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Q5T1V6

- DDX59_HUMAN

UniProt

Q5T1V6 - DDX59_HUMAN

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Protein

Probable ATP-dependent RNA helicase DDX59

Gene

DDX59

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

Functioni

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri104 – 13330HIT-typeAdd
BLAST
Nucleotide bindingi247 – 2548ATPPROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. helicase activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. RNA binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase DDX59 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 59
Zinc finger HIT domain-containing protein 5
Gene namesi
Name:DDX59
Synonyms:ZNHIT5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:25360. DDX59.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus 1 Publication
Note: Exhibits granular localization in the nucleus, as well as in the cytoplasm.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. intracellular Source: LIFEdb
  3. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Orofaciodigital syndrome 5 (OFD5) [MIM:174300]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD5 patients show the core features of cleft palate, lobulated tongue, and polydactyly. Additional features include frontal bossing and intellectual disability.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti367 – 3671V → G in OFD5; markedly reduced expression in fibroblasts compared to wild-type protein; impaired SHH signaling in SAG-treated fibroblasts. 1 Publication
VAR_070198
Natural varianti534 – 5341G → R in OFD5. 1 Publication
VAR_070199

Keywords - Diseasei

Ciliopathy, Disease mutation

Organism-specific databases

MIMi174300. phenotype.
Orphaneti369902. Orofaciodigital syndrome type 14.
PharmGKBiPA142672000.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 619619Probable ATP-dependent RNA helicase DDX59PRO_0000282713Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei64 – 641Phosphoserine1 Publication
Modified residuei160 – 1601Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ5T1V6.
PaxDbiQ5T1V6.
PRIDEiQ5T1V6.

PTM databases

PhosphoSiteiQ5T1V6.

Expressioni

Tissue specificityi

Expressed in fibroblasts (at protein level).1 Publication

Gene expression databases

BgeeiQ5T1V6.
CleanExiHS_DDX59.
ExpressionAtlasiQ5T1V6. baseline and differential.
GenevestigatoriQ5T1V6.

Organism-specific databases

HPAiHPA047166.

Interactioni

Protein-protein interaction databases

MINTiMINT-4714465.
STRINGi9606.ENSP00000330460.

Structurei

Secondary structure

1
619
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi109 – 1135Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi120 – 1223Combined sources
Beta strandi125 – 1284Combined sources
Helixi129 – 14315Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YQPNMR-A94-146[»]
ProteinModelPortaliQ5T1V6.
SMRiQ5T1V6. Positions 96-146, 168-572.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5T1V6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini234 – 405172Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini416 – 579164Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi203 – 23129Q motifAdd
BLAST
Motifi353 – 3564DEAD box

Domaini

The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 HIT-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri104 – 13330HIT-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0513.
GeneTreeiENSGT00770000120586.
HOGENOMiHOG000006599.
HOVERGENiHBG106120.
InParanoidiQ5T1V6.
OMAiEHPFILN.
OrthoDBiEOG7B8S3D.
PhylomeDBiQ5T1V6.
TreeFamiTF330866.

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.
IPR014014. RNA_helicase_DEAD_Q_motif.
IPR007529. Znf_HIT.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF04438. zf-HIT. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 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: Q5T1V6-1) [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
MFVPRSLKIK RNANDDGKSC VAKIIKPDPE DLQLDKSRDV PVDAVATEAA
60 70 80 90 100
TIDRHISESC PFPSPGGQLA EVHSVSPEQG AKDSHPSEEP VKSFSKTQRW
110 120 130 140 150
AEPGEPICVV CGRYGEYICD KTDEDVCSLE CKAKHLLQVK EKEEKSKLSN
160 170 180 190 200
PQKADSEPES PLNASYVYKE HPFILNLQED QIENLKQQLG ILVQGQEVTR
210 220 230 240 250
PIIDFEHCSL PEVLNHNLKK SGYEVPTPIQ MQMIPVGLLG RDILASADTG
260 270 280 290 300
SGKTAAFLLP VIMRALFESK TPSALILTPT RELAIQIERQ AKELMSGLPR
310 320 330 340 350
MKTVLLVGGL PLPPQLYRLQ QHVKVIIATP GRLLDIIKQS SVELCGVKIV
360 370 380 390 400
VVDEADTMLK MGFQQQVLDI LENIPNDCQT ILVSATIPTS IEQLASQLLH
410 420 430 440 450
NPVRIITGEK NLPCANVRQI ILWVEDPAKK KKLFEILNDK KLFKPPVLVF
460 470 480 490 500
VDCKLGADLL SEAVQKITGL KSISIHSEKS QIERKNILKG LLEGDYEVVV
510 520 530 540 550
STGVLGRGLD LISVRLVVNF DMPSSMDEYV HQIGRVGRLG QNGTAITFIN
560 570 580 590 600
NNSKRLFWDI AKRVKPTGSI LPPQLLNSPY LHDQKRKEQQ KDKQTQNDLV
610
TGANLMDIIR KHDKSNSQK
Length:619
Mass (Da):68,810
Last modified:December 21, 2004 - v1
Checksum:i2B4EE96C11CB48ED
GO
Isoform 2 (identifier: Q5T1V6-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     533-619: IGRVGRLGQN...RKHDKSNSQK → ENTYKSTWRN...KLGLKKNCSS

Note: No experimental confirmation available.

