CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015787
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Lysine-specific demethylase 3B 
Protein Synonyms/Alias
 JmjC domain-containing histone demethylation protein 2B; Jumonji domain-containing protein 1B; Nuclear protein 5qNCA 
Gene Name
 KDM3B 
Gene Synonyms/Alias
 C5orf7; JHDM2B; JMJD1B; KIAA1082 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
11AAASPVGKRLLLLFAubiquitination[1, 2, 3]
186NALISDQKLQEIFSRubiquitination[2, 4]
204SVQGHRVKIYQPEGEubiquitination[2]
361IRFATYTKENGRTLVacetylation[5]
449AAGTVPEKQKGSRSQacetylation[6]
795KAPFEAVKRFSLDERacetylation[3]
861ELLLGKSKGKQAPKGubiquitination[2]
876RPRTAPLKVGQSVLKubiquitination[2]
883KVGQSVLKDVSKVKKubiquitination[2]
892VSKVKKLKQSGEPFLubiquitination[2]
913NVAPHLHKCRECRLEubiquitination[2]
924CRLERYRKFKEQEQDubiquitination[2]
926LERYRKFKEQEQDDSubiquitination[2, 3]
1081EEVFSWLKCAKGQSHubiquitination[2]
1121ARGKWGIKANCPCISubiquitination[2]
1193IRSEEPLKTDSSASNubiquitination[4]
1249SLRSVLNKESHSPFGubiquitination[2, 7]
1265DSFNSTAKVSPLTPKubiquitination[2]
1272KVSPLTPKLFNSLLLubiquitination[7, 8]
1287GPTASNNKTEGSSLRubiquitination[2, 4]
1303LLHSGPGKLPQTPLDubiquitination[2, 4]
1327STSSAGVKSKASLPNubiquitination[4]
1347IASVVENKKTSDASKubiquitination[2]
1348ASVVENKKTSDASKRubiquitination[2]
1364CNLTDTQKEVKEMVMubiquitination[2]
1403PSNKNNWKIFRECWKubiquitination[2]
1423LVSGVHKKLKSELWKubiquitination[2]
1425SGVHKKLKSELWKPEubiquitination[2]
1458CAIISDVKVRDFWDGubiquitination[2]
1471DGFEIICKRLRSEDGubiquitination[2]
1484DGQPMVLKLKDWPPGubiquitination[2]
1516LPLPEYTKRDGRLNLubiquitination[2, 4]
1600GDADEVTKQRIHDGKubiquitination[2, 4]
1607KQRIHDGKEKPGALWubiquitination[2]
1609RIHDGKEKPGALWHIubiquitination[2]
1620LWHIYAAKDAEKIREubiquitination[2]
1631KIRELLRKVGEEQGQubiquitination[2]
1711FVSPEHVKHCFRLTQubiquitination[2]
1733THTNHEDKLQVKNIIubiquitination[2]
Reference
 [1] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [2] 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]
 [3] 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]
 [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]
 [5] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [6] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [7] 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]
 [8] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965] 
Functional Description
 Histone demethylase that specifically demethylates 'Lys- 9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity. 
Sequence Annotation
 DOMAIN 1498 1721 JmjC.
 ZN_FING 1031 1056 C6-type (Potential).
 MOTIF 1293 1297 LXXLL motif.
 METAL 1560 1560 Iron; catalytic (By similarity).
 METAL 1562 1562 Iron; catalytic (By similarity).
 METAL 1689 1689 Iron; catalytic (By similarity).
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 361 361 N6-acetyllysine.
 MOD_RES 773 773 Phosphoserine.
 MOD_RES 779 779 Phosphoserine.
 MOD_RES 798 798 Phosphoserine.  
