CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001129
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Lysine-specific demethylase 4A 
Protein Synonyms/Alias
 JmjC domain-containing histone demethylation protein 3A; Jumonji domain-containing protein 2A 
Gene Name
 KDM4A 
Gene Synonyms/Alias
 JHDM3A; JMJD2; JMJD2A; KIAA0677 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
51LAKVVPPKEWKPRASubiquitination[1]
105RKIANSDKYCTPRYSubiquitination[1, 2]
224KRLERLAKGFFPGSAubiquitination[1, 2, 3]
251LISPLMLKKYGIPFDubiquitination[1]
252ISPLMLKKYGIPFDKubiquitination[1, 4]
301RRWIEYGKQAVLCSCubiquitination[1]
336YKLWKAGKDNTVIDHubiquitination[1]
386DGEEGDLKTSLAKHRubiquitination[5]
820RSPVDVSKIPLPRFKubiquitination[1, 2]
885FITCFRHKIPNLERAubiquitination[1]
1012TLDEELPKRVKSRLSubiquitination[1]
1033FNEIFTEKEVKQEKKubiquitination[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] 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]
 [3] 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]
 [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] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094] 
Functional Description
 Histone demethylase that specifically demethylates 'Lys- 9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. 
Sequence Annotation
 DOMAIN 14 56 JmjN.
 DOMAIN 142 308 JmjC.
 DOMAIN 897 954 Tudor 1.
 DOMAIN 955 1011 Tudor 2.
 ZN_FING 709 767 PHD-type 1.
 ZN_FING 829 885 PHD-type 2.
 REGION 597 638 Interaction with NCOR1.
 METAL 188 188 Iron; catalytic.
 METAL 190 190 Iron; catalytic.
 METAL 234 234 Zinc.
 METAL 240 240 Zinc.
 METAL 276 276 Iron; catalytic.
 METAL 306 306 Zinc.
 METAL 308 308 Zinc.
 BINDING 132 132 Alpha-ketoglutarate.
 BINDING 198 198 Alpha-ketoglutarate.
 BINDING 206 206 Alpha-ketoglutarate.
 BINDING 945 945 Histone H3K4me3.
 BINDING 967 967 Histone H3K4me3.
 BINDING 973 973 Histone H3K4me3.
 MOD_RES 2 2 N-acetylalanine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Chromatin regulator; Complete proteome; Dioxygenase; Host-virus interaction; Iron; Metal-binding; Nucleus; Oxidoreductase; Polymorphism; Reference proteome; Repeat; Transcription; Transcription regulation; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1064 AA 
Protein Sequence
MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP KEWKPRASYD 60
DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI ANSDKYCTPR YSEFEELERK 120
YWKNLTFNPP IYGADVNGTL YEKHVDEWNI GRLRTILDLV EKESGITIEG VNTPYLYFGM 180
WKTSFAWHTE DMDLYSINYL HFGEPKSWYS VPPEHGKRLE RLAKGFFPGS AQSCEAFLRH 240
KMTLISPLML KKYGIPFDKV TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATRRWIEYG 300
KQAVLCSCRK DMVKISMDVF VRKFQPERYK LWKAGKDNTV IDHTLPTPEA AEFLKESELP 360
PRAGNEEECP EEDMEGVEDG EEGDLKTSLA KHRIGTKRHR VCLEIPQEVS QSELFPKEDL 420
SSEQYEMTEC PAALAPVRPT HSSVRQVEDG LTFPDYSDST EVKFEELKNV KLEEEDEEEE 480
QAAAALDLSV NPASVGGRLV FSGSKKKSSS SLGSGSSRDS ISSDSETSEP LSCRAQGQTG 540
VLTVHSYAKG DGRVTVGEPC TRKKGSAARS FSERELAEVA DEYMFSLEEN KKSKGRRQPL 600
SKLPRHHPLV LQECVSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN FEAEKEFNET 660
MAQQAPHCAV CMIFQTYHQV EFGGFNQNCG NASDLAPQKQ RTKPLIPEMC FTSTGCSTDI 720
NLSTPYLEED GTSILVSCKK CSVRVHASCY GVPPAKASED WMCSRCSANA LEEDCCLCSL 780
RGGALQRAND DRWVHVSCAV AILEARFVNI AERSPVDVSK IPLPRFKLKC IFCKKRRKRT 840
AGCCVQCSHG RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALQSIT 900
AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD CLQFGPPAEG 960
EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR DDVYTLDEEL PKRVKSRLSV 1020
ASDMRFNEIF TEKEVKQEKK RQRVINSRYR EDYIEPALYR AIME 1064 
Gene Ontology
 GO:0005813; C:centrosome; IDA:HPA.
 GO:0005737; C:cytoplasm; IDA:HPA.
 GO:0005730; C:nucleolus; IDA:HPA.
 GO:0051864; F:histone demethylase activity (H3-K36 specific); IDA:UniProtKB.
 GO:0035064; F:methylated histone residue binding; IDA:UniProtKB.
 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:0045892; P:negative regulation of transcription, DNA-dependent; IDA:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW. 
Interpro
 IPR003347; JmjC_dom.
 IPR003349; TF_JmjN.
 IPR002999; Tudor.
 IPR011011; Znf_FYVE_PHD.
 IPR001965; Znf_PHD.
 IPR013083; Znf_RING/FYVE/PHD. 
Pfam
 PF02373; JmjC
 PF02375; JmjN 
SMART
 SM00558; JmjC
 SM00545; JmjN
 SM00249; PHD
 SM00333; TUDOR 
PROSITE
 PS51184; JMJC
 PS51183; JMJN
 PS50304; TUDOR
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS