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Protein

Probable ATP-dependent RNA helicase DDX23

Gene

DDX23

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi435 – 442ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: ProtInc
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • cis assembly of pre-catalytic spliceosome Source: HGNC
  • mRNA splicing, via spliceosome Source: UniProtKB
  • RNA secondary structure unwinding Source: GO_Central
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000174243-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX23 (EC:3.6.4.13)
Alternative name(s):
100 kDa U5 snRNP-specific protein
DEAD box protein 23
PRP28 homolog
U5-100kD
Gene namesi
Name:DDX23
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:17347. DDX23.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • nucleolus Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • U5 snRNP Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi9416.
OpenTargetsiENSG00000174243.
PharmGKBiPA134934941.

Polymorphism and mutation databases

BioMutaiDDX23.
DMDMi160385708.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000551281 – 820Probable ATP-dependent RNA helicase DDX23Add BLAST820

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei14PhosphoserineCombined sources1
Modified residuei16PhosphoserineCombined sources1
Modified residuei107PhosphoserineCombined sources1
Modified residuei109PhosphoserineCombined sources1

Post-translational modificationi

In vitro phosphorylated by CLK1 and U1 snRNP-associated protein kinase. Phosphorylated by SRPK2 and this phosphorylation is required for its association with the tri-snRNP (U4/U6-U5 tri-small nuclear ribonucleoproteins) and subsequent spliceosomal B complex formation.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9BUQ8.
MaxQBiQ9BUQ8.
PaxDbiQ9BUQ8.
PeptideAtlasiQ9BUQ8.
PRIDEiQ9BUQ8.

PTM databases

iPTMnetiQ9BUQ8.
PhosphoSitePlusiQ9BUQ8.
SwissPalmiQ9BUQ8.

Expressioni

Gene expression databases

BgeeiENSG00000174243.
CleanExiHS_DDX23.
ExpressionAtlasiQ9BUQ8. baseline and differential.
GenevisibleiQ9BUQ8. HS.

Organism-specific databases

HPAiHPA038680.
HPA039037.

Interactioni

Subunit structurei

The phosphorylated form (by SRPK2) is a component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Identified in the spliceosome C complex. Interacts with ERBB4.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
TERF1P542742EBI-540096,EBI-710997

Protein-protein interaction databases

BioGridi114811. 80 interactors.
DIPiDIP-34974N.
IntActiQ9BUQ8. 23 interactors.
MINTiMINT-1572793.
STRINGi9606.ENSP00000310723.

Structurei

Secondary structure

1820
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi357 – 359Combined sources3
Helixi362 – 364Combined sources3
Helixi367 – 377Combined sources11
Beta strandi379 – 385Combined sources7
Turni393 – 395Combined sources3
Helixi400 – 409Combined sources10
Helixi416 – 425Combined sources10
Turni426 – 428Combined sources3
Beta strandi431 – 434Combined sources4
Helixi441 – 455Combined sources15
Helixi458 – 461Combined sources4
Beta strandi470 – 474Combined sources5
Helixi478 – 492Combined sources15
Helixi493 – 495Combined sources3
Beta strandi499 – 502Combined sources4
Beta strandi504 – 506Combined sources3
Helixi508 – 516Combined sources9
Beta strandi520 – 524Combined sources5
Helixi526 – 534Combined sources9
Beta strandi545 – 550Combined sources6
Helixi551 – 556Combined sources6
Helixi560 – 567Combined sources8
Helixi572 – 574Combined sources3
Helixi580 – 583Combined sources4
Helixi585 – 593Combined sources9
Helixi595 – 597Combined sources3
Beta strandi601 – 607Combined sources7
Helixi611 – 620Combined sources10
Beta strandi625 – 629Combined sources5
Helixi635 – 638Combined sources4
Beta strandi639 – 645Combined sources7
Helixi648 – 650Combined sources3
Helixi651 – 660Combined sources10
Beta strandi667 – 670Combined sources4
Helixi674 – 686Combined sources13
Beta strandi691 – 693Combined sources3
Helixi704 – 712Combined sources9
Beta strandi717 – 720Combined sources4
Beta strandi734 – 740Combined sources7
Helixi745 – 752Combined sources8
Helixi753 – 755Combined sources3
Beta strandi757 – 760Combined sources4
Beta strandi763 – 768Combined sources6
Helixi770 – 775Combined sources6
Helixi776 – 784Combined sources9
Helixi793 – 796Combined sources4
Helixi799 – 801Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00F1-820[»]
4NHOX-ray2.00A338-820[»]
ProteinModelPortaliQ9BUQ8.
SMRiQ9BUQ8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini422 – 627Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST206
Domaini651 – 799Helicase C-terminalPROSITE-ProRule annotationAdd BLAST149

