Protein:DDX5 |
Protein Summary |
 Gene summary |
| Gene name: DDX5 | ASpdb.0 ID: 1655 | Gene | Gene symbol | DDX5 | Gene ID | 1655 |
| Gene name | DEAD-box helicase 5 |
| Synonyms | G17P1|HLR1|HUMP68|p68 |
| Cytomap | 17q23.3 |
| Type of gene | protein-coding |
| Description | probable ATP-dependent RNA helicase DDX5ATP-dependent RNA helicase DDX5DEAD (Asp-Glu-Ala-Asp) box helicase 5DEAD (Asp-Glu-Ala-Asp) box polypeptide 5DEAD box protein 5DEAD box-5DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)RNA h |
| Modification date | 20240407 |
| UniProtAcc | P17844 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | DDX5 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 15298701 |
| Gene | DDX5 | GO:0000381 | regulation of alternative mRNA splicing, via spliceosome | 21343338 |
| Gene | DDX5 | GO:0000956 | nuclear-transcribed mRNA catabolic process | 23788676 |
| Gene | DDX5 | GO:0003730 | mRNA 3'-UTR binding | 23788676 |
| Gene | DDX5 | GO:0005634 | nucleus | 24910439 |
| Gene | DDX5 | GO:0005654 | nucleoplasm | - |
| Gene | DDX5 | GO:0005730 | nucleolus | 10837141 |
| Gene | DDX5 | GO:0016607 | nuclear speck | 24644279 |
| Gene | DDX5 | GO:0036002 | pre-mRNA binding | 21343338 |
| Gene | DDX5 | GO:0043021 | ribonucleoprotein complex binding | 23788676 |
| Gene | DDX5 | GO:0050681 | nuclear androgen receptor binding | 18829551 |
| Gene | DDX5 | GO:0070878 | primary miRNA binding | 18548003 |
| Gene | DDX5 | GO:0071013 | catalytic step 2 spliceosome | 11991638 |
| Gene | DDX5 | GO:1990904 | ribonucleoprotein complex | 18809582 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P17844-1 | P17844-1_4a4d_A.pdb | 4A4D | X-ray | 2.7 | A | 52 | 304 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P17844 | DDX5 | P17844-1 | P17844-2 | 614 | 535 | 85 | 163 | Deletion | none | none | 84 | 84 |
| Multiple sequence alignment of our canonical and alternatively spliced DDX5 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of DDX5 |
| UniProt-id | ENSG | ENST | ENSP |
| P17844-1 | ENSG00000108654.16 | ENST00000225792.10 | ENSP00000225792.5 |
| P17844-1 | ENSG00000108654.16 | ENST00000450599.7 | ENSP00000403085.3 |
| P17844-1 | ENSG00000108654.16 | ENST00000577922.6 | ENSP00000464337.2 |
| P17844-1 | ENSG00000108654.16 | ENST00000585111.2 | ENSP00000463168.2 |
| P17844-1 | ENSG00000108654.16 | ENST00000676785.1 | ENSP00000504794.1 |
| UniProt-id | NM ID | NP ID |
| P17844-1 | NM_001320595.1 | NP_001307524.1 |
| P17844-1 | NM_001320596.1 | NP_001307525.1 |
| P17844-1 | NM_004396.4 | NP_004387.1 |
| Amino acid sequences of our canonical and alternatively spliced DDX5 |
| accession_id | Protein sequence |
| P17844-1 | MSGYSSDRDRGRDRGFGAPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTAQEVETYRRSKEITVRGHNCP KPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELA QQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIR PDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKRRCDELTRK MRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYIHRIGRTARSTKTGTAYTFFTPNNI KQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDDRRDRYSAGKRGGFNTFRDRENYDRGYSSLLKRDFGAKTQNGVYSAANY |
| P17844-2 | MSGYSSDRDRGRDRGFGAPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTAQEVETYRRSKEITVRGDGPI CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFE PQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVE TKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYIHRIGRTARSTKTG TAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDDRRDRYSAGKRGGFNTFRDRENYDRGYSSLLKRDFGAK |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| DDX5 (go to UniProt):P17844 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P17844 | Domain | 125 | 300 | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 | Type=Deletion;Start=85;End=163 |
| P17844 | Motif | 94 | 122 | Note=Q motif | Type=Deletion;Start=85;End=163 |
Gene Isoform Structures and Expression Levels for DDX5 |
| Gene structures of our canonical and alternative spliced genes of DDX5 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P17844-1 |
| 3D view using mol* of P17844-2 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P17844-1 |
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| pLDDT distribution across the protein length of P17844-2 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P17844-1 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P17844-1 | 1.038 | 384 | 0.933 | 1060.556 | 0.539 | 0.755 | 0.955 | 0.227 | 1.412 | 0.16 | 0.594 | 80,81,85,96,109,112,114,115,116,117,118,119,121,12 5,137,138,139,140,141,142,143,144,145,146,148,150, 178,179,181,182,183,185,186,189,190,248,249,278,27 9,280,281,282,283,284,285,287,299,301,302,303,304, 305,306,307,308,309,310,311,312,313,381,384,385,38 8,403,404,405,406,407,408,409,410,426,427,429,430, 431,433,434,435,437,462 |
| P17844-2 | 0.971 | 258 | 0.994 | 626.318 | 0.608 | 0.653 | 0.818 | 0.294 | 1.037 | 0.284 | 0.847 | 172,175,176,194,195,196,197,198,199,200,201,202,20 3,204,205,206,207,208,211,214,215,216,218,219,220, 221,222,223,224,225,226,227,228,229,230,231,234,34 2,343,344,347,348,350,351,353,354,355,356,376,379, 380,383 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P17844-1_P17844-1_4a4d_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P17844-1_4a4d_A_P17844-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P17844-1_P17844-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P17844-1_vs_P17844-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P17844-1_vs_P17844-2.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to DDX5 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P17844 | DDX5 | DB11638 | Artenimol | approved, experimental, investigational | ligand |
