PDBsum entry 2hye

Protein binding

PDB id: 2hye

Contents

Protein chains

1140 a.a. *

180 a.a. *

719 a.a. *

90 a.a. *

Metals

_ZN ×5

* Residue conservation analysis

PDB id:

2hye

Name:

Protein binding

Title:

Crystal structure of the ddb1-cul4a-rbx1-sv5v complex

Structure:

DNA damage-binding protein 1. Chain: a. Synonym: damage-specific DNA-binding protein 1, uv-damaged DNA- binding factor, ddb p127 subunit, ddba, uv-damaged DNA-binding protein 1, uv-ddb 1, xeroderma pigmentosum group e- complementing protein, xpce, xpe-binding factor, xpe-bf, x- associated protein 1, xap-1. Engineered: yes. Nonstructural protein v.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ddb1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Simian virus 5. Organism_taxid: 11207. Gene: p/v.

Biol. unit:

Dimer (from PQS)

Resolution:

3.10Å R-factor: 0.250 R-free: 0.316

Authors:

S.Angers,T.Li,X.Yi,M.J.Maccoss,R.T.Moon,N.Zheng

Key ref:

S.Angers et al. (2006). Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature, 443, 590-593. PubMed id: 16964240 DOI: 10.1038/nature05175

Date:

05-Aug-06 Release date: 03-Oct-06

Protein chain

Q16531  (DDB1_HUMAN) -  DNA damage-binding protein 1 from Homo sapiens

Seq: 1140 a.a.

Struc: 1140 a.a.*

Protein chain

P11207  (V_PIV5) -  Non-structural protein V from Parainfluenza virus 5 (strain W3)

Seq: 222 a.a.

Struc: 180 a.a.

Protein chain

Q13619  (CUL4A_HUMAN) -  Cullin-4A from Homo sapiens

Seq: 759 a.a.

Struc: 719 a.a.

Protein chain

P62877  (RBX1_HUMAN) -  E3 ubiquitin-protein ligase RBX1 from Homo sapiens

Seq: 108 a.a.

Struc: 90 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain D: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 3: Chain D: E.C.2.3.2.32 - cullin-RING-type E3 NEDD8 transferase.
• Reaction: S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]- L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N₆-[NEDD8- protein]-yl-[cullin]-L-lysine

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/nature05175

Nature 443:590-593 (2006)

PubMed id: 16964240

Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.

S.Angers, T.Li, X.Yi, M.J.MacCoss, R.T.Moon, N.Zheng.

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 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.

Selected figure(s)

Figure 1.
Figure 1: Crystal structure of the DDB1–CUL4A–ROC1 ubiquitin ligase complex hijacked by the V protein of simian virus 5. a, b, Two orthogonal views of the complex structure are shown in ribbon diagram. DDB1, CUL4A, ROC1 and SV5-V are coloured in blue, green, red and magenta, respectively. The BPB domain of DDB1 is coloured in cyan. The zinc atoms in ROC1 and SV5-V are represented as orange spheres. A previously identified STAT2-binding site^17 of the viral protein, as well as the four domains of DDB1, are indicated.

Figure 2.
Figure 2: Binding interfaces and structural flexibility of DDB1 on CUL4A. a, An overall view of the structural elements mediating the binding of the DDB1 BPB domain (cyan) with the CUL4A NTD (green). b, The interface between the top surface of DDB1-BPB (cyan) and the H2–H5 helices of CUL4A (green) viewed from above with participating side chains shown as sticks (grey in DDB1 and green in CUL4A). c, Superposition of the H2–H5 helices of CUL4A (green) and CUL1 (grey) with CUL1-bound SKP1 (blue) shown in the background. The view is the same as that shown in panel b. CUL4A-bound DDB1 is not shown for clarity. d, The interface between the CUL4A N-terminal extension sequence (green) and the peripheral side of the DDB1 BPB domain (blue). e, Superposition analyses of DDB1 alone (right) and DDB1–SV5-V complex (left) structures in the context of the full DDB1–CUL4A–ROC1 complex. The models are docked through the BPB domain and viewed from the same angles as shown in Fig. 1b.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 443, 590-593) copyright 2006.

Figures were selected by an automated process.