Lysine-specific demethylase 5D

Details

Name
Lysine-specific demethylase 5D
Synonyms
  • 1.14.11.-
  • H-Y
  • Histocompatibility Y antigen
  • Histone demethylase JARID1D
  • HY
  • HYA
  • JARID1D
  • Jumonji/ARID domain-containing protein 1D
  • KIAA0234
  • Protein SmcY
  • SMCY
Gene Name
KDM5D
Organism
Humans
Amino acid sequence
>lcl|BSEQ0004347|Lysine-specific demethylase 5D
MEPGCDEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEV
DNFRFTPRVQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVI
EEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGANHVQCNTHP
FDNEVKDKEYKPHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEEDIEKHPELKKLQIYG
PGPKMMGLGLMAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTM
QLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPK
CILAECKQPPEAFGFEQATQEYSLQSFGEMADSFKSDYFNMPVHMVPTELVEKEFWRLVS
SIEEDVTVEYGADIHSKEFGSGFPVSNSKQNLSPEEKEYATSGWNLNVMPVLDQSVLCHI
NADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMK
MLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYN
FAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDLNLAVAVHKEM
FIMVQEERRLRKALLEKGVTEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVC
LSHINDLCKCSSSRQYLRYRYTLDELPTMLHKLKIRAESFDTWANKVRVALEVEDGRKRS
FEELRALESEARERRFPNSELLQRLKNCLSEVEACIAQVLGLVSGQVARMDTPQLTLTEL
RVLLEQMGSLPCAMHQIGDVKDVLEQVEAYQAEAREALATLPSSPGLLRSLLERGQQLGV
EVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASSPSVDKARAEL
QELLTIAERWEEKAHFCLEARQKHPPATLEAIIRETENIPVHLPNIQALKEALTKAQAWI
ADVDEIQNGDHYPCLDDLEGLVAVGRDLPVGLEELRQLELQVLTAHSWREKASKTFLKKN
SCYTLLEVLCPCADAGSDSTKRSRWMEKALGLYQCDTELLGLSAQDLRDPGSVIVAFKEG
EQKEKEGILQLRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGVLQCDLCQDWFHGQC
VSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLVALQRLPVRLP
EGEALQCLTERAIGWQDRARKALASEDVTALLRQLAELRQQLQAKPRPEEASVYTSATAC
DPIREGSGNNISKVQGLLENGDSVTSPENMAPGKGSDLELLSSLLPQLTGPVLELPEAIR
APLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLDRIRTLLELEKFEHQGSRTRSRALE
RRRRRQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDH
SPFLKGNQNSLQHKDSGSSAACPSLMPLLQLSYSDEQQL
Number of residues
1539
Molecular Weight
174071.34
Theoretical pI
5.66
GO Classification
Functions
DNA binding / histone demethylase activity (H3-K4 specific) / 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 / zinc ion binding
Processes
chromatin organization / histone H3-K4 demethylation
Components
nucleoplasm
General Function
Zinc ion binding
Specific Function
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'. May play a role in spermatogenesis.
Pfam Domain Function
Transmembrane Regions
Not Available
Cellular Location
Nucleus
Gene sequence
>lcl|BSEQ0011599|Lysine-specific demethylase 5D (KDM5D)
ATGGAACCGGGGTGTGACGAGTTCCTGCCGCCACCGGAGTGCCCGGTTTTTGAGCCTAGC
TGGGCTGAATTCCAAGACCCGCTTGGCTACATTGCGAAAATAAGGCCCATAGCAGAGAAG
TCTGGCATCTGCAAAATCCGCCCACCCGCGGATTGGCAGCCTCCTTTTGCAGTAGAAGTT
GACAATTTCAGATTTACTCCTCGCGTCCAAAGGCTAAATGAACTGGAGGCCCAAACTAGA
GTGAAATTGAACTATTTGGATCAGATTGCAAAATTCTGGGAAATTCAAGGCTCCTCTTTA
AAGATTCCCAATGTGGAGCGGAAGATCTTGGACCTCTACAGCCTTAGTAAGATTGTGATT
GAGGAAGGTGGCTATGAAGCCATCTGCAAGGATCGTCGGTGGGCTCGAGTTGCCCAGCGT
CTCCACTACCCACCAGGCAAAAACATTGGCTCCCTGCTACGATCACATTACGAACGCATT
ATTTACCCCTATGAAATGTTTCAGTCTGGAGCCAACCATGTGCAATGTAACACACACCCG
TTTGACAATGAGGTAAAAGATAAGGAATACAAGCCCCACAGCATCCCCCTTAGACAGTCT
GTGCAGCCTTCAAAGTTCAGCAGCTACAGTCGACGGGCAAAAAGGCTACAGCCTGATCCA
GAGCCTACAGAGGAGGACATTGAGAAGCATCCAGAGCTAAAGAAGTTACAGATATATGGG
CCAGGTCCCAAAATGATGGGCTTGGGCCTTATGGCTAAGGATAAGGATAAGACTGTGCAT
AAGAAAGTCACATGCCCCCCAACTGTTACGGTGAAGGATGAGCAAAGTGGAGGTGGGAAC
GTGTCATCAACATTGCTCAAGCAGCACTTGAGCCTAGAGCCCTGCACTAAGACAACCATG
CAACTTCGAAAGAATCACAGCAGTGCCCAGTTTATTGACTCATATATTTGCCAAGTATGC
TCCCGTGGGGATGAAGATGATAAGCTTCTTTTCTGTGATGGCTGTGATGACAATTACCAC
ATCTTCTGCTTGTTACCACCCCTTCCTGAAATCCCCAGAGGCATCTGGAGGTGCCCAAAA
TGTATCTTGGCGGAGTGTAAACAGCCTCCTGAAGCTTTTGGATTTGAACAGGCTACCCAG
GAGTACAGTTTGCAGAGTTTTGGTGAAATGGCTGATTCCTTCAAGTCCGACTACTTCAAC
ATGCCTGTACATATGGTGCCTACAGAACTTGTAGAGAAGGAATTCTGGAGGCTGGTGAGC
AGCATTGAGGAAGACGTGACAGTTGAATATGGAGCTGATATTCATTCCAAAGAATTTGGC
AGTGGCTTTCCTGTCAGCAATAGCAAACAAAACTTATCTCCTGAGGAGAAGAGACAAAGT
CTCACTGTGTTGACCAGGCTGATCTCAAGCTTCTGGGCTCAAGCAGTCCTCCCACCTTGG
CCTCCCAAAGTGTTGGGATTACAGGAGTATGCGACCAGTGGTTGGAACCTGAATGTGATG
CCAGTGCTAGATCAGTCTGTTCTCTGTCACATCAATGCAGACATCTCAGGCATGAAGGTG
CCCTGGCTGTACGTGGGCATGGTTTTCTCAGCATTTTGTTGGCATATTGAGGATCACTGG
AGTTACTCTATTAACTATCTGCATTGGGGTGAGCCGAAGACCTGGTATGGTGTACCCTCC
CTGGCAGCAGAGCATTTGGAGGAGGTGATGAAGATGCTGACACCTGAGCTGTTTGATAGC
CAGCCTGATCTCCTACACCAGCTTGTCACTCTCATGAATCCCAACACTTTGATGTCCCAT
GGTGTGCCAGTTGTCCGCACAAACCAGTGTGCAGGGGAGTTTGTCATCACTTTTCCTCGT
GCTTACCACAGTGGTTTTAACCAAGGCTACAATTTTGCTGAAGCTGTCAACTTTTGTACT
GCTGACTGGCTACCTGCTGGACGCCAGTGCATTGAACACTACCGCCGGCTCCGGCGCTAT
TGTGTCTTCTCCCACGAGGAGCTCATCTGCAAGATGGCTGCCTTCCCAGAGACGTTGGAT
CTCAATCTAGCAGTAGCTGTGCACAAGGAGATGTTCATTATGGTTCAGGAGGAGCGACGT
CTACGAAAGGCCCTTTTGGAGAAGGGCGTCACGGAGGCTGAGCGAGAGGCTTTTGAGCTG
CTCCCAGATGATGAACGCCAGTGCATCAAGTGCAAGACCACGTGCTTCTTGTCAGCCCTG
GCCTGCTACGACTGCCCAGATGGCCTTGTATGCCTTTCCCACATCAATGACCTCTGCAAG
TGCTCTAGTAGCCGACAGTACCTCCGGTATCGGTACACCTTGGATGAGCTCCCCACCATG
CTGCATAAACTGAAGATTCGGGCTGAGTCTTTTGACACCTGGGCCAACAAAGTGCGAGTG
GCCTTGGAGGTGGAGGATGGCCGTAAACGCAGCTTTGAAGAGCTAAGGGCACTGGAGTCT
GAGGCTCGTGAGAGGAGGTTTCCTAATAGTGAGCTGCTTCAGCGACTGAAGAACTGCCTG
AGTGAGGTGGAGGCTTGTATTGCTCAAGTCCTGGGGCTGGTCAGTGGTCAGGTGGCCAGG
ATGGACACTCCACAGCTGACCTTGACTGAACTCCGGGTCCTTCTTGAGCAGATGGGCAGC
CTGCCCTGTGCCATGCATCAGATTGGGGATGTCAAGGATGTCCTGGAACAGGTGGAGGCC
TATCAAGCTGAGGCTCGTGAGGCTCTGGCCACACTGCCCTCTAGTCCAGGGCTATTGCGG
TCCCTGTTGGAGAGGGGGCAGCAGCTGGGTGTAGAGGTGCCTGAAGCCCATCAGCTTCAG
CAGCAGGTGGAGCAGGCGCAATGGCTAGATGAAGTGAAGCAGGCCCTGGCCCCTTCTGCT
CACAGGGGCTCTCTGGTCATCATGCAGGGGCTTTTGGTTATGGGTGCCAAGATAGCCTCC
AGCCCTTCTGTGGACAAGGCCCGGGCTGAGCTGCAAGAACTACTGACCATTGCAGAGCGC
TGGGAAGAAAAGGCTCATTTCTGCCTGGAGGCCAGGCAGAAGCATCCACCAGCCACATTG
GAAGCCATAATTCGTGAGACAGAAAACATCCCTGTTCACCTGCCTAACATCCAGGCTCTC
AAAGAAGCTCTGACTAAGGCACAAGCTTGGATTGCTGATGTGGATGAGATCCAAAATGGT
GACCACTACCCCTGTCTAGATGACTTGGAGGGCCTGGTGGCTGTGGGCCGGGACCTGCCT
GTGGGGCTGGAAGAGCTGAGACAGCTAGAGCTGCAGGTATTGACAGCACATTCCTGGAGA
GAGAAGGCCTCCAAGACCTTTCTCAAGAAGAATTCTTGCTACACACTGCTTGAGGTGCTT
TGCCCGTGTGCAGACGCTGGCTCAGACAGCACCAAGCGTAGCCGGTGGATGGAGAAGGCG
CTGGGGTTGTACCAGTGTGACACAGAGCTGCTGGGGCTGTCTGCACAGGACCTCAGAGAC
CCAGGCTCTGTGATTGTGGCCTTCAAGGAAGGGGAACAGAAGGAGAAGGAGGGTATCCTG
CAGCTGCGTCGCACCAACTCAGCCAAGCCCAGTCCACTGGCACCATCCCTCATGGCCTCT
TCTCCGACTTCTATCTGTGTGTGTGGGCAGGTGCCAGCTGGGGTGGGAGTTCTGCAGTGT
GACCTGTGTCAGGACTGGTTCCATGGGCAGTGTGTGTCAGTGCCCCATCTCCTCACCTCT
CCAAAGCCCAGTCTCACTTCATCTCCACTGCTAGCCTGGTGGGAATGGGACACAAAATTC
CTGTGTCCACTGTGTATGCGCTCACGACGGCCACGCCTAGAGACAATCCTAGCCTTGCTG
GTTGCCCTGCAGAGGCTGCCCGTGCGGCTGCCTGAGGGTGAGGCCCTTCAGTGTCTCACA
GAGAGGGCCATTGGCTGGCAAGACCGTGCCAGAAAGGCTCTGGCCTCTGAAGATGTGACT
GCTCTGTTGCGACAGCTGGCTGAGCTTCGCCAACAGCTACAGGCCAAACCCAGACCAGAG
GAGGCCTCAGTCTACACTTCAGCCACTGCCTGTGACCCTATCAGAGAAGGCAGTGGCAAC
AATATTTCTAAGGTCCAAGGGCTGCTGGAGAATGGAGACAGTGTGACCAGTCCTGAGAAC
ATGGCTCCAGGAAAGGGCTCTGACCTGGAGCTACTGTCCTCACTGTTGCCGCAGTTGACT
GGCCCTGTGTTGGAGCTGCCTGAGGCAATCCGGGCTCCCCTGGAGGAGCTCATGATGGAA
GGGGACCTGCTTGAGGTGACCCTGGATGAGAACCACAGCATCTGGCAGCTGCTGCAGGCT
GGACAGCCTCCAGACCTGGACAGAATTCGCACACTTCTGGAGCTGGAAAAATTTGAACAT
CAAGGGAGTCGGACAAGGAGCCGGGCTCTGGAGAGGCGACGGCGGCGGCAGAAGGTGGAT
CAGGGTAGAAACGTTGAGAATCTTGTTCAACAGGAGCTTCAGTCAAAAAGGGCTCGGAGC
TCAGGGATTATGTCTCAGGTGGGCCGAGAAGAAGAACATTATCAGGAGAAAGCAGACCGT
GAAAATATGTTCCTGACACCTTCCACAGACCACAGCCCTTTCTTGAAAGGAAACCAAAAT
