Q9BY66 (KDM5D_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
January 25, 2012.
Version 98.
History...
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Lysine-specific demethylase 5D EC=1.14.11.- Alternative name(s): Histocompatibility Y antigen Short name=H-Y Histone demethylase JARID1D Jumonji/ARID domain-containing protein 1D Protein SmcY | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 1539 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| 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. Ref.9 Ref.10 Ref.11 |
| Cofactor | Ascorbate. Ref.9 Binds 1 Fe2+ ion per subunit. Ref.9 |
| Subunit structure | |
| Subcellular location | Nucleus Probable. |
| Domain | The JmjC domain is required for enzymatic activity. |
| Sequence similarities | Belongs to the JARID1 histone demethylase family. Contains 1 ARID domain. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers. |
| Sequence caution | The sequence BAA13241.2 differs from that shown. Reason: Erroneous initiation. |
Ontologies
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] Note: Additional isoforms seem to exist. | ||||||
| Isoform 1 (identifier: Q9BY66-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. | ||||||
| Isoform 2 (identifier: Q9BY66-2) The sequence of this isoform differs from the canonical sequence as follows: 118-174: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1539 | 1539 | Lysine-specific demethylase 5D | PRO_0000200588 | |||||||||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||||||||
| Domain | 14 – 55 | 42 | JmjN | ||||||||||||||||||||||||||||||
| Domain | 79 – 169 | 91 | ARID | ||||||||||||||||||||||||||||||
| Domain | 458 – 624 | 167 | JmjC | ||||||||||||||||||||||||||||||
| Zinc finger | 316 – 362 | 47 | PHD-type 1 | ||||||||||||||||||||||||||||||
| Zinc finger | 1174 – 1235 | 62 | PHD-type 2 | ||||||||||||||||||||||||||||||
Sites | |||||||||||||||||||||||||||||||||
| Metal binding | 504 | 1 | Iron; catalytic By similarity | ||||||||||||||||||||||||||||||
| Metal binding | 507 | 1 | Iron; catalytic By similarity | ||||||||||||||||||||||||||||||
| Metal binding | 592 | 1 | Iron; catalytic By similarity | ||||||||||||||||||||||||||||||
Natural variations | |||||||||||||||||||||||||||||||||
| Alternative sequence | 118 – 174 | 57 | Missing in isoform 2. | VSP_000317 | |||||||||||||||||||||||||||||
| Natural variant | 1186 | 1 | V → L. Ref.1 Corresponds to variant rs1050807 [ dbSNP | Ensembl ]. | VAR_032991 | |||||||||||||||||||||||||||||
Experimental info | |||||||||||||||||||||||||||||||||
| Mutagenesis | 534 | 1 | H → A: Abolishes enzymatic activity; when associated with A-536. Ref.9 | ||||||||||||||||||||||||||||||
| Mutagenesis | 536 | 1 | E → A: Abolishes enzymatic activity; when associated with A-534. Ref.9 | ||||||||||||||||||||||||||||||
| Sequence conflict | 327 | 1 | D → N in AAC50806. Ref.1 | ||||||||||||||||||||||||||||||
| Sequence conflict | 327 | 1 | D → N in AAC51135. Ref.7 | ||||||||||||||||||||||||||||||
| Sequence conflict | 1285 | 1 | S → F in AAC50806. Ref.1 | ||||||||||||||||||||||||||||||
| Sequence conflict | 1352 | 1 | P → L in AAK27839. Ref.8 | ||||||||||||||||||||||||||||||
| Sequence conflict | 1391 | 1 | D → G in AAC50806. Ref.1 | ||||||||||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||||||
| Helix | 81 – 96 | 16 | |||||||||||||||||||||||||||||||
| Beta strand | 106 – 109 | 4 | |||||||||||||||||||||||||||||||
| Helix | 112 – 122 | 11 | |||||||||||||||||||||||||||||||
| Helix | 125 – 130 | 6 | |||||||||||||||||||||||||||||||
| Turn | 131 – 133 | 3 | |||||||||||||||||||||||||||||||
| Helix | 134 – 140 | 7 | |||||||||||||||||||||||||||||||
| Helix | 149 – 159 | 11 | |||||||||||||||||||||||||||||||
