CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-007473
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Lysine-specific demethylase 5C 
Protein Synonyms/Alias
 Histone demethylase JARID1C; Jumonji/ARID domain-containing protein 1C; Protein SmcX; Protein Xe169 
Gene Name
 KDM5C 
Gene Synonyms/Alias
 DXS1272E; JARID1C; SMCX; XE169 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
40KIRPIAEKSGICKIRubiquitination[1]
45AEKSGICKIRPPADWubiquitination[1]
82LEAQTRVKLNYLDQIubiquitination[1]
91NYLDQIAKFWEIQGSubiquitination[1]
101EIQGSSLKIPNVERRubiquitination[1, 2, 3]
205RQSVQPSKFNSYGRRubiquitination[1]
235EKNPELKKLQIYGAGubiquitination[1]
307HSPEPCTKMTMRLRRubiquitination[1]
370KGVWRCPKCVMAECKubiquitination[1]
377KCVMAECKRPPEAFGubiquitination[1]
459GFPVSDSKRHLTPEEubiquitination[1]
550EHLEEVMKKLTPELFubiquitination[4]
657KMAACPEKLDLNLAAubiquitination[1]
682QEERRLRKALLEKGIubiquitination[1]
687LRKALLEKGITEAERubiquitination[4]
776SFDTWANKVRVALEVubiquitination[1]
935ARWLDEVKRTLAPSAubiquitination[1]
996LCLEARQKHPPATLEubiquitination[1]
1023LPNIQALKEALAKARubiquitination[1]
1092ASKTFLKKNSCYTLLubiquitination[1]
1114DAGSDSTKRSRWMEKubiquitination[1]
1121KRSRWMEKELGLYKSubiquitination[1, 2, 3]
1442RTLLELEKAERHGSRubiquitination[1]
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] 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]
 [3] 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]
 [4] 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
Functional Description
 Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. 
Sequence Annotation
 DOMAIN 14 55 JmjN.
 DOMAIN 79 169 ARID.
 DOMAIN 468 634 JmjC.
 ZN_FING 326 372 PHD-type 1.
 ZN_FING 1187 1248 PHD-type 2.
 METAL 514 514 Iron; catalytic (By similarity).
 METAL 517 517 Iron; catalytic (By similarity).
 METAL 602 602 Iron; catalytic (By similarity).
 MOD_RES 317 317 Phosphoserine.
 MOD_RES 1359 1359 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Chromatin regulator; Complete proteome; Dioxygenase; Disease mutation; Iron; Mental retardation; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Reference proteome; Repeat; Transcription; Transcription regulation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1560 AA 
Protein Sequence
MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 60
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVV 120
EEGGYEAICK DRRWARVAQR LNYPPGKNIG SLLRSHYERI VYPYEMYQSG ANLVQCNTRP 180
FDNEEKDKEY KPHSIPLRQS VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG 240
AGPKMMGLGL MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKVESTSPKT FLESKEELSH 300
SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH IFCLLPPLPE 360
IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM ADSFKADYFN MPVHMVPTEL 420
VEKEFWRLVN SIEEDVTVEY GADIHSKEFG SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP 480
VLEQSVLCHI NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL 540
AAEHLEEVMK KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA 600
YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAACPEKLDL 660
NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL PDDERQCIKC KTTCFLSALA 720
CYDCPDGLVC LSHINDLCKC SSSRQYLRYR YTLDELPAML HKLKVRAESF DTWANKVRVA 780
LEVEDGRKRS LEELRALESE ARERRFPNSE LLQQLKNCLS EAEACVSRAL GLVSGQEAGP 840
HRVAGLQMTL TELRAFLDQM NNLPCAMHQI GDVKGVLEQV EAYQAEAREA LASLPSSPGL 900
LQSLLERGRQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAVM RGLLVAGASV 960
APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA TLEAIIREAE NIPVHLPNIQ 1020
ALKEALAKAR AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS 1080
WREKASKTFL KKNSCYTLLE VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL 1140
RDPGSVIVAF KEGEQKEKEG ILQLRRTNSA KPSPLASSST ASSTTSICVC GQVLAGAGAL 1200
QCDLCQDWFH GRCVSVPRLL SSPRPNPTSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA 1260
LLVALQRLPV RLPEGEALQC LTERAISWQG RARQALASED VTALLGRLAE LRQRLQAEPR 1320
PEEPPNYPAA PASDPLREGS GKDMPKVQGL LENGDSVTSP EKVAPEEGSG KRDLELLSSL 1380
LPQLTGPVLE LPEATRAPLE ELMMEGDLLE VTLDENHSIW QLLQAGQPPD LERIRTLLEL 1440
EKAERHGSRA RGRALERRRR RKVDRGGEGD DPAREELEPK RVRSSGPEAE EVQEEEELEE 1500
ETGGEGPPAP IPTTGSPSTQ ENQNGLEPAE GTTSGPSAPF STLTPRLHLP CPQQPPQQQL 1560 
Gene Ontology
 GO:0005634; C:nucleus; IDA:MGI.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0032453; F:histone demethylase activity (H3-K4 specific); IDA:MGI.
 GO:0016706; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors; IEA:InterPro.
 GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:UniProtKB-KW.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR001606; ARID/BRIGHT_DNA-bd.
 IPR003347; JmjC_dom.
 IPR013637; Lys_sp_deMease_like_dom.
 IPR003349; TF_JmjN.
 IPR019786; Zinc_finger_PHD-type_CS.
 IPR004198; Znf_C5HC2.
 IPR011011; Znf_FYVE_PHD.
 IPR001965; Znf_PHD.
 IPR019787; Znf_PHD-finger.
 IPR013083; Znf_RING/FYVE/PHD. 
Pfam
 PF01388; ARID
 PF02373; JmjC
 PF02375; JmjN
 PF00628; PHD
 PF08429; PLU-1
 PF02928; zf-C5HC2 
SMART
 SM00501; BRIGHT
 SM00558; JmjC
 SM00545; JmjN
 SM00249; PHD 
PROSITE
 PS51011; ARID
 PS51184; JMJC
 PS51183; JMJN
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS