Molecular architecture and assembly of the DDB1–CUL4A ubiquitin ligase machinery
Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways 1 . Through a three-enzyme (E1–E2–E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best...
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| Published in | Nature Vol. 443; no. 7111; pp. 590 - 593 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
05.10.2006
Nature Publishing Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways
1
. Through a three-enzyme (E1–E2–E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes
2
,
3
. Conserved from yeast to human, the DDB1–CUL4–ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair
4
,
5
,
6
,
7
,
8
,
9
,
10
, DNA replication
11
,
12
,
13
,
14
and transcription
15
, and can also be subverted by pathogenic viruses to benefit viral infection
16
. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1–CUL4–ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1–CUL4A–ROC1 machinery, which show that DDB1 uses one β-propeller domain for cullin scaffold binding and a variably attached separate double-β-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. |
|---|---|
| AbstractList | Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways
1
. Through a three-enzyme (E1–E2–E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes
2
,
3
. Conserved from yeast to human, the DDB1–CUL4–ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair
4
,
5
,
6
,
7
,
8
,
9
,
10
, DNA replication
11
,
12
,
13
,
14
and transcription
15
, and can also be subverted by pathogenic viruses to benefit viral infection
16
. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1–CUL4–ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1–CUL4A–ROC1 machinery, which show that DDB1 uses one β-propeller domain for cullin scaffold binding and a variably attached separate double-β-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. [PUBLICATION ABSTRACT] Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication, and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one[greek small letter beta]-propeller domain for cullin scaffold binding and a variably attached separate double-[greek small letter beta]-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes. |
| Audience | Academic |
| Author | Angers, Stephane Li, Ti MacCoss, Michael J. Moon, Randall T. Zheng, Ning Yi, Xianhua |
| Author_xml | – sequence: 1 givenname: Stephane surname: Angers fullname: Angers, Stephane organization: Howard Hughes Medical Institute, Department of Pharmacology, Leslie Dan Faculty of Pharmacy, University of Toronto – sequence: 2 givenname: Ti surname: Li fullname: Li, Ti organization: Department of Pharmacology, Leslie Dan Faculty of Pharmacy, University of Toronto – sequence: 3 givenname: Xianhua surname: Yi fullname: Yi, Xianhua organization: Department of Pharmacology – sequence: 4 givenname: Michael J. surname: MacCoss fullname: MacCoss, Michael J. organization: Department of Genome Sciences – sequence: 5 givenname: Randall T. surname: Moon fullname: Moon, Randall T. email: rtmoon@u.washington.edu organization: Howard Hughes Medical Institute, Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine – sequence: 6 givenname: Ning surname: Zheng fullname: Zheng, Ning email: nzheng@u.washington.edu organization: Department of Pharmacology |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18148665$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/16964240$$D View this record in MEDLINE/PubMed |
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| Keywords | Molecular complex Carbon-nitrogen ligases Enzyme Ligases Molecular assembly Ubiquitin-protein ligase |
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| Snippet | Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways
1... Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways.... |
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| SubjectTerms | Amino Acid Motifs Amino Acid Sequence Binding Sites Biological and medical sciences Carrier Proteins - chemistry Carrier Proteins - metabolism Cellular biology Crystallography, X-Ray Cullin Proteins - chemistry Cullin Proteins - metabolism Deoxyribonucleic acid DNA DNA repair DNA-Binding Proteins - chemistry DNA-Binding Proteins - metabolism Enzymes Fundamental and applied biological sciences. Psychology Humanities and Social Sciences Humans Interactions. Associations Intermolecular phenomena letter Mass spectrometry Models, Molecular Molecular biophysics Molecular Sequence Data Molecular structure multidisciplinary Pliability Protein Binding Protein Structure, Quaternary Proteins Proteomics Science Science (multidisciplinary) Structure-Activity Relationship Substrate Specificity Substrates Ubiquitin - metabolism Ubiquitin-Protein Ligases - chemistry Ubiquitin-Protein Ligases - metabolism Viruses Yeasts |
| Title | Molecular architecture and assembly of the DDB1–CUL4A ubiquitin ligase machinery |
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