| Helix | 161 – 167 | 7 | |||||||||||||||||||||||||||||||
| Beta strand | 318 – 320 | 3 | |||||||||||||||||||||||||||||||
| Helix | 324 – 328 | 5 | |||||||||||||||||||||||||||||||
| Turn | 333 – 335 | 3 | |||||||||||||||||||||||||||||||
| Beta strand | 341 – 346 | 6 | |||||||||||||||||||||||||||||||
| Helix | 359 – 366 | 8 | |||||||||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Gene sequence and evolutionary conservation of human SMCY." Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S., Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A., Vandeberg J. Nat. Genet. 14:128-129(1996) [PubMed: 8841177] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT LEU-1186. |
| [2] | Erratum Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S., Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A., Vandeberg J. Nat. Genet. 14:252-252(1996) |
| [3] | "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." Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N. DNA Res. 3:321-329(1996) [PubMed: 9039502] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Bone marrow. |
| [4] | "Population genetic implications from sequence variation in four Y chromosome genes." Shen P., Wang F., Underhill P.A., Franco C., Yang W.-H., Roxas A., Sung R., Lin A.A., Hyman R.W., Vollrath D., Davis R.W., Cavalli-Sforza L.L., Oefner P.J. Proc. Natl. Acad. Sci. U.S.A. 97:7354-7359(2000) [PubMed: 10861003] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1). |
| [5] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [6] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). |
| [7] | "Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven." Agulnik A.I., Bishop C.E., Lerner J.L., Agulnik S.I., Solovyev V.V. Mamm. Genome 8:134-138(1997) [PubMed: 9060413] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-457 (ISOFORM 1). |
| [8] | "Exon-intron structure of SMCX and SMCY genes in bovine and swine." Poloumienko A., Blecher S. Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1340-1478. Tissue: Blood. |
| [9] | "Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein." Lee M.G., Norman J., Shilatifard A., Shiekhattar R. Cell 128:877-887(2007) [PubMed: 17320162] [Abstract] Cited for: FUNCTION, COFACTOR, INTERACTION WITH PCGF6, MUTAGENESIS OF HIS-534 AND GLU-536. |
| [10] | "The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases." Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y. Cell 128:1077-1088(2007) [PubMed: 17320160] [Abstract] Cited for: FUNCTION. |
| [11] | "The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase." Eissenberg J.C., Lee M.G., Schneider J., Ilvarsonn A., Shiekhattar R., Shilatifard A. Nat. Struct. Mol. Biol. 14:344-346(2007) [PubMed: 17351630] [Abstract] Cited for: FUNCTION. |
| [12] | "Spermatogenesis-specific association of SMCY and MSH5." Akimoto C., Kitagawa H., Matsumoto T., Kato S. Genes Cells 13:623-633(2008) [PubMed: 18459961] [Abstract] Cited for: INTERACTION WITH MSH5. |
| [13] | "Solution structure of the PHD domain and of the ARID domain of JARID1D/SMCY protein." RIKEN structural genomics initiative (RSGI) Submitted (APR-2008) to the PDB data bank Cited for: STRUCTURE BY NMR OF 79-384. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | U52191 mRNA. Translation: AAC50806.1. D87072 mRNA. Translation: BAA13241.2. Different initiation. AF273841 Genomic DNA. Translation: AAG00951.1. CH471202 Genomic DNA. Translation: EAW54663.1. BC132721 mRNA. Translation: AAI32722.1. BC146767 mRNA. Translation: AAI46768.1. U52365 mRNA. Translation: AAC51135.1. AF134849 Genomic DNA. Translation: AAK27839.1. | ||||||||||||||||||
| IPI | IPI00219940. IPI00329577. | ||||||||||||||||||
| RefSeq | NP_001140177.1. NM_001146705.1. NP_001140178.1. NM_001146706.1. NP_004644.2. NM_004653.4. | ||||||||||||||||||
