Q641Y8

PR
Gene name
Ddx1
Protein name
ATP-dependent RNA helicase DDX1
Names
DEAD box protein 1
Species
Rattus norvegicus (Rat)
KEGG Pathway
rno:84474
EC number
3.6.4.13: Acting on ATP; involved in cellular and subcellular movement
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

244-316 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

1 structures for Q641Y8

Entry ID Method Resolution Chain Position Source
AF-Q641Y8-F1 Predicted AlphaFoldDB

No variants for Q641Y8

Variant ID(s) Position Change Description Diseaes Association Provenance
No variants for Q641Y8

No associated diseases with Q641Y8

6 regional properties for Q641Y8

Type Name Position InterPro Accession
domain Helicase, C-terminal 493 - 681 IPR001650
domain B30.2/SPRY domain 70 - 247 IPR001870
domain SPRY domain 130 - 246 IPR003877
domain DEAD/DEAH box helicase domain 26 - 418 IPR011545
domain Helicase superfamily 1/2, ATP-binding domain 21 - 444 IPR014001
domain RNA helicase, DEAD-box type, Q motif 2 - 30 IPR014014

Functions

Description
EC Number 3.6.4.13 Acting on ATP; involved in cellular and subcellular movement
Subcellular Localization
  • Nucleus
  • Cytoplasm
  • Cytoplasmic granule
  • Cytoplasm, cytosol
  • Mitochondrion
  • Localized with MBNL1, TIAL1 and YBX1 in stress granules upon stress
  • Localized with CSTF2 in cleavage bodies
  • Forms large aggregates called DDX1 bodies
  • Relocalized into multiple foci (IR-induced foci or IRIF) after IR treatment, a process that depends on the presence of chromosomal DNA and/or RNA-DNA duplexes
  • Relocalized at sites of DNA double-strand breaks (DSBs) in an ATM-dependent manner after IR treatment
  • Colocalized with RELA in the nucleus upon TNF-alpha induction
  • Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low
  • Colocalizes in the cytosol with DDX21, DHX36 and TICAM1
  • Colocalizes in the mitochondria with TICAM1 and poly(I:C) RNA ligand
  • The multi-helicase-TICAM1 complex may translocate to the mitochondria upon poly(I:C) stimulation (By similarity)
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

8 GO annotations of cellular component

Name Definition
cleavage body A nuclear body that contains proteins involved in pre-mRNA 3'-end cleavage and polyadenylation, such as DDX1, CSTF2 and CPSFs, as well as the transcription factors TFIIE and TFIIF. Cleavage bodies are localized adjacent to Cajal bodies and are involved in mRNA3'-end processing.
cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasmic stress granule A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
ribonucleoprotein complex A macromolecular complex that contains both RNA and protein molecules.
tRNA-splicing ligase complex A protein complex that catalyzes the ligation of cleaved pre-tRNAs by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester.

11 GO annotations of molecular function

Name Definition
ATP binding Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
ATP hydrolysis activity Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
chromatin binding Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
DNA/RNA helicase activity Unwinding of a DNA/RNA duplex, i.e. a double helix in which a strand of DNA pairs with a complementary strand of RNA, driven by ATP hydrolysis.
double-stranded RNA binding Binding to double-stranded RNA.
exonuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids.
poly(A) binding Binding to a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
RNA helicase activity Unwinding of an RNA helix, driven by ATP hydrolysis.
transcription coregulator activity A transcription regulator activity that modulates the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators.

12 GO annotations of biological process

Name Definition
defense response to virus Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
DNA duplex unwinding The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
double-strand break repair The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
mRNA processing Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
nucleic acid phosphodiester bond hydrolysis The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
positive regulation of I-kappaB kinase/NF-kappaB signaling Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
positive regulation of myeloid dendritic cell cytokine production Any process that activates or increases the frequency, rate, or extent of myeloid dendritic cell cytokine production.
protein localization to cytoplasmic stress granule A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
response to exogenous dsRNA Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
response to virus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
tRNA splicing, via endonucleolytic cleavage and ligation Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

7 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q0IIK5 DDX1 ATP-dependent RNA helicase DDX1 Bos taurus (Bovine) PR
Q90WU3 DDX1 ATP-dependent RNA helicase DDX1 Gallus gallus (Chicken) PR
Q92499 DDX1 ATP-dependent RNA helicase DDX1 Homo sapiens (Human) PR
Q91VR5 Ddx1 ATP-dependent RNA helicase DDX1 Mus musculus (Mouse) PR
Q5RKI1 Eif4a2 Eukaryotic initiation factor 4A-II Rattus norvegicus (Rat) PR
Q62780 Ddx46 Probable ATP-dependent RNA helicase DDX46 Rattus norvegicus (Rat) PR
Q5XH91 ddx1 ATP-dependent RNA helicase DDX1 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) PR
10 20 30 40 50 60
MAAFSEMGVM PEIAQAVEEM DWLLPTDIQA ESIPLILGGG DVLMAAETGS GKTGAFSIPV
70 80 90 100 110 120
IQIVYETLKD QQEGKKGKAT IKTGASVLNK WQMNPYDRGS AFAIGSDGLC CQSREVKEWH
130 140 150 160 170 180
GCRATRGLLR GKHYYEVSCH DQGLCRVGWS TMQASLDLGT DKFGFGFGGT GKKSHNKQFD
190 200 210 220 230 240
NYGEEFTMHD TIGCYLDIDK GHVKFSKNGK DLGLAFEIPA HIKNQALFPA CVLKNAELKF
250 260 270 280 290 300
NFGEEEFKFP PKDGFVALSK APDSYVVKSQ HTGNAQVSQT KFLPNAPKAL IVEPSRELAE
310 320 330 340 350 360
QTLNNVKQFK KYIDNPKLRE LLIIGGVAAR DQLSVLDNGV DIVVGTPGRL DDLVSTGKLN
370 380 390 400 410 420
LSQVRFLVLD EADGLLSQGY SDFINRMHNQ IPQITSDGKR LQVIVCSATL HSFDVKKLSE
430 440 450 460 470 480
KIMHFPTWVD LKGEDSVPDT VHHVVVPVNP KTDRLWERLG KNHIRTDDVH AKDNTRPGAN
490 500 510 520 530 540
SPEMWSEAIK ILKGEYAVRA IKEHKMDQAI IFCRTKIDCD NLEQYFMQQG GGPDKKGHQF
550 560 570 580 590 600
SCVCLHGDRK PHERKQNLER FKKGDVRFLI CTDVAARGID IHGVPYVINV TLPDEKQNYV
610 620 630 640 650 660
HRIGRVGRAE RMGLAISLVA TEKEKVWYHV CSNRGKGCYN TRLKEDGGCT IWYNEMQLLS
670 680 690 700 710 720
EIEEHLNCTI SQVEPDIKVP VDEFDGKVTY GQKRAAGGGN YKGHVDILAP TVQELAALEK
730
EAQTSFLHLG YLPNQLFRTF