Reviewed,
UniProtKB/Swiss-Prot P29375 (KDM5A_HUMAN)
Last modified
June 16, 2009.
Version 91.
History...
Clusters with 100%,
90%,
50% identity |
Documents (6) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Lysine-specific demethylase 5A EC=1.14.11.- Alternative name(s): Histone demethylase JARID1A Jumonji/ARID domain-containing protein 1A Retinoblastoma-binding protein 2 Short name=RBBP-2 | ||||
| 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 | 1690 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| 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 stimulate transcription mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12. Ref.8 Ref.10 Ref.12 Ref.13 Ref.14 |
| Cofactor | Fe2+ By similarity. |
| Subunit structure | Interacts with the viral protein-binding domain of RB1. Interacts with ESR1, MYC, MYCN and LMO2. Ref.8 Ref.10 Ref.1 Ref.6 Ref.7 Ref.15 |
| Subcellular location | |
| Sequence similarities | Belongs to the JARID1 histone demethylase family. Contains 1 ARID domain. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 3 PHD-type zinc fingers. |
| Sequence caution | The sequence AAB28544.1 differs from that shown. Reason: Frameshift at several positions. |
Ontologies
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: P29375-1) 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: P29375-2) The sequence of this isoform differs from the canonical sequence as follows: 1623-1690: VDWVQCDGGC...LPMEDLKETS → GVVFVTEEERDKKY |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1690 | 1690 | Lysine-specific demethylase 5A | PRO_0000200584 | |||||
Regions | |||||||||
| Domain | 19 – 60 | 42 | JmjN | ||||||
| Domain | 84 – 174 | 91 | ARID | ||||||
| Domain | 437 – 603 | 167 | JmjC | ||||||
| Zinc finger | 293 – 343 | 51 | PHD-type 1 | ||||||
| Zinc finger | 1161 – 1218 | 58 | PHD-type 2 | ||||||
| Zinc finger | 1607 – 1661 | 55 | PHD-type 3 | ||||||
| Region | 1623 – 1690 | 68 | Interaction with LMO2 | ||||||
| Compositional bias | 1492 – 1587 | 96 | Lys-rich | ||||||
Amino acid modifications | |||||||||
| Modified residue | 1111 | 1 | Phosphoserine Ref.11 Ref.16 | ||||||
| Modified residue | 1331 | 1 | Phosphoserine Ref.16 Ref.9 | ||||||
| Modified residue | 1598 | 1 | Phosphoserine Ref.11 | ||||||
| Modified residue | 1603 | 1 | Phosphoserine Ref.11 | ||||||
| Modified residue | 1666 | 1 | Phosphoserine Ref.9 | ||||||
Natural variations | |||||||||
| Alternative sequence | 1623 – 1690 | 68 | VDWVQ…LKETS → GVVFVTEEERDKKY in isoform 2. | VSP_035746 | |||||
| Natural variant | 865 | 1 | M → T: dbSNP rs11062385. | VAR_032984 | |||||
| Natural variant | 1190 | 1 | P → A: dbSNP rs2229353. | VAR_032985 | |||||
Experimental info | |||||||||
| Sequence conflict | 1411 | 1 | Q → QVFFGK in AAB28544. Ref.1 | ||||||
| Sequence conflict | 1547 | 1 | E → K in AAB28544. Ref.1 | ||||||
| Sequence conflict | 1612 – 1614 | 3 | AQN → EPD in AAB28544. Ref.1 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Characterization of the retinoblastoma binding proteins RBP1 and RBP2." Fattaey A.R., Helin K., Dembski M.S., Dyson N., Harlow E., Vuocolo G.A., Hanobik M.G., Haskell K.M., Oliff A., Defeo-Jones D., Jones R.E. Oncogene 8:3149-3156(1993) [PubMed: 8414517] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH RB1. |
| [2] | "Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method." Nakajima D., Saito K., Yamakawa H., Kikuno R.F., Nakayama M., Ohara R., Okazaki N., Koga H., Nagase T., Ohara O. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). |
| [3] | "The finished DNA sequence of human chromosome 12." Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R. Gibbs R.A.Nature 440:346-351(2006) [PubMed: 16541075] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | "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] OF 1-1099 (ISOFORM 1/2). Tissue: Eye and Testis. |
| [5] | "Cloning of cDNAs for cellular proteins that bind to the retinoblastoma gene product." Defeo-Jones D., Huang P.S., Jones R.E., Haskell K.M., Vuocolo G.A., Hanobik M.G., Huber H.E., Oliff A. Nature 352:251-254(1991) [PubMed: 1857421] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1102-1564. |
| [6] | "Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein." Kim Y.W., Otterson G.A., Kratzke R.A., Coxon A.B., Kaye F.J. Mol. Cell. Biol. 14:7256-7264(1994) [PubMed: 7935440] [Abstract] Cited for: INTERACTION WITH RB1, SUBCELLULAR LOCATION. |
| [7] | "T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2." Mao S., Neale G.A.M., Goorha R.M. Oncogene 14:1531-1539(1997) [PubMed: 9129143] [Abstract] Cited for: INTERACTION WITH LMO2. |
| [8] | "Retinoblastoma-binding protein 2 (Rbp2) potentiates nuclear hormone receptor-mediated transcription." Chan S.W., Hong W. J. Biol. Chem. 276:28402-28412(2001) [PubMed: 11358960] [Abstract] Cited for: FUNCTION, INTERACTION WITH ESR1. |
