Reviewed,
UniProtKB/Swiss-Prot Q7LBC6 (KDM3B_HUMAN)
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June 16, 2009.
Version 43.
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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents
Names and origin
| Protein names | Recommended name: Lysine-specific demethylase 3B EC=1.14.11.- Alternative name(s): JmjC domain-containing histone demethylation protein 2B Jumonji domain-containing protein 1B Nuclear protein 5qNCA | ||||
| 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 | 1761 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-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity. Ref.7 |
| Cofactor | Binds 1 Fe2+ ion per subunit By similarity. |
| Subcellular location | Nucleus By similarity. |
| Tissue specificity | Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver. Ref.1 Ref.2 |
| Domain | Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors By similarity. |
| Miscellaneous | Its gene is located in the 5q region of the genome which is deleted in del(5q) interstitial deletion, a frequent deletion found in myeloid leukemias and myelodysplasias, suggesting that it may be a good candidate for the del(5q) tumor suppressor gene. |
| Sequence similarities | Belongs to the JHDM2 histone demethylase family. Contains 1 JmjC domain. |
Ontologies
Alternative products
| This entry describes 3 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q7LBC6-1) 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: Q7LBC6-2) The sequence of this isoform differs from the canonical sequence as follows: 1-344: Missing. 345-349: TFVPQ → MGAME | ||||||
| Isoform 3 (identifier: Q7LBC6-3) The sequence of this isoform differs from the canonical sequence as follows: 1-1002: Missing. | ||||||
| Note: No experimental confirmation available. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1761 | 1761 | Lysine-specific demethylase 3B | PRO_0000234373 | |||||
Regions | |||||||||
| Domain | 1498 – 1721 | 224 | JmjC | ||||||
| Zinc finger | 1031 – 1056 | 26 | C6-type Potential | ||||||
| Motif | 1293 – 1297 | 5 | LXXLL motif | ||||||
| Compositional bias | 647 – 744 | 98 | Ser-rich | ||||||
Sites | |||||||||
| Metal binding | 1560 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 1562 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 1689 | 1 | Iron; catalytic By similarity | ||||||
Amino acid modifications | |||||||||
| Modified residue | 291 | 1 | Phosphoserine Ref.6 | ||||||
| Modified residue | 773 | 1 | Phosphoserine Ref.9 | ||||||
| Modified residue | 779 | 1 | Phosphoserine Ref.9 | ||||||
| Modified residue | 798 | 1 | Phosphoserine Ref.8 | ||||||
Natural variations | |||||||||
| Alternative sequence | 1 – 1002 | 1002 | Missing in isoform 3. | VSP_018298 | |||||
| Alternative sequence | 1 – 344 | 344 | Missing in isoform 2. | VSP_018299 | |||||
| Alternative sequence | 345 – 349 | 5 | TFVPQ → MGAME in isoform 2. | VSP_018300 | |||||
| Natural variant | 256 | 1 | T → A: dbSNP rs6865472. Ref.2 | VAR_026221 | |||||
| Natural variant | 1201 | 1 | S → N: dbSNP rs7706614. | VAR_026222 | |||||
Experimental info | |||||||||
| Sequence conflict | 569 | 1 | C → R in AAF63765. Ref.1 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins." Lai F., Godley L.A., Fernald A.A., Orelli B.J., Pamintuan L., Zhao N., Le Beau M.M. Genomics 70:123-130(2000) [PubMed: 11087669] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY. Tissue: Bone marrow. |
| [2] | "A novel nuclear protein, 5qNCA (LOC51780) is a candidate for the myeloid leukemia tumor suppressor gene on chromosome 5 band q31." Hu Z., Gomes I., Horrigan S.K., Kravarusic J., Mar B., Arbieva Z., Chyna B., Fulton N., Edassery S., Raza A., Westbrook C.A. Oncogene 20:6946-6954(2001) [PubMed: 11687974] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANT ALA-256. |
| [3] | "Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro." Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 6:197-205(1999) [PubMed: 10470851] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain. |
| [4] | "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones." Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T. DNA Res. 9:99-106(2002) [PubMed: 12168954] [Abstract] Cited for: SEQUENCE REVISION. |
| [5] | "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] (ISOFORM 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 184-1761. Tissue: Brain and Eye. |
| [6] | "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-291, MASS SPECTROMETRY. Tissue: Epithelium. |
| [7] | "JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor." Yamane K., Toumazou C., Tsukada Y.I., Erdjument-Bromage H., Tempst P., Wong J., Zhang Y. Cell 125:483-495(2006) [PubMed: 16603237] [Abstract] Cited for: FUNCTION, ENZYME ACTIVITY. |
| [8] | "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-798, MASS SPECTROMETRY. Tissue: Epithelium. |
| [9] | "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-773 AND SER-779, MASS SPECTROMETRY. |
| [10] | Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. |
Cross-references
Sequence databases | |
|---|---|
| AF251039 mRNA. Translation: AAF63765.1. AF338242 mRNA. Translation: AAK13499.1. AB029005 mRNA. Translation: BAA83034.2. Different initiation. BC000539 mRNA. Translation: AAH00539.2. BC001202 mRNA. Translation: AAH01202.1. | |
| IPI | IPI00298935. IPI00748132. IPI00749486. |
| RefSeq | NP_057688.2. |
| UniGene | Hs.714832 |
3D structure databases | |
| ModBase | Search... |
PTM databases | |
| PhosphoSite | Q7LBC6. |
Proteomic databases | |
| PRIDE | Q7LBC6. |
Genome annotation databases | |
| Ensembl | ENSG00000120733. Homo sapiens. [Contig view] |
| GeneID | 51780. |
| KEGG | hsa:51780. |
Organism-specific databases | |
| GeneCards | GC05P137716. |
| H-InvDB | HIX0005211. |
| HGNC | HGNC:1337. KDM3B. |
| HPA | HPA016610. |
| MIM | 609373. gene. |
| PharmGKB | PA25918. |
| HUGE | Search... |
| GenAtlas | Search... |
Phylogenomic databases | |
| HOGENOM | Q7LBC6. |
| HOVERGEN | Q7LBC6. |
Gene expression databases | |
| ArrayExpress | Q7LBC6. |
| Bgee | Q7LBC6. |
| CleanEx | HS_JMJD1B. |
| GermOnline | ENSG00000120733. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. [Graphical view] |
| Pfam | PF02373. JmjC. 1 hit. [Graphical view] |
| SMART | SM00558. JmjC. 1 hit. [Graphical view] |
| PROSITE | PS51184. JMJC. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other Resources | |
| NextBio | 55912. |
| SOURCE | Search... |
Entry information
| Entry name | KDM3B_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q7LBC6 Secondary accession number(s): Q9BVH6  Q9UPS0 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
Relevant documents
| Human chromosome 5 Human chromosome 5: 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 |
| SIMILARITY comments Index of protein domains and families |
