PDBsum entry 1u6g

Ligase

PDB id: 1u6g

Contents

Protein chains

715 a.a. *

88 a.a. *

1146 a.a. *

Metals

_ZN ×3

Waters ×18

* Residue conservation analysis

PDB id:

1u6g

Name:

Ligase

Title:

Crystal structure of the cand1-cul1-roc1 complex

Structure:

Cullin homolog 1. Chain: a. Synonym: cul-1. Engineered: yes. Ring-box protein 1. Chain: b. Synonym: rbx1, regulator of cullins 1, ring finger protein 75, zyp protein, roc1. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cul1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rbx1, roc1, rnf75. Gene: cand1.

Biol. unit:

Trimer (from PQS)

Resolution:

3.10Å R-factor: 0.243 R-free: 0.317

Authors:

S.J.Goldenberg,S.D.Shumway,T.C.Cascio,K.C.Garbutt,J.Liu,Y.Xiong, N.Zheng

Key ref:

S.J.Goldenberg et al. (2004). Structure of the Cand1-Cul1-Roc1 complex reveals regulatory mechanisms for the assembly of the multisubunit cullin-dependent ubiquitin ligases. Cell, 119, 517-528. PubMed id: 15537541 DOI: 10.1016/j.cell.2004.10.019

Date:

29-Jul-04 Release date: 14-Dec-04

Protein chain

Q13616  (CUL1_HUMAN) -  Cullin-1 from Homo sapiens

Seq: 776 a.a.

Struc: 715 a.a.

Protein chain

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

Seq: 108 a.a.

Struc: 88 a.a.

Protein chain

Q86VP6  (CAND1_HUMAN) -  Cullin-associated NEDD8-dissociated protein 1 from Homo sapiens

Seq: 1230 a.a.

Struc: 1146 a.a.

Enzyme reactions

• Enzyme class 2: Chain B: 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 B: 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: 10.1016/j.cell.2004.10.019

Cell 119:517-528 (2004)

PubMed id: 15537541

Structure of the Cand1-Cul1-Roc1 complex reveals regulatory mechanisms for the assembly of the multisubunit cullin-dependent ubiquitin ligases.

S.J.Goldenberg, T.C.Cascio, S.D.Shumway, K.C.Garbutt, J.Liu, Y.Xiong, N.Zheng.

ABSTRACT

The SCF ubiquitin ligase complex regulates diverse cellular functions by ubiquitinating numerous protein substrates. Cand1, a 120 kDa HEAT repeat protein, forms a tight complex with the Cul1-Roc1 SCF catalytic core, inhibiting the assembly of the multisubunit E3 complex. The crystal structure of the Cand1-Cul1-Roc1 complex shows that Cand1 adopts a highly sinuous superhelical structure, clamping around the elongated SCF scaffold protein Cul1. At one end, a Cand1 beta hairpin protrusion partially occupies the adaptor binding site on Cul1, inhibiting its interactions with the Skp1 adaptor and the substrate-recruiting F box protein subunits. At the other end, two Cand1 HEAT repeats pack against a conserved Cul1 surface cleft and bury a Cul1 lysine residue, whose modification by the ubiquitin-like protein, Nedd8, is able to block Cand1-Cul1 association. Together with biochemical evidence, these structural results elucidate the mechanisms by which Cand1 and Nedd8 regulate the assembly-disassembly cycles of SCF and other cullin-dependent E3 complexes.

Selected figure(s)

Figure 3.
Figure 3. Cand1 Interacts with the SCF Scaffold through Multiple Interfaces as Shown in Three Dissected Views(A) Interactions between the C-terminal arch of Cand1 and the first two cullin repeats of Cul1. Two orthogonal views are shown with Cand1 in surface and Cul1 in ribbon representations. The helical elements of the two Cul1 cullin repeats are labeled. The unusual parts of the twenty-fifth and twenty-seventh Cand1 HEAT repeats projecting out from the Cand1 solenoid main body are indicated. Surfaces of the strictly conserved Cand1 residues are colored in bright yellow.(B) Interactions between the central arch of Cand1 and the entire Cul1 NTD. The A helix of each Cul1 cullin repeat is labeled.(C) Interactions between the N-terminal arch of Cand1 and the Cul1 CTD. For clarity, the third cullin repeat of the Cul1 NTD is shown together with the Cul1 CTD. The 4HB and WH-B domains of the Cul1 CTD and the apical ridge of the Cand1 arch are labeled and indicated with arrows.

Figure 5.
Figure 5. The N-terminal HEAT Repeats of Cand1 Interact with a Conserved Surface Cleft of the Cul1 CTD and Bury the Cul1 Neddylation Site Lysine Residue(A) Interactions between the first two Cand1 HEAT repeats and the Cul1 CTD surface cleft. The molecular surfaces of Cul1 and Roc1 are colored in green and red. Surfaces of conserved Cul1 residues are shown in yellow. Important structural elements of the proteins are labeled.(B) Closeup view of the interfaces among the Cul1 WH-B domain, Cand1's first HEAT repeat, and the Roc1 RING domain. Residues interacting with Cul1 Lys720, as well as several surrounding amino acids, are shown.(C) Zoomed-out view of (B) with surface representation. The ε-amino group of the Cul1 Lys720 residue is completely buried and invisible. Cul1 residues conserved among all human cullins are colored in yellow. The surface of three such conserved Cul1 residues located on the opposite side of the Cul1 WH-B domain where the Cand1-interacting surface cleft is found are indicated. This surface area represents a potential site on the Cul1 CTD for interacting with additional regulatory factors.

The above figures are reprinted by permission from Cell Press: Cell (2004, 119, 517-528) copyright 2004.

Figures were selected by an automated process.