Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Identification
HMDB Protein ID HMDBP09185
Secondary Accession Numbers
  • 14943
Name Lysine-specific demethylase 2B
Synonyms
  1. CXXC-type zinc finger protein 2
  2. F-box and leucine-rich repeat protein 10
  3. F-box protein FBL10
  4. F-box/LRR-repeat protein 10
  5. JmjC domain-containing histone demethylation protein 1B
  6. Jumonji domain-containing EMSY-interactor methyltransferase motif protein
  7. Protein JEMMA
  8. Protein-containing CXXC domain 2
  9. [Histone-H3]-lysine-36 demethylase 1B
Gene Name KDM2B
Protein Type Enzyme
Biological Properties
General Function Involved in DNA binding
Specific Function Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.
Pathways Not Available
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
lateral ventricle development
midbrain-hindbrain boundary morphogenesis
negative regulation of neural precursor cell proliferation
third ventricle development
spermatogenesis
negative regulation of neuron apoptotic process
negative regulation of transcription from RNA polymerase II promoter
midbrain development
transcription, DNA-dependent
histone H3-K36 demethylation
embryonic camera-type eye morphogenesis
fourth ventricle development
histone H2A monoubiquitination
initiation of neural tube closure
Cellular Component
nucleolus
nucleus
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
oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
zinc ion binding
DNA binding
histone demethylase activity (H3-K36 specific)
histone demethylase activity
rRNA binding
Cellular Location
  1. Nucleus
  2. nucleolus
Gene Properties
Chromosome Location 12
Locus 12q24.31
SNPs KDM2B
Gene Sequence
>4011 bp
ATGGCGGGTCCGCAAATGGGGGGATCTGCAGAGGATCACCCCCCACGAAAAAGACATGCA
GCAGAAAAGCAAAAAAAGAAAACAGTTATATATACAAAATGCTTTGAATTTGAGTCGGCC
ACACAGCGCCCGATTGACCGCCAGCGATACGACGAGAACGAGGACTTGTCGGACGTGGAG
GAGATCGTCAGCGTCCGCGGCTTCAGCCTGGAGGAGAAGCTTCGCAGCCAGCTGTACCAG
GGGGACTTCGTGCACGCCATGGAGGGCAAAGATTTCAACTATGAGTACGTACAGAGAGAA
GCTCTCAGGGTTCCCCTGATATTTCGAGAAAAGGATGGACTGGGAATTAAGATGCCTGAC
CCTGATTTCACAGTCCGAGACGTCAAACTCCTAGTGGGGAGCCGGCGGCTTGTGGACGTG
ATGGATGTGAACACCCAGAAGGGCACGGAGATGAGCATGTCCCAGTTTGTGCGTTACTAC
GAGACGCCCGAGGCCCAGCGGGACAAGCTGTACAACGTCATCAGCCTAGAGTTCAGCCAC
ACCAAGCTGGAGCACTTGGTCAAGCGTCCGACTGTGGTAGACCTGGTGGACTGGGTGGAC
AACATGTGGCCCCAGCATCTGAAGGAGAAGCAGACAGAAGCCACGAACGCCATTGCAGAG
ATGAAGTACCCGAAAGTGAAAAAGTACTGTCTGATGAGCGTGAAAGGTTGTTTCACCGAC
TTCCACATCGACTTTGGAGGCACTTCCGTTTGGTACCATGTTTTCCGGGGTGGGAAGATT
TTTTGGCTGATTCCTCCAACGCTGCACAATTTGGCGCTGTACGAGGAGTGGGTGCTGTCA
GGCAAACAGAGTGACATCTTTCTGGGAGACCGTGTGGAACGATGCCAAAGAATTGAGCTG
AAGCAGGGCTACACATTTTTCATCCCTTCCGGTTGGATCCATGCCGTCTACACCCCTGTA
GACTCTTTGGTGTTCGGCGGAAACATCCTGCACAGCTTTAACGTGCCCATGCAGCTGCGG
ATCTACGAGATCGAGGACAGGACGCGGGTGCAGCCCAAATTCCGTTACCCCTTCTACTAT