Keyword
 Acetylation; Alternative splicing; Chromatin regulator; Complete proteome; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Polymorphism; Reference proteome; Transcription; Transcription regulation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1761 AA 
Protein Sequence
MADAAASPVG KRLLLLFADT AASASASAPA AAAASGDPGP ALRTRAWRAG TVRAMSGAVP 60
QDLAIFVEFD GCNWKQHSWV KVHAEEVIVL LLEGSLVWAP REDPVLLQGI RVSIAQWPAL 120
TFTPLVDKLG LGSVVPVEYL LDRELRFLSD ANGLHLFQMG TDSQNQILLE HAALRETVNA 180
LISDQKLQEI FSRGPYSVQG HRVKIYQPEG EEGWLYGVVS HQDSITRLME VSVTESGEIK 240
SVDPRLIHVM LMDNSAPQSE GGTLKAVKSS KGKKKRESIE GKDGRRRKSA SDSGCDPASK 300
KLKGDRGEVD SNGSDGGEAS RGPWKGGNAS GEPGLDQRAK QPPSTFVPQI NRNIRFATYT 360
KENGRTLVVQ DEPVGGDTPA SFTPYSTATG QTPLAPEVGG AENKEAGKTL EQVGQGIVAS 420
AAVVTTASST PNTVRISDTG LAAGTVPEKQ KGSRSQASGE NSRNSILASS GFGAPLPSSS 480
QPLTFGSGRS QSNGVLATEN KPLGFSFGCS SAQEAQKDTD LSKNLFFQCM SQTLPTSNYF 540
TTVSESLADD SSSRDSFKQS LESLSSGLCK GRSVLGTDTK PGSKAGSSVD RKVPAESMPT 600
LTPAFPRSLL NARTPENHEN LFLQPPKLSR EEPSNPFLAF VEKVEHSPFS SFASQASGSS 660
SSATTVTSKV APSWPESHSS ADSASLAKKK PLFITTDSSK LVSGVLGSAL TSGGPSLSAM 720
GNGRSSSPTS SLTQPIEMPT LSSSPTEERP TVGPGQQDNP LLKTFSNVFG RHSGGFLSSP 780
ADFSQENKAP FEAVKRFSLD ERSLACRQDS DSSTNSDLSD LSDSEEQLQA KTGLKGIPEH 840
LMGKLGPNGE RSAELLLGKS KGKQAPKGRP RTAPLKVGQS VLKDVSKVKK LKQSGEPFLQ 900
DGSCINVAPH LHKCRECRLE RYRKFKEQEQ DDSTVACRFF HFRRLIFTRK GVLRVEGFLS 960
PQQSDPDAMN LWIPSSSLAE GIDLETSKYI LANVGDQFCQ LVMSEKEAMM MVEPHQKVAW 1020
KRAVRGVREM CDVCETTLFN IHWVCRKCGF GVCLDCYRLR KSRPRSETEE MGDEEVFSWL 1080
KCAKGQSHEP ENLMPTQIIP GTALYNIGDM VHAARGKWGI KANCPCISRQ NKSVLRPAVT 1140
NGMSQLPSIN PSASSGNETT FSGGGGPAPV TTPEPDHVPK ADSTDIRSEE PLKTDSSASN 1200
SNSELKAIRP PCPDTAPPSS ALHWLADLAT QKAKEETKEA GSLRSVLNKE SHSPFGLDSF 1260
NSTAKVSPLT PKLFNSLLLG PTASNNKTEG SSLRDLLHSG PGKLPQTPLD TGIPFPPVFS 1320
TSSAGVKSKA SLPNFLDHII ASVVENKKTS DASKRACNLT DTQKEVKEMV MGLNVLDPHT 1380
SHSWLCDGRL LCLHDPSNKN NWKIFRECWK QGQPVLVSGV HKKLKSELWK PEAFSQEFGD 1440
QDVDLVNCRN CAIISDVKVR DFWDGFEIIC KRLRSEDGQP MVLKLKDWPP GEDFRDMMPT 1500
RFEDLMENLP LPEYTKRDGR LNLASRLPSY FVRPDLGPKM YNAYGLITAE DRRVGTTNLH 1560
LDVSDAVNVM VYVGIPIGEG AHDEEVLKTI DEGDADEVTK QRIHDGKEKP GALWHIYAAK 1620
DAEKIRELLR KVGEEQGQEN PPDHDPIHDQ SWYLDQTLRK RLYEEYGVQG WAIVQFLGDA 1680
VFIPAGAPHQ VHNLYSCIKV AEDFVSPEHV KHCFRLTQEF RHLSNTHTNH EDKLQVKNII 1740
YHAVKDAVGT LKAHESKLAR S 1761 
Gene Ontology
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:UniProtKB-KW.
 GO:0016568; P:chromatin modification; IEA:UniProtKB-KW.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR003347; JmjC_dom. 
Pfam
 PF02373; JmjC 
SMART
 SM00558; JmjC 
PROSITE
 PS51184; JMJC 
PRINTS