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Showing Protein Lysine-specific demethylase 2A (HMDBP09184)

IdentificationBiological propertiesGene propertiesProtein propertiesExternal linksReferencesXMLShow 6 metabolites
Identification
HMDB Protein ID HMDBP09184
Secondary Accession Numbers
  • 14942
Name Lysine-specific demethylase 2A
Synonyms
  1. CXXC-type zinc finger protein 8
  2. F-box and leucine-rich repeat protein 11
  3. F-box protein FBL7
  4. F-box protein Lilina
  5. F-box/LRR-repeat protein 11
  6. JmjC domain-containing histone demethylation protein 1A
  7. [Histone-H3]-lysine-36 demethylase 1A
Gene Name KDM2A
Protein Type Enzyme
Biological Properties
General Function Involved in DNA binding
Specific Function Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis.
Pathways
  • The oncogenic action of 2-hydroxyglutarate
  • The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria
  • The Oncogenic Action of Fumarate
  • The oncogenic action of L-2-hydroxyglutarate in Hydroxygluaricaciduria
  • The Oncogenic Action of Succinate
Reactions
Protein N(6),N(6)-dimethyl-L-lysine + Oxoglutaric acid + Oxygen → protein N(6)-methyl-L-lysine + Succinic acid + Formaldehyde + CO(2) details
Protein N(6)-methyl-L-lysine + Oxoglutaric acid + Oxygen → protein L-lysine + Succinic acid + Formaldehyde + CO(2) details
Protein N6,N6-dimethyl-L-lysine + Oxoglutaric acid + Oxygen → Protein lysine + Succinic acid + Formaldehyde + Carbon dioxide details
GO Classification
Biological Process
regulation of transcription, DNA-dependent
transcription, DNA-dependent
histone H3-K36 demethylation
Cellular Component
nucleoplasm
nuclear chromatin
Function
ion binding
cation binding
metal ion binding
binding
transition metal ion binding
zinc ion binding
protein binding
nucleic acid binding
dna binding
Molecular Function
metal ion binding
unmethylated CpG binding
oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
zinc ion binding
histone demethylase activity (H3-K36 specific)
Cellular Location
  1. Nucleus
  2. nucleoplasm
Gene Properties
Chromosome Location 11
Locus 11q13.2
SNPs KDM2A
Gene Sequence 
>3489 bp
ATGGAACCCGAAGAAGAAAGGATTCGTTACAGCCAGAGATTGCGTGGTACCATGCGACGA
CGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGAAAAAGAACTTTTGACTTG
GAAGAGAAACTGCACACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAAGGAAAA
GATTTTAATGTAGAGTATATTCAGCGGGGTGGCTTGAGAGATCCTCTGATTTTCAAGAAT
TCTGATGGACTCGGAATAAAAATGCCGGATCCAGACTTCACTGTGAATGATGTCAAAATG
TGTGTGGGGAGTCGTCGCATGGTGGATGTCATGGACGTGAACACACAGAAAGGCATTGAA
ATGACCATGGCTCAGTGGACACGCTACTATGAGACCCCAGAGGAGGAGCGAGAGAAACTC
TATAATGTCATCAGCCTCGAGTTTAGCCACACCAGGCTGGAGAATATGGTGCAGAGGCCC
TCCACGGTGGATTTCATTGACTGGGTAGACAACATGTGGCCAAGGCACTTGAAGGAAAGC
CAGACTGAATCAACAAATGCCATCTTGGAGATGCAGTACCCTAAAGTGCAGAAGTACTGT
CTAATGAGTGTTCGAGGCTGCTATACTGACTTCCATGTGGACTTTGGTGGTACCTCTGTT
TGGTATCACATCCATCAAGGGGGAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAAC
CTGGAGCTGTACGAGAATTGGCTGCTGTCAGGGAAACAGGGAGACATCTTTCTGGGTGAC
CGGGTATCAGATTGTCAGCGCATTGAGCTCAAGCAGGGCTATACCTTCGTCATTCCCTCA
GGCTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGGGGCAATTTTTTG
CATAGCTTCAACATCCCTATGCAGTTAAAAATATACAACATTGAAGATCGGACACGGGTT
CCAAATAAGTTTCGCTATCCATTCTACTATGAGATGTGTTGGTATGTGTTGGAGCGCTAT
