KDM5D

KDM5D
Available structures
PDB	Ortholog search: PDBe RCSB
List of PDB id codes
	2E6R, 2YQE
Identifiers
Aliases	KDM5D, HY, HYA, JARID1D, SMCY, lysine demethylase 5D
External IDs	OMIM: 426000 MGI: 99780 HomoloGene: 55838 GeneCards: KDM5D
Gene location (Human)
Chr.	Y chromosome (human)[1]
End	19,744,939 bp[1]
Gene location (Mouse)
Chr.	Y chromosome (mouse)[2]
End	956,786 bp[2]
RNA expression pattern
	More reference expression data
Gene ontology
Molecular function	• histone demethylase activity (H3-K4 specific); • DNA binding; • oxidoreductase activity; • dioxygenase activity; • metal ion binding; • histone demethylase activity; • androgen receptor binding; • GO:0001948 protein binding; • GO:0001200, GO:0001133, GO:0001201 DNA-binding transcription factor activity, RNA polymerase II-specific; • GO:0001078, GO:0001214, GO:0001206 DNA-binding transcription repressor activity, RNA polymerase II-specific; • chromatin binding; • histone demethylase activity (H3-trimethyl-K4 specific); • methylated histone binding;
Cellular component	• cell nucleus; • nucleoplasm; • fibrillar center; • cellular component; • histone methyltransferase complex;
Biological process	• histone H3-K4 demethylation; • oxidation-reduction process; • T cell antigen processing and presentation; • transcription, DNA-templated; • regulation of transcription, DNA-templated; • regulation of androgen receptor signaling pathway; • chromatin organization; • regulation of transcription from RNA polymerase II promoter; • negative regulation of transcription from RNA polymerase II promoter; • histone H3-K4 demethylation, trimethyl-H3-K4-specific; • chromatin remodeling;
	Sources:Amigo / QuickGO
Orthologs
	8284
	20592
	ENSG00000012817
	ENSMUSG00000056673
	Q9BY66
	Q62240
	NM_001146705; NM_001146706; NM_004653
	NM_011419
	NP_001140177; NP_001140178; NP_004644
	NP_035549
	Wikidata
View/Edit Human	View/Edit Mouse

Lysine-specific demethylase 5D is an enzyme that in humans is encoded by the KDM5D gene.[5][6][7] KDM5D belongs to the alpha-ketoglutarate-dependent hydroxylases superfamily.

This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient.[7]

References

GRCh38: Ensembl release 89: ENSG00000012817 - Ensembl, May 2017
GRCm38: Ensembl release 89: ENSMUSG00000056673 - Ensembl, May 2017
"Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
"Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
Froggatt P (Feb 1977). "The foundation of the "Inst" medical department and its association with the Belfast Fever Hospital". The Ulster Medical Journal. 45 (2): 107–45. PMC 2385577. PMID 795123.
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 (October 1996). "Gene sequence and evolutionary conservation of human SMCY". Nature Genetics. 14 (2): 128–9. doi:10.1038/ng1096-128. PMID 8841177. S2CID 23054699.
"Entrez Gene: JARID1D jumonji, AT rich interactive domain 1D".