| [9] | "Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1331 AND SER-1666, MASS SPECTROMETRY. Tissue: Epithelium. |
| [10] | "Binding of pRB to the PHD protein RBP2 promotes cellular differentiation." Benevolenskaya E.V., Murray H.L., Branton P., Young R.A., Kaelin W.G. Jr. Mol. Cell 18:623-635(2005) [PubMed: 15949438] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH RB1, FUNCTION. |
| [11] | "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1111; SER-1598 AND SER-1603, MASS SPECTROMETRY. Tissue: Epithelium. |
| [12] | "The retinoblastoma binding protein RBP2 is an H3K4 demethylase." Klose R.J., Yan Q., Tothova Z., Yamane K., Erdjument-Bromage H., Tempst P., Gilliland D.G., Zhang Y., Kaelin W.G. Jr. Cell 128:889-900(2007) [PubMed: 17320163] [Abstract] Cited for: FUNCTION. |
| [13] | "RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3." Christensen J., Agger K., Cloos P.A.C., Pasini D., Rose S., Sennels L., Rappsilber J., Hansen K.H., Salcini A.E., Helin K. Cell 128:1063-1076(2007) [PubMed: 17320161] [Abstract] Cited for: FUNCTION. |
| [14] | "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. |
| [15] | "The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth." Secombe J., Li L., Carlos L., Eisenman R.N. Genes Dev. 21:537-551(2007) [PubMed: 17311883] [Abstract] Cited for: INTERACTION WITH MYC AND MYCN. |
| [16] | "A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1111 AND SER-1331, MASS SPECTROMETRY. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S66431 mRNA. Translation: AAB28544.1. Frameshift. AB209999 mRNA. Translation: BAE06081.1. Different initiation. AC005844 Genomic DNA. No translation available. AC007406 Genomic DNA. No translation available. BC048307 mRNA. Translation: AAH48307.1. Different termination. BC053893 mRNA. Translation: AAH53893.1. Different termination. BC110916 mRNA. Translation: AAI10917.1. Different termination. | |||||||||||||||||||||||||||||||
| IPI | IPI00619935. IPI00872073. | ||||||||||||||||||||||||||||||
| PIR | I78879. | ||||||||||||||||||||||||||||||
| RefSeq | NP_001036068.1. NP_005047.2. | ||||||||||||||||||||||||||||||
| UniGene | Hs.76272 | ||||||||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||||||||
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| ModBase | Search... | ||||||||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||||||||
| DIP | DIP:472N. | ||||||||||||||||||||||||||||||
PTM databases | |||||||||||||||||||||||||||||||
| PhosphoSite | P29375. | ||||||||||||||||||||||||||||||
Proteomic databases | |||||||||||||||||||||||||||||||
| PRIDE | P29375. | ||||||||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||||||||
| Ensembl | ENSG00000073614. Homo sapiens. [Contig view] | ||||||||||||||||||||||||||||||
| GeneID | 5927. | ||||||||||||||||||||||||||||||
| KEGG | hsa:5927. | ||||||||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||||||||
| GeneCards | GC12M000263. | ||||||||||||||||||||||||||||||
| H-InvDB | HIX0010308. | ||||||||||||||||||||||||||||||
| HGNC | HGNC:9886. KDM5A. | ||||||||||||||||||||||||||||||
| HPA | HPA006201. | ||||||||||||||||||||||||||||||
| MIM | 180202. gene. | ||||||||||||||||||||||||||||||
| PharmGKB | PA34250. | ||||||||||||||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||||||||
| HOVERGEN | P29375. | ||||||||||||||||||||||||||||||
Gene expression databases | |||||||||||||||||||||||||||||||
| ArrayExpress | P29375. | ||||||||||||||||||||||||||||||
| Bgee | P29375. | ||||||||||||||||||||||||||||||
| CleanEx | HS_JARID1A. HS_RBP2. | ||||||||||||||||||||||||||||||
| GermOnline | ENSG00000073614. Homo sapiens. | ||||||||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||||||||
| InterPro | IPR001606. ARID. IPR013637. PLU-1. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. IPR019786. Zinc_finger_PHD-type_CS. IPR004198. Znf_C5HC2. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. [Graphical view] | ||||||||||||||||||||||||||||||
| Gene3D | G3DSA:1.10.150.60. ARID. 1 hit. | ||||||||||||||||||||||||||||||
| Pfam | PF01388. ARID. 1 hit. PF02373. JmjC. 1 hit. PF02375. JmjN. 1 hit. PF00628. PHD. 3 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. 3 hits. [Graphical view] | ||||||||||||||||||||||||||||||
| PROSITE | PS51011. ARID. 1 hit. PS51184. JMJC. 1 hit. PS51183. JMJN. 1 hit. PS01359. ZF_PHD_1. 2 hits. PS50016. ZF_PHD_2. 3 hits. [Graphical view] | ||||||||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||||||||
Other Resources | |||||||||||||||||||||||||||||||
| NextBio | 23088. | ||||||||||||||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||||||||||||||
Entry information
| Entry name | KDM5A_HUMAN | ||||||||
| Accession | Primary (citable) accession number: P29375 Secondary accession number(s): A8MV76, Q4LE72, Q86XZ1 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
Relevant documents
| Human chromosome 12 Human chromosome 12: 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