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi391 – 419Q motifAdd BLAST29
Motifi549 – 552DEAD box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi20 – 122Arg-richAdd BLAST103
Compositional biasi128 – 240Glu-richAdd BLAST113

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG0333. Eukaryota.
ENOG410XNVG. LUCA.
GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268796.
HOVERGENiHBG102054.
InParanoidiQ9BUQ8.
KOiK12858.
OMAiNPIYKEK.
OrthoDBiEOG091G032I.
PhylomeDBiQ9BUQ8.
TreeFamiTF300527.

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.
IPR000629. RNA-helicase_DEAD-box_CS.
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. 2 hits.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. 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. AlignAdd to basket

Isoform 1 (identifier: Q9BUQ8-1) [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
MAGELADKKD RDASPSKEER KRSRTPDRER DRDRDRKSSP SKDRKRHRSR
60 70 80 90 100
DRRRGGSRSR SRSRSKSAER ERRHKERERD KERDRNKKDR DRDKDGHRRD
110 120 130 140 150
KDRKRSSLSP GRGKDFKSRK DRDSKKDEED EHGDKKPKAQ PLSLEELLAK
160 170 180 190 200
KKAEEEAEAK PKFLSKAERE AEALKRRQQE VEERQRMLEE ERKKRKQFQD
210 220 230 240 250
LGRKMLEDPQ ERERRERRER MERETNGNED EEGRQKIREE KDKSKELHAI
260 270 280 290 300
KERYLGGIKK RRRTRHLNDR KFVFEWDASE DTSIDYNPLY KERHQVQLLG
310 320 330 340 350
RGFIAGIDLK QQKREQSRFY GDLMEKRRTL EEKEQEEARL RKLRKKEAKQ
360 370 380 390 400
RWDDRHWSQK KLDEMTDRDW RIFREDYSIT TKGGKIPNPI RSWKDSSLPP
410 420 430 440 450
HILEVIDKCG YKEPTPIQRQ AIPIGLQNRD IIGVAETGSG KTAAFLIPLL
460 470 480 490 500
VWITTLPKID RIEESDQGPY AIILAPTREL AQQIEEETIK FGKPLGIRTV
510 520 530 540 550
AVIGGISRED QGFRLRMGCE IVIATPGRLI DVLENRYLVL SRCTYVVLDE
560 570 580 590 600
ADRMIDMGFE PDVQKILEHM PVSNQKPDTD EAEDPEKMLA NFESGKHKYR
610 620 630 640 650
QTVMFTATMP PAVERLARSY LRRPAVVYIG SAGKPHERVE QKVFLMSESE
660 670 680 690 700
KRKKLLAILE QGFDPPIIIF VNQKKGCDVL AKSLEKMGYN ACTLHGGKGQ
710 720 730 740 750
EQREFALSNL KAGAKDILVA TDVAGRGIDI QDVSMVVNYD MAKNIEDYIH
760 770 780 790 800
RIGRTGRAGK SGVAITFLTK EDSAVFYELK QAILESPVSS CPPELANHPD
810 820
AQHKPGTILT KKRREETIFA
Length:820
Mass (Da):95,583
Last modified:October 23, 2007 - v3
Checksum:i01DD5BCF8BFBA2DB
GO
Isoform 2 (identifier: Q9BUQ8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     107-108: SL → RH
     109-820: Missing.