Simpson E, Scott D, Chandler P (1997). "The male-specific histocompatibility antigen, H-Y: a history of transplantation, immune response genes, sex determination and expression cloning". Annual Review of Immunology. 15: 39–61. doi:10.1146/annurev.immunol.15.1.39. PMID 9143681.
Wolf U (1998). "The serologically detected H-Y antigen revisited". Cytogenetics and Cell Genetics. 80 (1–4): 232–5. doi:10.1159/000014986. PMID 9678364. S2CID 25908189.
Agulnik AI, Mitchell MJ, Lerner JL, Woods DR, Bishop CE (June 1994). "A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens". Human Molecular Genetics. 3 (6): 873–8. doi:10.1093/hmg/3.6.873. PMID 7524912.
Wang W, Meadows LR, den Haan JM, Sherman NE, Chen Y, Blokland E, Shabanowitz J, Agulnik AI, Hendrickson RC, Bishop CE (September 1995). "Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein". Science. 269 (5230): 1588–90. doi:10.1126/science.7667640. hdl:1887/2988. PMID 7667640.
Nagase T, Seki N, Ishikawa K, Ohira M, Kawarabayasi Y, Ohara O, Tanaka A, Kotani H, Miyajima N, Nomura N (October 1996). "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 Research. 3 (5): 321–9, 341–54. doi:10.1093/dnares/3.5.321. PMID 9039502.
Agulnik AI, Bishop CE, Lerner JL, Agulnik SI, Solovyev VV (February 1997). "Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven". Mammalian Genome. 8 (2): 134–8. doi:10.1007/s003359900372. PMID 9060413. S2CID 8099911.
Rufer N, Wolpert E, Helg C, Tiercy JM, Gratwohl A, Chapuis B, Jeannet M, Goulmy E, Roosnek E (October 1998). "HA-1 and the SMCY-derived peptide FIDSYICQV (H-Y) are immunodominant minor histocompatibility antigens after bone marrow transplantation". Transplantation. 66 (7): 910–6. doi:10.1097/00007890-199810150-00016. PMID 9798702.
Lau YF, Zhang J (April 2000). "Expression analysis of thirty one Y chromosome genes in human prostate cancer". Molecular Carcinogenesis. 27 (4): 308–21. doi:10.1002/(SICI)1098-2744(200004)27:4<308::AID-MC9>3.0.CO;2-R. PMID 10747295.
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 (June 2000). "Population genetic implications from sequence variation in four Y chromosome genes". Proceedings of the National Academy of Sciences of the United States of America. 97 (13): 7354–9. doi:10.1073/pnas.97.13.7354. PMC 16549. PMID 10861003.
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 (June 2003). "The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes". Nature. 423 (6942): 825–37. doi:10.1038/nature01722. PMID 12815422.
Agate RJ, Choe M, Arnold AP (February 2004). "Sex differences in structure and expression of the sex chromosome genes CHD1Z and CHD1W in zebra finches". Molecular Biology and Evolution. 21 (2): 384–96. doi:10.1093/molbev/msh027. PMID 14660691.
Miklos DB, Kim HT, Miller KH, Guo L, Zorn E, Lee SJ, Hochberg EP, Wu CJ, Alyea EP, Cutler C, Ho V, Soiffer RJ, Antin JH, Ritz J (April 2005). "Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission". Blood. 105 (7): 2973–8. doi:10.1182/blood-2004-09-3660. PMC 1350982. PMID 15613541.
Piper KP, McLarnon A, Arrazi J, Horlock C, Ainsworth J, Kilby MD, Martin WL, Moss PA (January 2007). "Functional HY-specific CD8+ T cells are found in a high proportion of women following pregnancy with a male fetus". Biology of Reproduction. 76 (1): 96–101. doi:10.1095/biolreprod.106.055426. PMID 16988213.
Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y (March 2007). "The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases". Cell. 128 (6): 1077–88. doi:10.1016/j.cell.2007.02.017. PMID 17320160. S2CID 14729302.
Lee MG, Norman J, Shilatifard A, Shiekhattar R (March 2007). "Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein". Cell. 128 (5): 877–87. doi:10.1016/j.cell.2007.02.004. PMID 17320162. S2CID 6519228.

External links

JARID1D+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH)
Overview of all the structural information available in the PDB for UniProt: Q9BY66 (Lysine-specific demethylase 5D) at the PDBe-KB.

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.

[refGRCh38Ensembl-1] GRCh38: Ensembl release 89: ENSG00000012817 - Ensembl, May 2017

[refGRCm38Ensembl-2] GRCm38: Ensembl release 89: ENSMUSG00000056673 - Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[pmid795123-5] Froggatt P (Feb 1977). "The foundation of the "Inst" medical department and its association with the Belfast Fever Hospital". The Ulster Medical Journal. 45 (2): 107–45. PMC 2385577. PMID 795123.

[pmid8841177-6] 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 (October 1996). "Gene sequence and evolutionary conservation of human SMCY". Nature Genetics. 14 (2): 128–9. doi:10.1038/ng1096-128. PMID 8841177. S2CID 23054699.

[entrez-7] "Entrez Gene: JARID1D jumonji, AT rich interactive domain 1D".

Oxidoreductases: dioxygenases, including steroid hydroxylases (EC 1.14)
1.14.11: 2-oxoglutarate	Prolyl hydroxylase HIF prolyl-hydroxylase EGLN1 EGLN2 EGLN3 P4HTM Lysyl hydroxylase
1.14.13: NADH or NADPH	Flavin-containing monooxygenase FMO1 FMO2 FMO3 FMO4 FMO5 Nitric oxide synthase NOS1 NOS2 NOS3 Cholesterol 7 alpha-hydroxylase Methane monooxygenase 3A4 14α-demethylase 24-hydroxycholesterol 7α-hydroxylase
1.14.14: reduced flavin or flavoprotein	19A1 2D6 2E1
1.14.15: reduced iron-sulfur protein	11B1 11B2 11A1
1.14.16: reduced pteridine (BH4 dependent)	Phenylalanine hydroxylase Tyrosine hydroxylase Tryptophan hydroxylase
1.14.17: reduced ascorbate	Dopamine beta-hydroxylase
1.14.18-19: other	Tyrosinase Stearoyl-CoA desaturase-1
1.14.99 - miscellaneous	Cyclooxygenase Heme oxygenase (HMOX1) Squalene monooxygenase 17A1 21A2 Ecdysone 20-monooxygenase

Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

KDM5D

References

Further reading

External links