Related Diseases to DDX5 |
| Previous studies relating to the alternative splicing of DDX5 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| DDX5 | 16230076 | Beta-catenin interacts with the FUS proto-oncogene product and regulates pre-mRNA splicing. | beta-Catenin is a downstream effector of the Wnt signaling pathway and is believed to exert its oncogenic function by activating T-cell factor (TCF)/lymphoid enhancer factor (LEF) family transcriptional factors. However, it is still uncertain whether the diverse effects of beta-catenin are caused solely by aberrant gene transactivation. In this study, we used a proteomics approach to obtain further insight into the functional properties of nuclear beta-catenin. | D015179 | Colorectal Neoplasms |
| DDX5 | 21345143 | RNA helicases p68 and p72: multifunctional proteins with important implications for cancer development. | The DEAD box RNA helicases p68 (DDX5) and p72 (DDX17) play important roles in multiple cellular processes that are commonly dysregulated in cancers, including transcription, pre-mRNA processing/alternative splicing and miRNA processing. Although p68 and p72 appear to have some overlapping functions, they clearly also have distinct, nonredundant functions. Furthermore, their ability to interact with a variety of different factors and act as multifunctional proteins has the potential to impact on several different processes, and alterations in expression or function of p68 and/or p72 could have profound implications for cancer development. However, their roles are likely to be context-dependent and both proteins have been reported to have pro-proliferation or even oncogenic functions as well as antiproliferative or tumor cosuppressor roles. Therefore, eludicating the precise role of these proteins in cancer is likely to be complex and to depend on the cellular environment and interacting factors. In this article, we review the many functions that have been attributed to p68 and p72 and discuss their potential roles in cancer development. | D009369 | Neoplasms |
| DDX5 | 22156369 | New function for the RNA helicase p68/DDX5 as a modifier of MBNL1 activity on expanded CUG repeats. | Myotonic Dystrophy type I (DM1) is caused by an abnormal expansion of CTG triplets in the 3' UTR of the dystrophia myotonica protein kinase (DMPK) gene, leading to the aggregation of the mutant transcript in nuclear RNA foci. The expanded mutant transcript promotes the sequestration of the MBNL1 splicing factor, resulting in the misregulation of a subset of alternative splicing events. In this study, we identify the DEAD-box RNA helicase p68 (DDX5) in complexes assembled onto in vitro-transcribed CUG repeats. We showed that p68 colocalized with RNA foci in cells expressing the 3'UTR of the DMPK gene containing expanded CTG repeats. We found that p68 increased MBNL1 binding onto pathological repeats and the stem-loop structure regulatory element within the cardiac Troponin T (TNNT2) pre-mRNA, splicing of which is misregulated in DM1. Mutations in the helicase core of p68 prevented both the stimulatory effect of the protein on MBNL1 binding and the colocalization of p68 with CUG repeats, suggesting that remodeling of RNA secondary structure by p68 facilitates MBNL1 binding. We also found that the competence of p68 for regulating TNNT2 exon 5 inclusion depended on the integrity of MBNL1 binding sites. We propose that p68 acts as a modifier of MBNL1 activity on splicing targets and pathogenic RNA. | D009223 | Myotonic Dystrophy |
| DDX5 | 23022728 | Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness. | Both epigenetic and splicing regulation contribute to tumor progression, but the potential links between these two levels of gene-expression regulation in pathogenesis are not well understood. Here, we report that the mouse and human RNA helicases Ddx17 and Ddx5 contribute to tumor-cell invasiveness by regulating alternative splicing of several DNA- and chromatin-binding factors, including the macroH2A1 histone. We show that macroH2A1 splicing isoforms differentially regulate the transcription of a set of genes involved in redox metabolism. In particular, the SOD3 gene that encodes the extracellular superoxide dismutase and plays a part in cell migration is regulated in an opposite manner by macroH2A1 splicing isoforms. These findings reveal a new regulatory pathway in which splicing factors control the expression of histone variant isoforms that in turn drive a transcription program to switch tumor cells to an invasive phenotype. | D009361 | Neoplasm Invasiveness |
| DDX5 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D004392 | Dwarfism |
| DDX5 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D006130 | Growth Disorders |
| DDX5 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D009123 | Muscle Hypotonia |
Clinically important variants in DDX5 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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