CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-021445
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ATP-dependent RNA helicase YTHDC2 
Protein Synonyms/Alias
  
Gene Name
 YTHDC2 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
90QSLGLVSKSKGKGANubiquitination[1]
180GIPQIPVKRGESEFDubiquitination[2]
236FLLDDCFKNGIPCRIubiquitination[1]
285LESRVSPKTLLTFCTubiquitination[1]
399KEMLKYKKEKQQEEKacetylation[3]
406KEKQQEEKQQTTLTEacetylation[3]
423SAQENSFKPESQRQRubiquitination[1]
647DRILFDDKRFADSTHubiquitination[1]
1016LSQPQYKKIPPANGQubiquitination[1]
1143RRMRAPSKPWSQVDEubiquitination[1]
1307NLEISQQKGIWSTTPubiquitination[1, 4, 5]
1356SSEIGREKSQDWGSAubiquitination[1]
1426ERLPLGEKNTTD***ubiquitination[1, 2, 6]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [4] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [5] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [6] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302
Functional Description
  
Sequence Annotation
 DOMAIN 38 106 R3H.
 DOMAIN 203 369 Helicase ATP-binding.
 REPEAT 506 538 ANK 1.
 REPEAT 539 571 ANK 2.
 DOMAIN 612 784 Helicase C-terminal.
 DOMAIN 1288 1418 YTH.
 NP_BIND 216 223 ATP (By similarity).
 MOTIF 316 319 DEAH box.
 MOD_RES 23 23 Phosphoserine.
 MOD_RES 1089 1089 Phosphoserine.
 MOD_RES 1092 1092 Phosphoserine.
 MOD_RES 1281 1281 Phosphoserine.  
Keyword
 3D-structure; ANK repeat; ATP-binding; Complete proteome; Helicase; Hydrolase; Nucleotide-binding; Phosphoprotein; Polymorphism; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1430 AA 
Protein Sequence
MSRPSSVSPR QPAPGGGGGG GPSPCGPGGG GRAKGLKDIR IDEEVKIAVN IALERFRYGD 60
QREMEFPSSL TSTERAFIHR LSQSLGLVSK SKGKGANRYL TVKKKDGSET AHAMMTCNLT 120
HNTKHAVRSL IQRFPVTNKE RTELLPKTER GNVFAVEAEN REMSKTSGRL NNGIPQIPVK 180
RGESEFDSFR QSLPVFEKQE EIVKIIKENK VVLIVGETGS GKTTQIPQFL LDDCFKNGIP 240
CRIFCTQPRR LAAIAVAERV AAERRERIGQ TIGYQIRLES RVSPKTLLTF CTNGVLLRTL 300
MAGDSTLSTV THVIVDEVHE RDRFSDFLLT KLRDLLQKHP TLKLILSSAA LDVNLFIRYF 360
GSCPVIYIQG RPFEVKEMFL EDILRTTGYT NKEMLKYKKE KQQEEKQQTT LTEWYSAQEN 420
SFKPESQRQR TVLNVTDEYD LLDDGGDAVF SQLTEKDVNC LEPWLIKEMD ACLSDIWLHK 480
DIDAFAQVFH LILTENVSVD YRHSETSATA LMVAAGRGFA SQVEQLISMG ANVHSKASNG 540
WMALDWAKHF GQTEIVDLLE SYSATLEFGN LDESSLVQTN GSDLSAEDRE LLKAYHHSFD 600
DEKVDLDLIM HLLYNICHSC DAGAVLIFLP GYDEIVGLRD RILFDDKRFA DSTHRYQVFM 660
LHSNMQTSDQ KKVLKNPPAG VRKIILSTNI AETSITVNDV VFVIDSGKVK EKSFDALNFV 720
TMLKMVWISK ASAIQRKGRA GRCRPGICFR LFSRLRFQNM LEFQTPELLR MPLQELCLHT 780
KLLAPVNCPI ADFLMKAPEP PPALIVRNAV QMLKTIDAMD TWEDLTELGY HLADLPVEPH 840
LGKMVLCAVV LKCLDPILTI ACTLAYRDPF VLPTQASQKR AAMLCRKRFT AGAFSDHMAL 900
LRAFQAWQKA RSDGWERAFC EKNFLSQATM EIIIGMRTQL LGQLRASGFV RARGGGDIRD 960
VNTNSENWAV VKAALVAGMY PNLVHVDREN LVLTGPKEKK VRFHPASVLS QPQYKKIPPA 1020
NGQAAAIKAL PTDWLIYDEM TRAHRIANIR CCSAVTPVTI LVFCGPARLA SNALQEPSSF 1080
RVDGIPNDSS DSEMEDKTTA NLAALKLDEW LHFTLEPEAA SLLLQLRQKW HSLFLRRMRA 1140
PSKPWSQVDE ATIRAIIAVL STEEQSAGLQ QPSGIGQRPR PMSSEELPLA SSWRSNNSRK 1200
SSADTEFSDE CTTAERVLMK SPSPALHPPQ KYKDRGILHP KRGTEDRSDQ SSLKSTDSSS 1260
YPSPCASPSP PSSGKGSKSP SPRPNMPVRY FIMKSSNLRN LEISQQKGIW STTPSNERKL 1320
NRAFWESSIV YLVFSVQGSG HFQGFSRMSS EIGREKSQDW GSAGLGGVFK VEWIRKESLP 1380
FQFAHHLLNP WNDNKKVQIS RDGQELEPLV GEQLLQLWER LPLGEKNTTD 1430 
Gene Ontology
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0008026; F:ATP-dependent helicase activity; IEA:InterPro.
 GO:0003676; F:nucleic acid binding; IEA:InterPro. 
Interpro
 IPR002110; Ankyrin_rpt.
 IPR020683; Ankyrin_rpt-contain_dom.
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR011709; DUF1605.
 IPR007502; Helicase-assoc_dom.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR001374; R3H_ss-bd.
 IPR007275; YTH_domain. 
Pfam
 PF12796; Ank_2
 PF00270; DEAD
 PF04408; HA2
 PF00271; Helicase_C
 PF07717; OB_NTP_bind
 PF01424; R3H
 PF04146; YTH 
SMART
 SM00248; ANK
 SM00487; DEXDc
 SM00847; HA2
 SM00490; HELICc 
PROSITE
 PS50297; ANK_REP_REGION
 PS50088; ANK_REPEAT
 PS00690; DEAH_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS51061; R3H
 PS50882; YTH 
PRINTS