Q13838 · DX39B_HUMAN
- ProteinSpliceosome RNA helicase DDX39B
- GeneDDX39B
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids428 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA (PubMed:15833825, PubMed:15998806, PubMed:17190602).
The TREX complex is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NXF1 pathway (PubMed:15833825, PubMed:15998806, PubMed:17190602).
The THOC1-THOC2-THOC3 core complex alone is sufficient to promote ATPase activity of DDX39B; in the complex THOC2 is the only component that directly interacts with DDX39B (PubMed:33191911).
Associates with SARNP/CIP29, which facilitates RNA binding of DDX39B and likely plays a role in mRNA export (PubMed:37578863).
May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC4 and CHTOP onto mRNA. Also associates with pre-mRNA independent of ALYREF/THOC4. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability
Catalytic activity
- ATP + H2O = ADP + H+ + phosphate
Kinetics
KM | SUBSTRATE | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|---|
3.3 μM | ATP |
Vmax | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|
0.126 μM/min/mg | with ATP as substrate |
Features
Showing features for binding site.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | nuclear speck | |
Cellular Component | nucleoplasm | |
Cellular Component | nucleus | |
Cellular Component | spliceosomal complex | |
Cellular Component | transcription export complex | |
Cellular Component | U4 snRNP | |
Cellular Component | U6 snRNP | |
Molecular Function | ATP binding | |
Molecular Function | ATP hydrolysis activity | |
Molecular Function | ATP-dependent activity, acting on RNA | |
Molecular Function | ATP-dependent protein binding | |
Molecular Function | identical protein binding | |
Molecular Function | mRNA binding | |
Molecular Function | RNA binding | |
Molecular Function | RNA helicase activity | |
Molecular Function | U4 snRNA binding | |
Molecular Function | U6 snRNA binding | |
Biological Process | mRNA export from nucleus | |
Biological Process | mRNA splicing, via spliceosome | |
Biological Process | RNA export from nucleus | |
Biological Process | RNA secondary structure unwinding | |
Biological Process | RNA splicing | |
Biological Process | spliceosomal complex assembly |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Protein family/group databases
Names & Taxonomy
Protein names
- Recommended nameSpliceosome RNA helicase DDX39B
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ13838
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Keywords
- Cellular component
Disease & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 94-96 | Loss of ATPase and helicase activity. | ||||
Sequence: GKT → AAA | ||||||
Mutagenesis | 95 | Loss of ATPase and helicase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 197 | Loss of ATPase and helicase activity. | ||||
Sequence: E → A | ||||||
Mutagenesis | 198 | No effect on ATPase activity. | ||||
Sequence: C → A | ||||||
Mutagenesis | 199 | Increased ATPase activity and loss of helicase activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 228-230 | Decreased ATPase activity and loss of helicase activity. | ||||
Sequence: SAT → AAA | ||||||
Mutagenesis | 283 | Abolishes interaction with SARNP; when associated with 2-A--T-258 del. | ||||
Sequence: D → R |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 415 variants from UniProt as well as other sources including ClinVar and dbSNP.
Organism-specific databases
Miscellaneous
Chemistry
Genetic variation databases
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain, modified residue (large scale data), cross-link.
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Initiator methionine | 1 | UniProt | Removed | ||||
Sequence: M | |||||||
Modified residue | 2 | UniProt | N-acetylalanine | ||||
Sequence: A | |||||||
Chain | PRO_0000055071 | 2-428 | UniProt | Spliceosome RNA helicase DDX39B | |||
Sequence: AENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR | |||||||
Modified residue (large scale data) | 13 | PRIDE | Phosphotyrosine | ||||
Sequence: Y | |||||||
Modified residue (large scale data) | 20 | PRIDE | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue | 36 | UniProt | N6-acetyllysine; alternate | ||||
Sequence: K | |||||||
Cross-link | 36 | UniProt | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate | ||||
Sequence: K | |||||||
Modified residue | 38 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 38 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 39 | PRIDE | Phosphotyrosine | ||||
Sequence: Y | |||||||
Modified residue | 41 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 41 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 44 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 172 | UniProt | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue (large scale data) | 172 | PRIDE | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue (large scale data) | 266 | PRIDE | Phosphotyrosine | ||||
Sequence: Y |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Interaction
Subunit
DDX39B interacts with the THO subcomplex to form the THO-DDX39B complex which multimerizes into a 28-subunit tetrameric assembly (PubMed:33191911, PubMed:37020021).
Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; in the complex interacts with THOC2 (PubMed:33191911, PubMed:37020021).
THOC1-THOC2-THOC3-DDX39B subcomplex is sufficient for the interaction with export factor NXF1-NXT1 (PubMed:33191911).
TREX seems to have a dynamic structure involving ATP-dependent remodeling (PubMed:23222130).
Within the TREX complex bridges ALYREF/THOC4 and the THO subcomplex, and, in a ATP-dependent manner, ALYREF/THOC4 and SARNP/CIP29 (PubMed:11675789, PubMed:14667819, PubMed:15833825, PubMed:15998806, PubMed:17984224, PubMed:20844015, PubMed:23299939).
Component of the spliceosome. Interacts directly with U2AF2 (PubMed:9242493).
Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1, MX1 and POLDIP3 (PubMed:12944400, PubMed:15870275, PubMed:19836239, PubMed:21859714, PubMed:22928037).
Interacts with LUZP4 (PubMed:25662211).
Interacts with SARNP/CIP29 (via the C-terminal domain); the interaction is direct and facilitates RNA binding of DDX39B (PubMed:37578863).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q13838 | ALYREF Q86V81 | 5 | EBI-348622, EBI-347640 | |
BINARY | Q13838 | API5 Q9BZZ5 | 2 | EBI-348622, EBI-1048422 | |
BINARY | Q13838 | CHTOP Q9Y3Y2 | 8 | EBI-348622, EBI-347794 | |
BINARY | Q13838 | CHTOP Q9Y3Y2-3 | 5 | EBI-348622, EBI-11984237 | |
BINARY | Q13838 | DDX39A O00148 | 6 | EBI-348622, EBI-348253 | |
BINARY | Q13838 | DDX39B Q13838 | 4 | EBI-348622, EBI-348622 | |
BINARY | Q13838 | FYTTD1 Q96QD9 | 5 | EBI-348622, EBI-724553 | |
BINARY | Q13838 | LUZP4 Q9P127 | 3 | EBI-348622, EBI-10198848 | |
BINARY | Q13838 | RNF4 P78317 | 3 | EBI-348622, EBI-2340927 | |
BINARY | Q13838 | SARNP P82979 | 7 | EBI-348622, EBI-347495 | |
BINARY | Q13838 | SDCBP O00560 | 3 | EBI-348622, EBI-727004 | |
BINARY | Q13838 | SNRPA P09012 | 4 | EBI-348622, EBI-607085 | |
BINARY | Q13838 | U2AF2 P26368-2 | 3 | EBI-348622, EBI-11097439 | |
BINARY | Q13838 | UBE2I Q7KZS0 | 3 | EBI-348622, EBI-10180829 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for compositional bias, region, motif, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-22 | Acidic residues | ||||
Sequence: MAENDVDNELLDYEDDEVETAA | ||||||
Region | 1-31 | Disordered | ||||
Sequence: MAENDVDNELLDYEDDEVETAAGGDGAEAPA | ||||||
Motif | 45-73 | Q motif | ||||
Sequence: SGFRDFLLKPELLRAIVDCGFEHPSEVQH | ||||||
Domain | 76-249 | Helicase ATP-binding | ||||
Sequence: IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI | ||||||
Motif | 196-199 | DECD box | ||||
Sequence: DECD | ||||||
Domain | 261-422 | Helicase C-terminal | ||||
Sequence: GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISS |
Domain
Sequence similarities
Phylogenomic databases
Family and domain databases
Sequence & Isoform
- Sequence statusComplete
This entry describes 2 isoforms produced by Alternative splicing.
Q13838-1
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.