Show »
Length:580
Mass (Da):64,572
Checksum:i11BD25D69906898E
GO

Sequence cautioni

The sequence AAH14183.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence starting in position 433.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti77 – 771P → T in a breast cancer sample; somatic mutation. 1 Publication
VAR_035842
Natural varianti107 – 1071I → V.
Corresponds to variant rs3795634 [ dbSNP | Ensembl ].
VAR_031424
Natural varianti367 – 3671V → G in OFD5; markedly reduced expression in fibroblasts compared to wild-type protein; impaired SHH signaling in SAG-treated fibroblasts. 1 Publication
VAR_070198
Natural varianti472 – 4721S → R.1 Publication
Corresponds to variant rs17854157 [ dbSNP | Ensembl ].
VAR_033001
Natural varianti534 – 5341G → R in OFD5. 1 Publication
VAR_070199

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei533 – 61987IGRVG…SNSQK → ENTYKSTWRNPQHFQQDVRM TLGYVGKAQWEEDNQLKVKL GLKKNCSS in isoform 2. 1 PublicationVSP_024227Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL136611 mRNA. Translation: CAB66546.1.
AL445483 Genomic DNA. Translation: CAI17055.1.
AL445483 Genomic DNA. Translation: CAI17056.1.
BC014183 mRNA. Translation: AAH14183.1. Sequence problems.
BC041801 mRNA. Translation: AAH41801.1.
CCDSiCCDS30964.1. [Q5T1V6-1]
RefSeqiNP_001026895.2. NM_001031725.4. [Q5T1V6-1]
UniGeneiHs.497332.

Genome annotation databases

EnsembliENST00000331314; ENSP00000330460; ENSG00000118197. [Q5T1V6-1]
ENST00000447706; ENSP00000394367; ENSG00000118197. [Q5T1V6-2]
GeneIDi83479.
KEGGihsa:83479.
UCSCiuc009wzk.3. human. [Q5T1V6-1]

Polymorphism databases

DMDMi74762230.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL136611 mRNA. Translation: CAB66546.1 .
AL445483 Genomic DNA. Translation: CAI17055.1 .
AL445483 Genomic DNA. Translation: CAI17056.1 .
BC014183 mRNA. Translation: AAH14183.1 . Sequence problems.
BC041801 mRNA. Translation: AAH41801.1 .
CCDSi CCDS30964.1. [Q5T1V6-1 ]
RefSeqi NP_001026895.2. NM_001031725.4. [Q5T1V6-1 ]
UniGenei Hs.497332.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2YQP NMR - A 94-146 [» ]
ProteinModelPortali Q5T1V6.
SMRi Q5T1V6. Positions 96-146, 168-572.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

MINTi MINT-4714465.
STRINGi 9606.ENSP00000330460.

PTM databases

PhosphoSitei Q5T1V6.

Polymorphism databases

DMDMi 74762230.

Proteomic databases

MaxQBi Q5T1V6.
PaxDbi Q5T1V6.
PRIDEi Q5T1V6.

Protocols and materials databases

DNASUi 83479.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000331314 ; ENSP00000330460 ; ENSG00000118197 . [Q5T1V6-1 ]
ENST00000447706 ; ENSP00000394367 ; ENSG00000118197 . [Q5T1V6-2 ]
GeneIDi 83479.
KEGGi hsa:83479.
UCSCi uc009wzk.3. human. [Q5T1V6-1 ]

Organism-specific databases

CTDi 83479.
GeneCardsi GC01M200594.
HGNCi HGNC:25360. DDX59.
HPAi HPA047166.
MIMi 174300. phenotype.
615464. gene.
neXtProti NX_Q5T1V6.
Orphaneti 369902. Orofaciodigital syndrome type 14.
PharmGKBi PA142672000.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0513.
GeneTreei ENSGT00770000120586.
HOGENOMi HOG000006599.
HOVERGENi HBG106120.
InParanoidi Q5T1V6.
OMAi EHPFILN.
OrthoDBi EOG7B8S3D.
PhylomeDBi Q5T1V6.
TreeFami TF330866.

Miscellaneous databases

EvolutionaryTracei Q5T1V6.
GeneWikii DDX59.
GenomeRNAii 83479.
NextBioi 72419.
PROi Q5T1V6.
SOURCEi Search...

Gene expression databases

Bgeei Q5T1V6.
CleanExi HS_DDX59.
ExpressionAtlasi Q5T1V6. baseline and differential.
Genevestigatori Q5T1V6.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
IPR007529. Znf_HIT.
[Graphical view ]
Pfami PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF04438. zf-HIT. 1 hit.
[Graphical view ]
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 2 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Fetal brain.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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), VARIANT ARG-472.
    Tissue: Brain and Lung.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-64, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  5. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-160, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  6. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Solution structure of the ZF-hit domain in DEAD (Asp-Glu-Ala-Asp) box polypeptide 59."
    RIKEN structural genomics initiative (RSGI)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 94-146.
  9. Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-77.
  10. "Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome."
    Shamseldin H.E., Rajab A., Alhashem A., Shaheen R., Al-Shidi T., Alamro R., Al Harassi S., Alkuraya F.S.
    Am. J. Hum. Genet. 93:555-560(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS OFD5 GLY-367 AND ARG-534, CHARACTERIZATION OF VARIANT OFD5 GLY-367, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.

Entry informationi

Entry nameiDDX59_HUMAN
AccessioniPrimary (citable) accession number: Q5T1V6
Secondary accession number(s): Q6PJL2, Q8IVW3, Q9H0W3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: December 21, 2004
Last modified: November 26, 2014
This is version 103 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3