GTGTACTGCATAACCAACCGTTCCCACCTAACTAAGGAATTTCAGAAAGAGTCCCTCAGC
ATGGATTTGGAGTTAAATGGGTTGGAGTCTGGGAATGGGGATGAGGAAGCAGTGGATCGA
GAACCCCGACGCTTGAGCAGCAGGCGTTCTGTCCTCACTAGCCCTGTAGCGAATGGAGTC
AACCTGGATTATGATGGACTGGGCAAAACCTGCCGAAGTCTTCCAAGTCTGAAGAAAACT
TTGGCTGGGGACTCATCTTCTGACTGTAGCCGGGGCTCCCACAATGGACAAGTGTGGGAT
CCCCAGTGTGCTCCCCGAAAGGACAGGCAAGTGCATCTGACCCATTTTGAGCTTGAAGGC
CTTCGCTGCCTTGTAGATAAGTTGGAGTCTCTGCCACTGCACAAGAAATGTGTCCCCACA
GGGATAGAAGATGAAGATGCTCTCATTGCTGATGTAAAGATTTTGCTGGAGGAGCTTGCC
AACAGCGATCCCAAGTTAGCCCTCACTGGAGTTCCTATAGTACAGTGGCCAAAAAGGGAT
AAGCTTAAATTCCCCACTCGGCCAAAGGTGCGGGTTCCTACCATCCCCATTACGAAGCCT
CACACTATGAAACCAGCTCCACGGTTAACACCTGTGAGGCCAGCTGCTGCCTCCCCGATT
GTGTCAGGAGCCAGACGGAGACGAGTGCGATGTCGAAAATGCAAAGCCTGTGTGCAAGGA
GAGTGTGGTGTTTGCCACTACTGCAGAGACATGAAGAAGTTTGGGGGGCCTGGACGCATG
AAGCAGTCCTGTGTCCTCCGACAGTGCTTGGCACCCAGACTGCCTCACTCAGTCACATGT
TCCCTCTGTGGAGAGGTGGATCAGAATGAAGAGACACAAGACTTTGAGAAGAAACTCATG
GAATGCTGTATCTGCAATGAGATTGTTCATCCTGGCTGCCTCCAGATGGACGGAGAGGGG
TTGCTTAACGAAGAATTGCCAAATTGCTGGGAATGTCCAAAGTGCTACCAGGAGGACAGC
TCGGAGAAAGCCCAGAAGCGGAAAATGGAAGAGAGTGACGAAGAAGCTGTGCAAGCCAAA
GTCCTGCGGCCCCTGCGGAGCTGCGATGAGCCTCTCACGCCCCCGCCTCATTCACCCACT
TCCATGCTGCAGCTCATCCATGACCCGGTTTCCCCCCGGGGTATGGTGACTCGGTCATCC
CCTGGGGCTGGCCCCAGCGACCACCACAGTGCCAGCCGCGATGAGCGCTTCAAACGGCGG
CAGTTGCTGCGGCTGCAGGCCACAGAGCGCACCATGGTACGGGAAAAGGAGAACAATCCC
AGCGGCAAAAAGGAGCTGTCTGAAGTTGAGAAAGCCAAGATCCGGGGATCGTACCTCACT
GTCACGCTACAGAGGCCCACCAAAGAGCTCCACGGGACATCCATTGTGCCCAAGCTGCAG
GCCATCACGGCCTCCTCTGCCAACCTTCGCCATTCCCCCCGTGTGCTAGTGCAGCACTGC
CCAGCCCGAACCCCCCAGCGTGGGGATGAGGAGGGGCTGGGGGGAGAGGAGGAGGAAGAG
GAGGAGGAGGAGGAGGAAGATGACAGTGCAGAGGAGGGGGGTGCAGCCAGGCTGAATGGC
CGGGGCAGTTGGGCTCAGGATGGAGACGAAAGCTGGATGCAGCGGGAGGTCTGGATGTCT
GTCTTCCGCTACCTCAGCCGCAGAGAACTTTGTGAATGTATGCGAGTGTGCAAGACGTGG
TATAAATGGTGCTGCGACAAGAGACTTTGGACAAAAATTGACTTGAGTAGGTGTAAGGCC
ATTGTGCCCCAGGCCCTCAGTGGCATCATCAAGAGGCAGCCAGTCAGCCTTGACCTCAGT
TGGACCAACATCTCTAAAAAGCAACTGACATGGCTCGTCAATAGGCTGCCAGGACTGAAA
GACCTCCTCCTAGCAGGCTGCTCCTGGTCTGCAGTCTCTGCCCTCAGCACCTCCAGCTGC
CCCCTTCTCAGGACCCTTGATCTTCGGTGGGCAGTAGGAATCAAGGACCCTCAAATTCGG
GACTTGCTTACTCCACCGGCTGATAAACCAGGTCAGGACAATCGCAGCAAGCTCCGGAAC
ATGACCGACTTCCGGCTGGCAGGCCTTGACATCACAGATGCCACGCTTCGCCTCATAATT
CGCCACATGCCCCTCCTGTCTCGACTCGACCTCAGTCACTGCAGCCACCTTACAGATCAG
TCCTCCAATCTACTCACTGCTGTCGGGTCTTCCACTCGCTACTCTCTCACAGAGCTCAAT
ATGGCAGGTTGCAATAAATTGACAGACCAGACCCTGATCTACCTACGGCGCATTGCCAAC
GTCACCTTGATCGACCTTCGAGGATGCAAGCAGATCACTCGAAAAGCCTGCGAGCACTTC
ATCTCAGACTTGTCCATCAACAGCCTCTACTGCCTGTCTGACGAGAAGCTGATACAGAAG
ATCAGCTAA
Protein Properties
Number of Residues 1162
Molecular Weight 81677.13
Theoretical pI 8.752
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence 
>Lysine-specific demethylase 2A
MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLHTNKYNANFVTFMEGK
DFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIE
MTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKES
QTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHN
LELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFL
HSFNIPMQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLS
MDLELNGLESGNGDEEAVDREPRRLSSRRSVLTSPVANGVNLDYDGLGKTCRSLPSLKKT
LAGDSSSDCSRGSHNGQVWDPQCAPRKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPT
GIEDEDALIADVKILLEELANSDPKLALTGVPIVQWPKRDKLKFPTRPKVRVPTIPITKP
HTMKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRM
KQSCVLRQCLAPRLPHSVTCSLCGEVDQNEETQDFEKKLMECCICNEIVHPGCLQMDGEG
LLNEELPNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCDEPLTPPPHSPT
SMLQLIHDPVSPRGMVTRSSPGAGPSDHHSASRDERFKRRQLLRLQATERTMVREKENNP
SGKKELSEVEKAKIRGSYLTVTLQRPTKELHGTSIVPKLQAITASSANLRHSPRVLVQHC
PARTPQRGDEEGLGGEEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGDESWMQREVWMS
VFRYLSRRELCECMRVCKTWYKWCCDKRLWTKIDLSRCKAIVPQALSGIIKRQPVSLDLS
WTNISKKQLTWLVNRLPGLKDLLLAGCSWSAVSALSTSSCPLLRTLDLRWAVGIKDPQIR
DLLTPPADKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRLDLSHCSHLTDQ
SSNLLTAVGSSTRYSLTELNMAGCNKLTDQTLIYLRRIANVTLIDLRGCKQITRKACEHF
ISDLSINSLYCLSDEKLIQKIS
GenBank ID Protein 16306580
UniProtKB/Swiss-Prot ID Q9Y2K7
UniProtKB/Swiss-Prot Entry Name KDM2A_HUMAN
PDB IDs
GenBank Gene ID NM_012308.2
GeneCard ID KDM2A
GenAtlas ID KDM2A
HGNC ID HGNC:13606
References
General References
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  2. Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP: A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31. [PubMed:18669648 ]
  3. Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007. [PubMed:19690332 ]
  4. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006 Nov 3;127(3):635-48. [PubMed:17081983 ]
  5. Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD: Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra. J Proteome Res. 2007 Nov;6(11):4150-62. Epub 2007 Oct 9. [PubMed:17924679 ]
  6. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ: ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science. 2007 May 25;316(5828):1160-6. [PubMed:17525332 ]
  7. Nakajima D, Okazaki N, Yamakawa H, Kikuno R, Ohara O, Nagase T: Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. DNA Res. 2002 Jun 30;9(3):99-106. [PubMed:12168954 ]
  8. Bechtel S, Rosenfelder H, Duda A, Schmidt CP, Ernst U, Wellenreuther R, Mehrle A, Schuster C, Bahr A, Blocker H, Heubner D, Hoerlein A, Michel G, Wedler H, Kohrer K, Ottenwalder B, Poustka A, Wiemann S, Schupp I: The full-ORF clone resource of the German cDNA Consortium. BMC Genomics. 2007 Oct 31;8:399. [PubMed:17974005 ]
  9. Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd: Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. J Proteome Res. 2008 Mar;7(3):1346-51. doi: 10.1021/pr0705441. Epub 2008 Jan 26. [PubMed:18220336 ]
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  12. Hattori A, Okumura K, Nagase T, Kikuno R, Hirosawa M, Ohara O: Characterization of long cDNA clones from human adult spleen. DNA Res. 2000 Dec 31;7(6):357-66. [PubMed:11214971 ]
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  14. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y: Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006 Feb 16;439(7078):811-6. Epub 2005 Dec 18. [PubMed:16362057 ]
  15. Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, Basrur V, Elenitoba-Johnson KS, Katz RA, Pagano M: KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle. 2008 Nov 15;7(22):3539-47. Epub 2008 Nov 24. [PubMed:19001877 ]
  16. Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ: CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23;38(2):179-90. doi: 10.1016/j.molcel.2010.04.009. [PubMed:20417597 ]