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Protein

Probable ATP-dependent RNA helicase YTHDC2

Gene

YTHDC2

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

Functioni

Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (PubMed:26318451). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:26318451).1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei1310N6-methyladenosineBy similarity1
Binding sitei1360N6-methyladenosineBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi216 – 223ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: GO_Central
  • N6-methyladenosine-containing RNA binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • RNA-dependent ATPase activity Source: AgBase
  • RNA polymerase binding Source: AgBase

GO - Biological processi

  • positive regulation by host of viral genome replication Source: AgBase
  • response to interleukin-1 Source: AgBase
  • response to tumor necrosis factor Source: AgBase
  • RNA processing Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000047188-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ATP-dependent RNA helicase YTHDC2 (EC:3.6.4.13)
Alternative name(s):
YTH domain-containing protein 2
Gene namesi
Name:YTHDC2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:24721. YTHDC2.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: AgBase
  • nucleus Source: GO_Central
Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

DisGeNETi64848.
OpenTargetsiENSG00000047188.
PharmGKBiPA134912676.

Polymorphism and mutation databases

BioMutaiYTHDC2.
DMDMi239938805.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002493401 – 1430Probable ATP-dependent RNA helicase YTHDC2Add BLAST1430

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1089PhosphoserineCombined sources1
Modified residuei1090PhosphoserineBy similarity1
Modified residuei1092PhosphoserineCombined sources1
Modified residuei1202PhosphoserineCombined sources1
Modified residuei1263PhosphoserineBy similarity1
Modified residuei1267PhosphoserineBy similarity1
Modified residuei1281PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H6S0.
MaxQBiQ9H6S0.
PaxDbiQ9H6S0.
PeptideAtlasiQ9H6S0.
PRIDEiQ9H6S0.

PTM databases

iPTMnetiQ9H6S0.
PhosphoSitePlusiQ9H6S0.

Expressioni

Gene expression databases

BgeeiENSG00000047188.
CleanExiHS_YTHDC2.
ExpressionAtlasiQ9H6S0. baseline and differential.
GenevisibleiQ9H6S0. HS.

Organism-specific databases

HPAiHPA037364.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
Irak1Q99J342EBI-1057466,EBI-6117042From a different organism.
IRF4Q153062EBI-1057466,EBI-751345
MeiocA2AG062EBI-1057466,EBI-11664020From a different organism.

GO - Molecular functioni

  • RNA polymerase binding Source: AgBase

Protein-protein interaction databases

BioGridi122321. 36 interactors.
IntActiQ9H6S0. 19 interactors.
MINTiMINT-6944358.
STRINGi9606.ENSP00000161863.

Structurei

Secondary structure

11430
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1289 – 1298Combined sources10
Helixi1299 – 1306Combined sources8
Beta strandi1309 – 1311Combined sources3
Helixi1317 – 1326Combined sources10
Beta strandi1330 – 1342Combined sources13
Beta strandi1344 – 1348Combined sources5
Beta strandi1352 – 1354Combined sources3
Beta strandi1368 – 1375Combined sources8
Helixi1381 – 1384Combined sources4
Beta strandi1404 – 1406Combined sources3
Helixi1410 – 1415Combined sources6
Helixi1416 – 1419Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YU6NMR-A1288-1421[»]
ProteinModelPortaliQ9H6S0.
SMRiQ9H6S0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H6S0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini38 – 106R3HPROSITE-ProRule annotationAdd BLAST69
Domaini203 – 369Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST167
Repeati506 – 538ANK 1Add BLAST33
Repeati539 – 571ANK 2Add BLAST33
Domaini612 – 784Helicase C-terminalPROSITE-ProRule annotationAdd BLAST173
Domaini1288 – 1418YTHPROSITE-ProRule annotationAdd BLAST131

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1294 – 1296N6-methyladenosine bindingBy similarity3

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi316 – 319DEAH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi15 – 31Gly-richAdd BLAST17
Compositional biasi1248 – 1281Ser-richAdd BLAST34

Domaini

The YTH domain mediates RNA-binding.By similarity

Sequence similaritiesi

Contains 2 ANK repeats.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 R3H domain.PROSITE-ProRule annotation
Contains 1 YTH domain.PROSITE-ProRule annotation

