Reviewed,
UniProtKB/Swiss-Prot Q640I9 (JHD1B_XENLA)
Last modified
November 25, 2008.
Version 36.
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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: JmjC domain-containing histone demethylation protein 1B EC=1.14.11.27 Alternative name(s): [Histone-H3]-lysine-36 demethylase 1B F-box and leucine-rich repeat protein 10 F-box/LRR-repeat protein 10 | ||||
| Gene names |
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| Organism | Xenopus laevis (African clawed frog) | ||||
| Taxonomic identifier | 8355 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus |
Protein attributes
| Sequence length | 1259 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence at transcript level. |
General annotation (Comments)
| Function | Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylted H3 'Lys-36' By similarity. |
| Catalytic activity | Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2). Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2). |
| Cofactor | Binds 1 Fe(2+) ion per subunit By similarity. |
| Subcellular location | NucleusBy similarity. |
| Domain | The JmjC domain mediates the demethylation activity By similarity. |
| Sequence similarities | Belongs to the JHDM1 histone demethylase family. Contains 1 CXXC-type zinc finger. Contains 1 F-box domain. Contains 1 JmjC domain. Contains 4 LRR (leucine-rich) repeats. Contains 1 PHD-type zinc finger. |
Ontologies
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q640I9-1) 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: Q640I9-2) The sequence of this isoform differs from the canonical sequence as follows: 1-521: Missing. 522-539: NLAISGVPVVMWPKKPSK → MALSLSNDDEEYDSEQEQ | ||||||
| Notes: No experimental confirmation available. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1259 | 1259 | JmjC domain-containing histone demethylation protein 1B | PRO_0000226786 | |||||
Regions | |||||||||
| Domain | 147 – 315 | 169 | JmjC | ||||||
| Domain | 985 – 1030 | 46 | F-box | ||||||
| Repeat | 1071 – 1094 | 24 | LRR 1 | ||||||
| Repeat | 1135 – 1158 | 24 | LRR 2 | ||||||
| Repeat | 1192 – 1216 | 25 | LRR 3 | ||||||
| Repeat | 1217 – 1259 | 43 | LRR 4 | ||||||
| Zinc finger | 567 – 613 | 47 | CXXC-type | ||||||
| Zinc finger | 620 – 686 | 67 | PHD-type | ||||||
| Coiled coil | 864 – 891 | 28 | Potential | ||||||
| Compositional bias | 688 – 799 | 112 | Lys-rich | ||||||
Sites | |||||||||
| Metal binding | 211 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 213 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 283 | 1 | Iron; catalytic By similarity | ||||||
| Binding site | 208 | 1 | Substrate By similarity | ||||||
| Binding site | 228 | 1 | Substrate By similarity | ||||||
Natural variations | |||||||||
| Alternative sequence | 1 – 521 | 521 | Missing in isoform 2. | VSP_017479 | |||||
| Alternative sequence | 522 – 539 | 18 | NLAIS…KKPSK → MALSLSNDDEEYDSEQEQ in isoform 2. | VSP_017480 | |||||
Experimental info | |||||||||
| Sequence conflict | 919 | 1 | N → H in AAH73414. Ref.1 | ||||||
Sequences
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References
| [1] | NIH - Xenopus Gene Collection (XGC) project Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Embryo. |
Cross-references
Sequence databases | |
|---|---|
| BC073414 mRNA. Translation: AAH73414.1. BC082636 mRNA. Translation: AAH82636.1. | |
| RefSeq | NP_001085840.1. |
| UniGene | Xl.52422 |
3D structure databases | |
| SMR | Q640I9. Positions 35-361. |
| ModBase | Search... |
Genome annotation databases | |
| GeneID | 444267. |
| KEGG | xla:444267. |
Organism-specific databases | |
| Xenbase | XB-FEAT-990505. fbxl10. |
Phylogenomic databases | |
| HOVERGEN | Q640I9. |
Family and domain databases | |
| InterPro | IPR001810. F-box. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR002857. Znf_CXXC. IPR001965. Znf_PHD. [Graphical view] |
| Pfam | PF00646. F-box. 1 hit. PF02373. JmjC. 1 hit. PF02008. zf-CXXC. 1 hit. [Graphical view] |
| SMART | SM00558. JmjC. 1 hit. SM00249. PHD. 1 hit. [Graphical view] |
| PROSITE | PS50181. FBOX. False negative. PS51184. JMJC. 1 hit. PS51058. ZF_CXXC. 1 hit. PS01359. ZF_PHD_1. False negative. PS50016. ZF_PHD_2. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Entry information
| Entry name | JHD1B_XENLA | ||||||||
| Accession | Primary (citable) accession number: Q640I9 Secondary accession number(s): Q6GNT8 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | Xenopus annotation project | ||||||||