- Name1
- Length428
- Mass (Da)48,991
- Last updated1996-11-01 v1
- Checksum7A55167BF576FB6F
Q13838-2
- Name2
- Differences from canonical
- 114-114: V → VYLGRVLGRGFWLGLV
Computationally mapped potential isoform sequences
There are 28 potential isoforms mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
F6QYI9 | F6QYI9_HUMAN | DDX39B | 187 | ||
F6R6M7 | F6R6M7_HUMAN | DDX39B | 197 | ||
F6WLT2 | F6WLT2_HUMAN | DDX39B | 289 | ||
H0YCC6 | H0YCC6_HUMAN | DDX39B | 141 | ||
F6S4E6 | F6S4E6_HUMAN | DDX39B | 231 | ||
F6S2B7 | F6S2B7_HUMAN | DDX39B | 132 | ||
Q5STU3 | Q5STU3_HUMAN | DDX39B | 425 | ||
H0Y400 | H0Y400_HUMAN | DDX39B | 187 | ||
A0A140T9X3 | A0A140T9X3_HUMAN | DDX39B | 325 | ||
A0A140T9X9 | A0A140T9X9_HUMAN | DDX39B | 179 | ||
A0A140T9L4 | A0A140T9L4_HUMAN | DDX39B | 131 | ||
A0A140T9K1 | A0A140T9K1_HUMAN | DDX39B | 138 | ||
A0A140T9K2 | A0A140T9K2_HUMAN | DDX39B | 64 | ||
A0A140T9N3 | A0A140T9N3_HUMAN | DDX39B | 97 | ||
A0A140T9Q9 | A0A140T9Q9_HUMAN | DDX39B | 32 | ||
A0A140T9A8 | A0A140T9A8_HUMAN | DDX39B | 21 | ||
A0A140T9B4 | A0A140T9B4_HUMAN | DDX39B | 25 | ||
A0A140T973 | A0A140T973_HUMAN | DDX39B | 135 | ||
A0A140T996 | A0A140T996_HUMAN | DDX39B | 189 | ||
A0A0A0MT12 | A0A0A0MT12_HUMAN | DDX39B | 235 | ||
F6SXL5 | F6SXL5_HUMAN | DDX39B | 136 | ||
A0A140TA18 | A0A140TA18_HUMAN | DDX39B | 247 | ||
F6UJC5 | F6UJC5_HUMAN | DDX39B | 245 | ||
F6U6E2 | F6U6E2_HUMAN | DDX39B | 125 | ||
F6TRA5 | F6TRA5_HUMAN | DDX39B | 238 | ||
A0A0G2JJZ9 | A0A0G2JJZ9_HUMAN | DDX39B | 328 | ||
A0A0G2JHN7 | A0A0G2JHN7_HUMAN | DDX39B | 95 | ||
A0A0G2JJL7 | A0A0G2JJL7_HUMAN | DDX39B | 187 |
Features
Showing features for compositional bias, alternative sequence, sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-22 | Acidic residues | ||||
Sequence: MAENDVDNELLDYEDDEVETAA | ||||||
Alternative sequence | VSP_026347 | 114 | in isoform 2 | |||
Sequence: V → VYLGRVLGRGFWLGLV | ||||||
Sequence conflict | 289 | in Ref. 3; BAD96632 | ||||
Sequence: Q → R |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
Z37166 EMBL· GenBank· DDBJ | CAA85523.1 EMBL· GenBank· DDBJ | mRNA | ||
BT009909 EMBL· GenBank· DDBJ | AAP88911.1 EMBL· GenBank· DDBJ | mRNA | ||
AK222912 EMBL· GenBank· DDBJ | BAD96632.1 EMBL· GenBank· DDBJ | mRNA | ||
AB088115 EMBL· GenBank· DDBJ | BAC54953.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AB103621 EMBL· GenBank· DDBJ | BAF31287.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AB202112 EMBL· GenBank· DDBJ | BAE78637.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BA000025 EMBL· GenBank· DDBJ | BAB63306.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AL662801 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
AL662847 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
BX001040 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
BX248516 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
BX927320 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CR753820 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CR753864 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CH471081 EMBL· GenBank· DDBJ | EAX03404.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BC000361 EMBL· GenBank· DDBJ | AAH00361.1 EMBL· GenBank· DDBJ | mRNA | ||
BC013006 EMBL· GenBank· DDBJ | AAH13006.1 EMBL· GenBank· DDBJ | mRNA | ||
AF029061 EMBL· GenBank· DDBJ | AAB94615.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AF029062 EMBL· GenBank· DDBJ | AAC63046.1 EMBL· GenBank· DDBJ | Genomic DNA |