GAGATGTGCTGGTATGTCCTGGAGAGATACGTGTACTGTGTGACCCAGCGCTCCCACCTC
ACTCAGGAATACCAGAGGGAGTCGATGCTTATTGATGCCCCGAGGAAGCCCAGCATAGAC
GGCTTCTCTTCGGATTCCTGGCTGGAGATGGAGGAGGAGGCCTGTGATCAGCAGCCTCAG
GAGGAGGAGGAGAAGGACGAGGAGGGCGAGGGCAGGGACAGGGCACCCAAACCGCCCACC
GATGGCTCCACTTCACCCACCAGCACGCCCTCTGAGGACCAGGAGGCCCTCGGGAAGAAG
CCCAAAGCACCTGCCCTGCGATTCCTCAAAAGGACTTTGTCTAATGAGTCGGAGGAAAGT
GTGAAGTCCACCACATTGGCCGTAGACTACCCCAAGACCCCCACCGGCTCTCCCGCCACG
GAGGTCTCTGCCAAATGGACCCATCTCACTGAGTTTGAACTGAAGGGCCTGAAAGCTCTG
GTGGAGAAACTGGAATCCCTCCCGGAGAACAAGAAGTGTGTCCCCGAGGGCATCGAGGAC
CCCCAGGCACTCCTGGAGGGTGTGAAGAACGTCCTGAAGGAGCACGCAGATGATGACCCT
AGTCTGGCCATCACTGGGGTCCCTGTGGTGACTTGGCCAAAGAAGACTCCAAAGAACCGG
GCTGTGGGTCGGCCCAAGGGGAAGCTGGGCCCGGCCTCCGCGGTGAAGTTGGCCGCCAAC
CGGACAACGGCAGGAGCTCGGCGGCGCCGGACGCGATGCCGCAAGTGCGAGGCCTGCCTG
CGGACCGAGTGCGGAGAGTGCCACTTCTGCAAGGACATGAAGAAGTTCGGGGGCCCCGGG
CGCATGAAGCAGAGCTGCATCATGCGGCAGTGCATCGCGCCAGTGCTGCCCCACACCGCC
GTGTGCCTTGTGTGTGGCGAGGCGGGGAAGGAAGACACGGTGGAAGAGGAGGAAGGCAAG
TTTAACCTCATGCTCATGGAGTGCTCCATCTGCAATGAAATCATCCACCCTGGATGCCTT
AAGATTAAGGAGTCAGAGGGTGTGGTCAACGACGAGCTTCCAAACTGCTGGGAGTGTCCG
AAGTGTAACCACGCCGGCAAGACCGGGAAACAAAAGCGTGGCCCTGGCTTTAAGTACGCC
TCCAACCTGCCCGGCTCCCTGCTCAAGGAGCAGAAGATGAACCGGGACAACAAGGAAGGG
CAGGAACCTGCCAAGCGGAGGAGTGAGTGTGAGGAGGCGCCCCGGCGCAGGTCGGATGAG
CACTCGAAGAAGGTGCCGCCGGACGGCCTTCTGCGCAGAAAGTCTGACGACGTGCACCTG
AGGAAGAAGCGGAAATACGAGAAGCCCCAGGAGCTGAGTGGACGCAAGCGGGCCTCATCG
CTTCAAACGTCCCCCGGTTCCTCCTCTCACCTCTCGCCGAGGCCCCCTCTAGGCAGCAGC
CTCAGCCCCTGGTGGAGATCCAGTCTCACTTACTTCCAGCAGCAGCTCAAACCTGGCAAA
GAAGATAAGCTTTTCAGGAAAAAGCGGCGGTCCTGGAAGAACGCCGAGGACCGCATGGCG
CTGGCCAACAAGCCCCTCCGGCGCTTCAAGCAGGAACCCGAGGACGAACTGCCCGAGGCG
CCCCCCAAGACCAGGGAGAGCGACCACTCCCGCTCCAGCTCCCCCACCGCGGGACCCAGC
ACCGAAGGGGCCGAGGGCCCGGAGGAGAAGAAGAAGGTGAAGATGCGCCGGAAGCGGCGG
CTTCCCAACAAGGAGCTGAGCAGGGAGCTGAGCAAGGAGCTCAACCACGAGATCCAGAGG
ACGGAGAACAGCCTGGCCAACGAGAACCAGCAGCCCATCAAGTCGGAGCCTGAGAGCGAG
GGCGAGGAGCCCAAGCGGCCCCCGGGCATCTGCGAGCGTCCCCACCGCTTCAGCAAGGGG
CTCAACGGCACCCCCCGGGAGCTGCGGCACCAGCTGGGGCCCAGCCTGCGCAGCCCGCCC
CGTGTCATCTCCCGGCCCCCACCCTCCGTGTCCCCGCCCAAGTGTATCCAGATGGAGCGC
CATGTGATCCGGCCACCCCCCATCAGCCCCCCGCCTGACTCGCTACCCCTGGACGATGGG
GCAGCCCACGTCATGCACAGGGAGGTGTGGATGGCCGTCTTCAGCTACCTCAGCCACCAA
GACCTGTGTGTGTGCATGCGGGTCTGCAGGACCTGGAACCGCTGGTGCTGCGATAAGCGG
TTGTGGACCCGCATTGACCTGAACCACTGCAAGTCTATCACACCCCTGATGCTGAGTGGC
ATCATCCGGCGACAGCCCGTCTCCCTCGACCTCAGCTGGACCAATATCTCCAAGAAGCAG
CTGAGCTGGCTCATCAACCGGCTGCCTGGGCTCCGGGACTTGGTGCTGTCAGGCTGCTCA
TGGATCGCGGTCTCGGCCCTTTGCAGCTCCAGTTGTCCGCTGCTCCGGACCCTGGATGTC
CAGTGGGTGGAGGGACTAAAGGATGCCCAGATGCGGGATCTCCTGTCCCCGCCCACAGAC
AACAGGCCAGGTCAGATGGACAATCGGAGCAAGCTCCGGAACATCGTGGAGCTGCGCCTG
GCAGGCCTGGACATCACAGATGCCTCCCTGCGGCTCATCATCCGCCACATGCCCCTGCTC
TCCAAGCTCCACCTCAGTTACTGTAACCACGTCACCGACCAGTCTATCAACCTGCTCACT
GCTGTTGGCACCACCACCCGAGACTCCTTAACCGAGATCAACCTGTCTGACTGCAATAAG