AGCTTACAACACAAGGATTCAGGCTCTTCAGCTGCTTGTCCTTCTTTAATGCCTTTGCTA
CAACTCTCCTACTCTGATGAGCAACAGTTGTGA
Chromosome Location
Y
Locus
Yq11|Yq11
External Identifiers
ResourceLink
UniProtKB IDQ9BY66
UniProtKB Entry NameKDM5D_HUMAN
GenBank Protein ID1661016
GenBank Gene IDU52191
GenAtlas IDJARID1D
HGNC IDHGNC:11115
General References
  1. Kent-First MG, Maffitt M, Muallem A, Brisco P, Shultz J, Ekenberg S, Agulnik AI, Agulnik I, Shramm D, Bavister B, Abdul-Mawgood A, VandeBerg J: Gene sequence and evolutionary conservation of human SMCY. Nat Genet. 1996 Oct;14(2):128-9. [PubMed:8841177]
  2. Nagase T, Seki N, Ishikawa K, Ohira M, Kawarabayasi Y, Ohara O, Tanaka A, Kotani H, Miyajima N, Nomura N: Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. DNA Res. 1996 Oct 31;3(5):321-9, 341-54. [PubMed:9039502]
  3. Shen P, Wang F, Underhill PA, Franco C, Yang WH, Roxas A, Sung R, Lin AA, Hyman RW, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ: Population genetic implications from sequence variation in four Y chromosome genes. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7354-9. [PubMed:10861003]
  4. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC: The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 Jun 19;423(6942):825-37. [PubMed:12815422]
  5. 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]
  6. Agulnik AI, Bishop CE, Lerner JL, Agulnik SI, Solovyev VV: Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven. Mamm Genome. 1997 Feb;8(2):134-8. [PubMed:9060413]
  7. Lee MG, Norman J, Shilatifard A, Shiekhattar R: Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell. 2007 Mar 9;128(5):877-87. Epub 2007 Feb 22. [PubMed:17320162]
  8. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y: The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell. 2007 Mar 23;128(6):1077-88. Epub 2007 Feb 22. [PubMed:17320160]
  9. Eissenberg JC, Lee MG, Schneider J, Ilvarsonn A, Shiekhattar R, Shilatifard A: The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat Struct Mol Biol. 2007 Apr;14(4):344-6. Epub 2007 Mar 11. [PubMed:17351630]
  10. Akimoto C, Kitagawa H, Matsumoto T, Kato S: Spermatogenesis-specific association of SMCY and MSH5. Genes Cells. 2008 Jun;13(6):623-33. doi: 10.1111/j.1365-2443.2008.01193.x. Epub 2008 May 4. [PubMed:18459961]

Drug Relations

Drug Relations
DrugBank IDNameDrug groupPharmacological action?ActionsDetails
DB00126Ascorbic acidapproved, nutraceuticalunknownDetails