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

eggNOGiKOG0920. Eukaryota.
KOG0922. Eukaryota.
KOG1902. Eukaryota.
COG1643. LUCA.
GeneTreeiENSGT00760000119189.
HOGENOMiHOG000155703.
HOVERGENiHBG063891.
InParanoidiQ9H6S0.
KOiK20099.
OMAiDAMDTWE.
OrthoDBiEOG091G0CXN.
PhylomeDBiQ9H6S0.
TreeFamiTF318311.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
3.30.1370.50. 1 hit.
3.40.50.1820. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR029058. AB_hydrolase.
IPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001374. R3H_dom.
IPR007275. YTH_domain.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
PF01424. R3H. 1 hit.
PF04146. YTH. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
SM00393. R3H. 1 hit.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF82708. SSF82708. 1 hit.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51061. R3H. 1 hit.
PS50882. YTH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9H6S0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRPSSVSPR QPAPGGGGGG GPSPCGPGGG GRAKGLKDIR IDEEVKIAVN
60 70 80 90 100
IALERFRYGD QREMEFPSSL TSTERAFIHR LSQSLGLVSK SKGKGANRYL
110 120 130 140 150
TVKKKDGSET AHAMMTCNLT HNTKHAVRSL IQRFPVTNKE RTELLPKTER
160 170 180 190 200
GNVFAVEAEN REMSKTSGRL NNGIPQIPVK RGESEFDSFR QSLPVFEKQE
210 220 230 240 250
EIVKIIKENK VVLIVGETGS GKTTQIPQFL LDDCFKNGIP CRIFCTQPRR
260 270 280 290 300
LAAIAVAERV AAERRERIGQ TIGYQIRLES RVSPKTLLTF CTNGVLLRTL
310 320 330 340 350
MAGDSTLSTV THVIVDEVHE RDRFSDFLLT KLRDLLQKHP TLKLILSSAA
360 370 380 390 400
LDVNLFIRYF GSCPVIYIQG RPFEVKEMFL EDILRTTGYT NKEMLKYKKE
410 420 430 440 450
KQQEEKQQTT LTEWYSAQEN SFKPESQRQR TVLNVTDEYD LLDDGGDAVF
460 470 480 490 500
SQLTEKDVNC LEPWLIKEMD ACLSDIWLHK DIDAFAQVFH LILTENVSVD
510 520 530 540 550
YRHSETSATA LMVAAGRGFA SQVEQLISMG ANVHSKASNG WMALDWAKHF
560 570 580 590 600
GQTEIVDLLE SYSATLEFGN LDESSLVQTN GSDLSAEDRE LLKAYHHSFD
610 620 630 640 650
DEKVDLDLIM HLLYNICHSC DAGAVLIFLP GYDEIVGLRD RILFDDKRFA
660 670 680 690 700
DSTHRYQVFM LHSNMQTSDQ KKVLKNPPAG VRKIILSTNI AETSITVNDV
710 720 730 740 750
VFVIDSGKVK EKSFDALNFV TMLKMVWISK ASAIQRKGRA GRCRPGICFR
760 770 780 790 800
LFSRLRFQNM LEFQTPELLR MPLQELCLHT KLLAPVNCPI ADFLMKAPEP
810 820 830 840 850
PPALIVRNAV QMLKTIDAMD TWEDLTELGY HLADLPVEPH LGKMVLCAVV
860 870 880 890 900
LKCLDPILTI ACTLAYRDPF VLPTQASQKR AAMLCRKRFT AGAFSDHMAL
910 920 930 940 950
LRAFQAWQKA RSDGWERAFC EKNFLSQATM EIIIGMRTQL LGQLRASGFV
960 970 980 990 1000
RARGGGDIRD VNTNSENWAV VKAALVAGMY PNLVHVDREN LVLTGPKEKK
1010 1020 1030 1040 1050
VRFHPASVLS QPQYKKIPPA NGQAAAIKAL PTDWLIYDEM TRAHRIANIR
1060 1070 1080 1090 1100
CCSAVTPVTI LVFCGPARLA SNALQEPSSF RVDGIPNDSS DSEMEDKTTA
1110 1120 1130 1140 1150
NLAALKLDEW LHFTLEPEAA SLLLQLRQKW HSLFLRRMRA PSKPWSQVDE
1160 1170 1180 1190 1200
ATIRAIIAVL STEEQSAGLQ QPSGIGQRPR PMSSEELPLA SSWRSNNSRK
1210 1220 1230 1240 1250
SSADTEFSDE CTTAERVLMK SPSPALHPPQ KYKDRGILHP KRGTEDRSDQ
1260 1270 1280 1290 1300
SSLKSTDSSS YPSPCASPSP PSSGKGSKSP SPRPNMPVRY FIMKSSNLRN
1310 1320 1330 1340 1350
LEISQQKGIW STTPSNERKL NRAFWESSIV YLVFSVQGSG HFQGFSRMSS
1360 1370 1380 1390 1400
EIGREKSQDW GSAGLGGVFK VEWIRKESLP FQFAHHLLNP WNDNKKVQIS
1410 1420 1430
RDGQELEPLV GEQLLQLWER LPLGEKNTTD
Length:1,430
Mass (Da):160,248
Last modified:June 16, 2009 - v2
Checksum:iA0C3B45771A3DE16
GO