| UniGene | Hs.80358. | ||||||||||||||||||
3D structure databases | |||||||||||||||||||
| PDBe RCSB PDB PDBj |
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| ProteinModelPortal | Q9BY66. | ||||||||||||||||||
| SMR | Q9BY66. Positions 47-171, 309-641, 1169-1235. | ||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||
| IntAct | Q9BY66. 1 interaction. | ||||||||||||||||||
| STRING | Q9BY66. | ||||||||||||||||||
PTM databases | |||||||||||||||||||
| PhosphoSite | Q9BY66. | ||||||||||||||||||
Polymorphism databases | |||||||||||||||||||
| DMDM | 17368706. | ||||||||||||||||||
Proteomic databases | |||||||||||||||||||
| PRIDE | Q9BY66. | ||||||||||||||||||
Protocols and materials databases | |||||||||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||||||||
Genome annotation databases | |||||||||||||||||||
| Ensembl | ENST00000317961; ENSP00000322408; ENSG00000012817. | ||||||||||||||||||
| GeneID | 8284. | ||||||||||||||||||
| KEGG | hsa:8284. | ||||||||||||||||||
| UCSC | uc004fug.1. human. uc010nwy.1. human. | ||||||||||||||||||
Organism-specific databases | |||||||||||||||||||
| CTD | 8284. | ||||||||||||||||||
| GeneCards | GC0YM021865. | ||||||||||||||||||
| H-InvDB | HIX0017195. | ||||||||||||||||||
| HGNC | HGNC:11115. KDM5D. | ||||||||||||||||||
| MIM | 426000. gene. | ||||||||||||||||||
| neXtProt | NX_Q9BY66. | ||||||||||||||||||
| PharmGKB | PA162392425. PA164721742. PA35965. | ||||||||||||||||||
| HUGE | Search... | ||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||
| eggNOG | prNOG08641. | ||||||||||||||||||
| GeneTree | ENSGT00530000063118. | ||||||||||||||||||
| InParanoid | Q9BY66. | ||||||||||||||||||
| OMA | WRILETM. | ||||||||||||||||||
| OrthoDB | EOG4894KP. | ||||||||||||||||||
| PhylomeDB | Q9BY66. | ||||||||||||||||||
Gene expression databases | |||||||||||||||||||
| ArrayExpress | Q9BY66. | ||||||||||||||||||
| Bgee | Q9BY66. | ||||||||||||||||||
| CleanEx | HS_JARID1D. | ||||||||||||||||||
| Genevestigator | Q9BY66. | ||||||||||||||||||
| GermOnline | ENSG00000012817. Homo sapiens. | ||||||||||||||||||
Family and domain databases | |||||||||||||||||||
| InterPro | IPR001606. ARID/BRIGHT_DNA-bd. IPR013637. Lys_sp_deMease_like_dom. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. IPR019786. Zinc_finger_PHD-type_CS. IPR004198. Znf_C5HC2. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. IPR013083. Znf_RING/FYVE/PHD. [Graphical view] | ||||||||||||||||||
| Gene3D | G3DSA:1.10.150.60. ARID. 1 hit. G3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 2 hits. | ||||||||||||||||||
| KO | K11446. | ||||||||||||||||||
| Pfam | PF01388. ARID. 1 hit. PF02373. JmjC. 1 hit. PF02375. JmjN. 1 hit. PF00628. PHD. 2 hits. PF08429. PLU-1. 1 hit. PF02928. zf-C5HC2. 1 hit. [Graphical view] | ||||||||||||||||||
| SMART | SM00501. BRIGHT. 1 hit. SM00558. JmjC. 1 hit. SM00545. JmjN. 1 hit. SM00249. PHD. 2 hits. [Graphical view] | ||||||||||||||||||
| SUPFAM | SSF46774. ARID. 1 hit. SSF57903. FYVE_PHD_ZnF. 2 hits. | ||||||||||||||||||
| PROSITE | PS51011. ARID. 1 hit. PS51184. JMJC. 1 hit. PS51183. JMJN. 1 hit. PS01359. ZF_PHD_1. 2 hits. PS50016. ZF_PHD_2. 1 hit. [Graphical view] | ||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||
Other | |||||||||||||||||||
| DrugBank | DB00126. Vitamin C. | ||||||||||||||||||
| NextBio | 31049. | ||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||
Entry information
| Entry name | KDM5D_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q9BY66 Secondary accession number(s): A2RU19 Q9HCU1 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome Y Human chromosome Y: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with