83197

2D gel databases

SWISS-2DPAGEiQ9NY93

PTM databases

iPTMnetiQ9NY93
PhosphoSitePlusiQ9NY93
SwissPalmiQ9NY93

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000136271 Expressed in 221 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_DDX21
HS_DDX56
ExpressionAtlasiQ9NY93 baseline and differential
GenevisibleiQ9NY93 HS

Organism-specific databases

HPAiCAB037320
HPA019749

Interactioni

Subunit structurei

May form homooligomeric complexes.

Protein-protein interaction databases

BioGridi120075, 101 interactors
IntActiQ9NY93, 31 interactors
MINTiQ9NY93
STRINGi9606.ENSP00000258772

Structurei

3D structure databases

ProteinModelPortaliQ9NY93
SMRiQ9NY93
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini38 – 218Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST181
Domaini230 – 424Helicase C-terminalPROSITE-ProRule annotationAdd BLAST195

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi7 – 35Q motifAdd BLAST29
Motifi166 – 169DEAD box4

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0346 Eukaryota
ENOG410XR15 LUCA
GeneTreeiENSGT00550000074946
HOGENOMiHOG000253015
HOVERGENiHBG051334
InParanoidiQ9NY93
KOiK14810
OMAiRYRMEDA
OrthoDBiEOG091G04UR
PhylomeDBiQ9NY93
TreeFamiTF300620

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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
        10         20         30         40         50
MEDSEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR
60 70 80 90 100
ARTGSGKTAA YAIPMLQLLL HRKATGPVVE QAVRGLVLVP TKELARQAQS
110 120 130 140 150
MIQQLATYCA RDVRVANVSA AEDSVSQRAV LMEKPDVVVG TPSRILSHLQ
160 170 180 190 200
QDSLKLRDSL ELLVVDEADL LFSFGFEEEL KSLLCHLPRI YQAFLMSATF
210 220 230 240 250
NEDVQALKEL ILHNPVTLKL QESQLPGPDQ LQQFQVVCET EEDKFLLLYA
260 270 280 290 300
LLKLSLIRGK SLLFVNTLER SYRLRLFLEQ FSIPTCVLNG ELPLRSRCHI
310 320 330 340 350
ISQFNQGFYD CVIATDAEVL GAPVKGKRRG RGPKGDKASD PEAGVARGID
360 370 380 390 400
FHHVSAVLNF DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI
410 420 430 440 450
EELLSGENRG PILLPYQFRM EEIEGFRYRC RDAMRSVTKQ AIREARLKEI
460 470 480 490 500
KEELLHSEKL KTYFEDNPRD LQLLRHDLPL HPAVVKPHLG HVPDYLVPPA
510 520 530 540
LRGLVRPHKK RKKLSSSCRK AKRAKSQNPL RSFKHKGKKF RPTAKPS
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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WDT8F8WDT8_HUMAN
Probable ATP-dependent RNA helicase...
DDX56
185Annotation score:
F8WEI3F8WEI3_HUMAN
Probable ATP-dependent RNA helicase...
DDX56
103Annotation score:
G3V0G3G3V0G3_HUMAN
DEAD (Asp-Glu-Ala-Asp) box polypept...
DDX56 hCG_18300
375Annotation score:
H7C3E9H7C3E9_HUMAN
Probable ATP-dependent RNA helicase...
DDX56
396Annotation score:
H7BZN7H7BZN7_HUMAN
Probable ATP-dependent RNA helicase...
DDX56
182Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti30P → S in CAG33494 (Ref. 5) Curated1
Sequence conflicti145I → T in BAB14238 (PubMed:14702039).Curated1
Sequence conflicti402E → D in AK315363 (PubMed:14702039).Curated1
Sequence conflicti518C → Y in CAG33494 (Ref. 5) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_044869298 – 337Missing in isoform 2. 1 PublicationAdd BLAST40

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.5 human [Q9NY93-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

3D structure databases

ProteinModelPortaliQ9NY93
SMRiQ9NY93
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120075, 101 interactors
IntActiQ9NY93, 31 interactors
MINTiQ9NY93
STRINGi9606.ENSP00000258772

PTM databases

iPTMnetiQ9NY93
PhosphoSitePlusiQ9NY93
SwissPalmiQ9NY93

Polymorphism and mutation databases

BioMutaiDDX56
DMDMi20139238

2D gel databases

SWISS-2DPAGEiQ9NY93

Proteomic databases

EPDiQ9NY93
MaxQBiQ9NY93
PaxDbiQ9NY93
PeptideAtlasiQ9NY93
PRIDEiQ9NY93
ProteomicsDBi83197

Protocols and materials databases

DNASUi54606
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000258772; ENSP00000258772; ENSG00000136271 [Q9NY93-1]
ENST00000431640; ENSP00000393488; ENSG00000136271 [Q9NY93-2]
GeneIDi54606
KEGGihsa:54606
UCSCiuc003tlg.5 human [Q9NY93-1]

Organism-specific databases

CTDi54606
DisGeNETi54606
EuPathDBiHostDB:ENSG00000136271.10
GeneCardsiDDX56
HGNCiHGNC:18193 DDX56
HPAiCAB037320
HPA019749
MIMi608023 gene
neXtProtiNX_Q9NY93
OpenTargetsiENSG00000136271
PharmGKBiPA134916346
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0346 Eukaryota
ENOG410XR15 LUCA
GeneTreeiENSGT00550000074946
HOGENOMiHOG000253015
HOVERGENiHBG051334
InParanoidiQ9NY93
KOiK14810
OMAiRYRMEDA
OrthoDBiEOG091G04UR
PhylomeDBiQ9NY93
TreeFamiTF300620

Miscellaneous databases

ChiTaRSiDDX56 human
GeneWikiiDDX56
GenomeRNAii54606
PROiPR:Q9NY93
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000136271 Expressed in 221 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_DDX21
HS_DDX56
ExpressionAtlasiQ9NY93 baseline and differential
GenevisibleiQ9NY93 HS

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDDX56_HUMAN
AccessioniPrimary (citable) accession number: Q9NY93
Secondary accession number(s): A4D2K9
, C9JV95, Q6IAE2, Q9H9I8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: October 1, 2000
Last modified: November 7, 2018
This is version 171 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
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