Note: No experimental confirmation available.
Show »
Length:108
Mass (Da):13,401
Checksum:iE188544D668BD767
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti137P → L in AAB87902 (PubMed:9409622).Curated1
Sequence conflicti281D → E in AAB87902 (PubMed:9409622).Curated1
Sequence conflicti309L → F in AAB87902 (PubMed:9409622).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_056575107 – 108SL → RH in isoform 2. 1 Publication2
Alternative sequenceiVSP_056576109 – 820Missing in isoform 2. 1 PublicationAdd BLAST712

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF026402 mRNA. Translation: AAB87902.1.
AK294877 mRNA. Translation: BAG57976.1.
AK312379 mRNA. Translation: BAG35297.1.
AC117498 Genomic DNA. No translation available.
CH471111 Genomic DNA. Translation: EAW58011.1.
BC002366 mRNA. Translation: AAH02366.1.
CCDSiCCDS8770.1. [Q9BUQ8-1]
RefSeqiNP_004809.2. NM_004818.2. [Q9BUQ8-1]
UniGeneiHs.130098.

Genome annotation databases

EnsembliENST00000308025; ENSP00000310723; ENSG00000174243. [Q9BUQ8-1]
ENST00000547135; ENSP00000446770; ENSG00000174243. [Q9BUQ8-2]
GeneIDi9416.
KEGGihsa:9416.
UCSCiuc001rsm.4. human. [Q9BUQ8-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF026402 mRNA. Translation: AAB87902.1.
AK294877 mRNA. Translation: BAG57976.1.
AK312379 mRNA. Translation: BAG35297.1.
AC117498 Genomic DNA. No translation available.
CH471111 Genomic DNA. Translation: EAW58011.1.
BC002366 mRNA. Translation: AAH02366.1.
CCDSiCCDS8770.1. [Q9BUQ8-1]
RefSeqiNP_004809.2. NM_004818.2. [Q9BUQ8-1]
UniGeneiHs.130098.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00F1-820[»]
4NHOX-ray2.00A338-820[»]
ProteinModelPortaliQ9BUQ8.
SMRiQ9BUQ8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114811. 80 interactors.
DIPiDIP-34974N.
IntActiQ9BUQ8. 23 interactors.
MINTiMINT-1572793.
STRINGi9606.ENSP00000310723.

PTM databases

iPTMnetiQ9BUQ8.
PhosphoSitePlusiQ9BUQ8.
SwissPalmiQ9BUQ8.

Polymorphism and mutation databases

BioMutaiDDX23.
DMDMi160385708.

Proteomic databases

EPDiQ9BUQ8.
MaxQBiQ9BUQ8.
PaxDbiQ9BUQ8.
PeptideAtlasiQ9BUQ8.
PRIDEiQ9BUQ8.

Protocols and materials databases

DNASUi9416.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000308025; ENSP00000310723; ENSG00000174243. [Q9BUQ8-1]
ENST00000547135; ENSP00000446770; ENSG00000174243. [Q9BUQ8-2]
GeneIDi9416.
KEGGihsa:9416.
UCSCiuc001rsm.4. human. [Q9BUQ8-1]

Organism-specific databases

CTDi9416.
DisGeNETi9416.
GeneCardsiDDX23.
HGNCiHGNC:17347. DDX23.
HPAiHPA038680.
HPA039037.
MIMi612172. gene.
neXtProtiNX_Q9BUQ8.
OpenTargetsiENSG00000174243.
PharmGKBiPA134934941.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0333. Eukaryota.
ENOG410XNVG. LUCA.
GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268796.
HOVERGENiHBG102054.
InParanoidiQ9BUQ8.
KOiK12858.
OMAiNPIYKEK.
OrthoDBiEOG091G032I.
PhylomeDBiQ9BUQ8.
TreeFamiTF300527.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000174243-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiDDX23. human.
GeneWikiiDDX23.
GenomeRNAii9416.
PROiQ9BUQ8.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000174243.
CleanExiHS_DDX23.
ExpressionAtlasiQ9BUQ8. baseline and differential.
GenevisibleiQ9BUQ8. HS.

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.
IPR000629. RNA-helicase_DEAD-box_CS.
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. 2 hits.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDX23_HUMAN
AccessioniPrimary (citable) accession number: Q9BUQ8
Secondary accession number(s): B2R600, B4DH15, O43188
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: October 23, 2007
Last modified: November 2, 2016
This is version 150 of the entry and version 3 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.