GTCACTGATCAGTGCCTGTCCTTCTTCAAACGCTGTGGAAACATCTGTCATATTGACCTG
AGGTACTGCAAGCAAGTCACCAAGGAAGGCTGTGAGCAGTTCATAGCCGAGATGTCTGTG
AGTGTCCAGTTTGGGCAAGTAGAAGAAAAACTCCTGCAAAAACTGAGTTAG
Protein Properties
Number of Residues 1336
Molecular Weight 144767.43
Theoretical pI 8.415
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence
>Lysine-specific demethylase 2B
MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESATQRPIDRQRYDENEDLSDVE
EIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLIFREKDGLGIKMPD
PDFTVRDVKLLVGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSH
TKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNAIAEMKYPKVKKYCLMSVKGCFTD
FHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIEL
KQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIEDRTRVQPKFRYPFYY
EMCWYVLERYVYCVTQRSHLTQEYQRESMLIDAPRKPSIDGFSSDSWLEMEEEACDQQPQ
EEEEKDEEGEGRDRAPKPPTDGSTSPTSTPSEDQEALGKKPKAPALRFLKRTLSNESEES
VKSTTLAVDYPKTPTGSPATEVSAKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIED
PQALLEGVKNVLKEHADDDPSLAITGVPVVTWPKKTPKNRAVGRPKGKLGPASAVKLAAN
RTTAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTA
VCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECP
KCNHAGKTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDE
HSKKVPPDGLLRRKSDDVHLRKKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSS
LSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAEDRMALANKPLRRFKQEPEDELPEA
PPKTRESDHSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLPNKELSRELSKELNHEIQR
TENSLANENQQPIKSEPESEGEEPKRPPGICERPHRFSKGLNGTPRELRHQLGPSLRSPP
RVISRPPPSVSPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYLSHQ
DLCVCMRVCRTWNRWCCDKRLWTRIDLNHCKSITPLMLSGIIRRQPVSLDLSWTNISKKQ
LSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTD
NRPGQMDNRSKLRNIVELRLAGLDITDASLRLIIRHMPLLSKLHLSYCNHVTDQSINLLT
AVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSV
SVQFGQVEEKLLQKLS
GenBank ID Protein 54112382
UniProtKB/Swiss-Prot ID Q8NHM5
UniProtKB/Swiss-Prot Entry Name KDM2B_HUMAN
PDB IDs Not Available
GenBank Gene ID NM_032590.4
GeneCard ID KDM2B
GenAtlas ID KDM2B
HGNC ID HGNC:13610
References
General References
  1. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004 Jan;36(1):40-5. Epub 2003 Dec 21. [PubMed:14702039 ]
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed:15489334 ]
  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. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP: Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12130-5. Epub 2004 Aug 9. [PubMed:15302935 ]
  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. 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 ]
  7. 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 ]
  8. Frescas D, Guardavaccaro D, Bassermann F, Koyama-Nasu R, Pagano M: JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature. 2007 Nov 8;450(7167):309-13. [PubMed:17994099 ]