Sequence cautioni

The sequence BAB15183 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti860I → V in BAB15183 (PubMed:14702039).Curated1
Sequence conflicti993L → S in BAB15183 (PubMed:14702039).Curated1
Sequence conflicti1230Q → R in BAB15183 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_058002652S → N.Corresponds to variant rs10071816dbSNPEnsembl.1
Natural variantiVAR_0580031409L → Q.1 PublicationCorresponds to variant rs1132528dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC093208 Genomic DNA. No translation available.
AC010389 Genomic DNA. No translation available.
BC137285 mRNA. Translation: AAI37286.1.
AK025593 mRNA. Translation: BAB15183.1. Different initiation.
CCDSiCCDS4113.1.
RefSeqiNP_073739.3. NM_022828.4.
XP_016865219.1. XM_017009730.1.
UniGeneiHs.231942.

Genome annotation databases

EnsembliENST00000161863; ENSP00000161863; ENSG00000047188.
GeneIDi64848.
KEGGihsa:64848.
UCSCiuc003kqn.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC093208 Genomic DNA. No translation available.
AC010389 Genomic DNA. No translation available.
BC137285 mRNA. Translation: AAI37286.1.
AK025593 mRNA. Translation: BAB15183.1. Different initiation.
CCDSiCCDS4113.1.
RefSeqiNP_073739.3. NM_022828.4.
XP_016865219.1. XM_017009730.1.
UniGeneiHs.231942.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YU6NMR-A1288-1421[»]
ProteinModelPortaliQ9H6S0.
SMRiQ9H6S0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122321. 36 interactors.
IntActiQ9H6S0. 19 interactors.
MINTiMINT-6944358.
STRINGi9606.ENSP00000161863.

PTM databases

iPTMnetiQ9H6S0.
PhosphoSitePlusiQ9H6S0.

Polymorphism and mutation databases

BioMutaiYTHDC2.
DMDMi239938805.

Proteomic databases

EPDiQ9H6S0.
MaxQBiQ9H6S0.
PaxDbiQ9H6S0.
PeptideAtlasiQ9H6S0.
PRIDEiQ9H6S0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000161863; ENSP00000161863; ENSG00000047188.
GeneIDi64848.
KEGGihsa:64848.
UCSCiuc003kqn.4. human.

Organism-specific databases

CTDi64848.
DisGeNETi64848.
GeneCardsiYTHDC2.
HGNCiHGNC:24721. YTHDC2.
HPAiHPA037364.
MIMi616530. gene.
neXtProtiNX_Q9H6S0.
OpenTargetsiENSG00000047188.
PharmGKBiPA134912676.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0920. Eukaryota.
KOG0922. Eukaryota.
KOG1902. Eukaryota.
COG1643. LUCA.
GeneTreeiENSGT00760000119189.
HOGENOMiHOG000155703.
HOVERGENiHBG063891.
InParanoidiQ9H6S0.
KOiK20099.
OMAiDAMDTWE.
OrthoDBiEOG091G0CXN.
PhylomeDBiQ9H6S0.
TreeFamiTF318311.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000047188-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9H6S0.
GenomeRNAii64848.
PROiQ9H6S0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000047188.
CleanExiHS_YTHDC2.
ExpressionAtlasiQ9H6S0. baseline and differential.
GenevisibleiQ9H6S0. HS.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
3.30.1370.50. 1 hit.
3.40.50.1820. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR029058. AB_hydrolase.
IPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001374. R3H_dom.
IPR007275. YTH_domain.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
PF01424. R3H. 1 hit.
PF04146. YTH. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
SM00393. R3H. 1 hit.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF82708. SSF82708. 1 hit.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51061. R3H. 1 hit.
PS50882. YTH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYTDC2_HUMAN
AccessioniPrimary (citable) accession number: Q9H6S0
Secondary accession number(s): B2RP66
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: June 16, 2009
Last modified: November 30, 2016
This is version 119 of the entry and version 2 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 5
    Human chromosome 5: 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

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.