Q9U6M1 · JBP1_LEITA
- ProteinThymine dioxygenase JBP1
- GeneJBP1
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids827 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Dioxygenase that catalyzes the first step of DNA base J (beta-d-glucosyl-HOMedU) biosynthesis by converting thymine to 5-hydroxymethyluracil (HOMedU). DNA base J is a hypermodified thymidine residue found in the genome of kinetoplastid parasites, which is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. Also specifically binds to base J-containing DNA (J-DNA). Involved in propagation and maintenance of DNA base J synthesis initiated by JBP2 by specifically binding already synthesized DNA base J and propagating J synthesis. Thymine dioxygenase activity and J-DNA-binding are independent functions.
Catalytic activity
- 2-oxoglutarate + O2 + thymine = 5-hydroxymethyluracil + CO2 + succinate
Cofactor
Note: Binds 1 Fe2+ ion per subunit.
Features
Showing features for binding site, site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 189 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 191 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 239 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 255 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Site | 525 | Involved in J base recognition and binding, conferring specificity towards J-DNA | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | nucleus | |
Molecular Function | DNA binding | |
Molecular Function | metal ion binding | |
Molecular Function | thymine dioxygenase activity | |
Biological Process | base J metabolic process |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameThymine dioxygenase JBP1
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Discoba > Euglenozoa > Kinetoplastea > Metakinetoplastina > Trypanosomatida > Trypanosomatidae > Leishmaniinae > Leishmania > lizard Leishmania
Accessions
- Primary accessionQ9U6M1
Organism-specific databases
Subcellular Location
UniProt Annotation
GO Annotation
Note: Localizes to discrete spots in the nucleus, probably the J-rich telomeres.
Keywords
- Cellular component
Phenotypes & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 189 | Impairs DNA base J biosynthesis. | ||||
Sequence: H → A | ||||||
Mutagenesis | 191 | Impairs DNA base J biosynthesis. | ||||
Sequence: D → A | ||||||
Mutagenesis | 239 | Impairs DNA base J biosynthesis. | ||||
Sequence: H → A | ||||||
Mutagenesis | 255 | Impairs DNA base J biosynthesis. | ||||
Sequence: R → A | ||||||
Mutagenesis | 259 | No effect. | ||||
Sequence: V → A | ||||||
Mutagenesis | 391 | No effect. | ||||
Sequence: E → A | ||||||
Mutagenesis | 436 | No effect. | ||||
Sequence: K → A | ||||||
Mutagenesis | 465 | No effect. | ||||
Sequence: D → A | ||||||
Mutagenesis | 468 | No effect. | ||||
Sequence: E → A | ||||||
Mutagenesis | 487-488 | No effect. | ||||
Sequence: EE → AA | ||||||
Mutagenesis | 518 | Decreases binding affinity for both J-DNA and normal DNA. | ||||
Sequence: K → A | ||||||
Mutagenesis | 522 | Decreases binding affinity for both J-DNA and normal DNA. | ||||
Sequence: K → A | ||||||
Mutagenesis | 524 | Slightly decreases binding affinity for both J-DNA and normal DNA. | ||||
Sequence: K → A | ||||||
Mutagenesis | 525 | Abolishes preference for J-DNA-binding. | ||||
Sequence: D → A | ||||||
Mutagenesis | 532 | Decreases binding affinity for both J-DNA and normal DNA. | ||||
Sequence: R → A | ||||||
Mutagenesis | 535 | No effect. | ||||
Sequence: K → A | ||||||
Mutagenesis | 536 | No effect. | ||||
Sequence: D → A | ||||||
Mutagenesis | 540-541 | No effect. | ||||
Sequence: EE → AA | ||||||
Mutagenesis | 553 | No effect. | ||||
Sequence: E → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000377554 | 1-827 | Thymine dioxygenase JBP1 | |||
Sequence: MEPDSKKVKLDIFNFPTTRETRTPEEVAESYAEAVKSHPFYDNVHSVVDFYDSGTIKDGRGQIIGVVLREALPKYAASMASELLTSAAVRTSLRSMMFGGEPPLSGIAGYFDYRGSPVELKSRKTSFTYEHEAAWPAVFPVVDYVSEIYRHVAPERWKAQNDAIPDLVRIHGTPFSTLTINSRFRTASHTDVGDFDAGYSCIACLDGQFKGLALSFDDFGINVLLQPRDVMIFDSHHFHSNTEVELSFSGEDWKRLTCVFYYRAALGEPASYAEYQRRLEKSKTDTRFTPVVHHVRVKENGTSVNRPSPVYPISQSPFWVPMVAHCLQHCASAAQCVHEAMTADGSRLAEMMFGESLSTSDGIPLRGEDEKVKANGDSTPRPLSRLGGFSETNLMVSTAVEKKKYLDSEFLLHCISAQLLDMWKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMPEVAMSLRKLNVKLKDFNFGGTRYFKDMPPEEKKRRMERKQRIEEARRHGMPSGSHEKRANWLTNDSFDYQTEDCVIDYAQHKWVLPALHAKEVTKTVRTGELPTTERVVRVLVVIPDPQSKLENVDCKLEVPDMVGSSSEWERLMSSPAVHRVLSAAQRNLQLPDSVTHGNVQTHFAFHSTLPTDIYDFVVLQHVLSRIPDDAQASAYIRRAAALCSGCLFVVETDVQCRQYYTLKYSIRCSYDTVAPLFFQQLHRVCYGTKTARVRTKGELESLIPTVCCARYKLQGSPLNTTVHVVSPFPSCEVQNLSSALCDRA |
Interaction
Subunit
Monomer. Binds to DNA as a monomer.
Structure
Family & Domains
Features
Showing features for region, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 62-264 | Thymine dioxygenase | ||||
Sequence: QIIGVVLREALPKYAASMASELLTSAAVRTSLRSMMFGGEPPLSGIAGYFDYRGSPVELKSRKTSFTYEHEAAWPAVFPVVDYVSEIYRHVAPERWKAQNDAIPDLVRIHGTPFSTLTINSRFRTASHTDVGDFDAGYSCIACLDGQFKGLALSFDDFGINVLLQPRDVMIFDSHHFHSNTEVELSFSGEDWKRLTCVFYYRA | ||||||
Region | 364-383 | Disordered | ||||
Sequence: PLRGEDEKVKANGDSTPRPL | ||||||
Region | 392-561 | DNA-binding JBP1 domain | ||||
Sequence: TNLMVSTAVEKKKYLDSEFLLHCISAQLLDMWKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMPEVAMSLRKLNVKLKDFNFGGTRYFKDMPPEEKKRRMERKQRIEEARRHGMP | ||||||
Compositional bias | 539-564 | Basic and acidic residues | ||||
Sequence: PEEKKRRMERKQRIEEARRHGMPSGS | ||||||
Region | 539-568 | Disordered | ||||
Sequence: PEEKKRRMERKQRIEEARRHGMPSGSHEKR |
Domain
The DNA-binding JBP1 domain (DB-JBP1) is necessary and sufficient for binding to J-DNA.
Sequence similarities
Belongs to the TET family. JBP1 subfamily.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length827
- Mass (Da)93,403
- Last updated2000-05-01 v1
- Checksum5A4B502DE70A4BFE
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 539-564 | Basic and acidic residues | ||||
Sequence: PEEKKRRMERKQRIEEARRHGMPSGS |
Keywords
- Technical term