PDBsum entry: 1nex

Ligase, cell cycle

PDB-id: 1nex

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

129 a.a. *

444 a.a. *

Ligands

LEU-TPO-PRO-PRO

LEU-LEU-TPO-PRO-PRO-GLN-SER-GLY

Waters ×72

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, trimer
(*as deduced by PQS)

PDB id:

1nex

Name:

Ligase, cell cycle

Title:

Crystal structure of scskp1-sccdc4-cpd peptide complex

Structure:

Centromere DNA-binding protein complex cbf3 subunit d. Chain: a, c. Fragment: residues 36-63 deleted. Synonym: scskp1, suppressor of kinetochore protein 1. Engineered: yes. Cdc4 protein. Chain: b, d. Fragment: residues 601-604 and 609-624 deleted.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: cbf3d or skp1 or ydr328c or d9798.14. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Trimer (from PQS)

UniProt:

Chains A, C: P52286 (SKP1_YEAST)

Seq:	194 a.a.
Struc:	129 a.a.

Chains B, D: P07834 (CDC4_YEAST)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

779 a.a.

Struc:

444 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Resolution:

2.70Å

R-factor:

0.239

R-free:

0.273

Authors:

S.Orlicky,X.Tang,A.Willems,M.Tyers,F.Sicheri

Key ref:

S.Orlicky et al. (2003). Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase.. Cell, 112, 243-256. [PubMed id: 12553912] [DOI: 10.1016/S0092-8674(03)00034-5]

Date:

12-Dec-02

Release date:

18-Feb-03

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1016/S0092-8674(03)00034-5

Cell 112:243-256 (2003)

PubMed id: 12553912

Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase.

S.Orlicky, X.Tang, A.Willems, M.Tyers, F.Sicheri.

ABSTRACT

Cell cycle progression depends on precise elimination of cyclins and cyclin-dependent kinase (CDK) inhibitors by the ubiquitin system. Elimination of the CDK inhibitor Sic1 by the SCFCdc4 ubiquitin ligase at the onset of S phase requires phosphorylation of Sic1 on at least six of its nine Cdc4-phosphodegron (CPD) sites. A 2.7 A X-ray crystal structure of a Skp1-Cdc4 complex bound to a high-affinity CPD phosphopeptide from human cyclin E reveals a core CPD motif, Leu-Leu-pThr-Pro, bound to an eight-bladed WD40 propeller domain in Cdc4. The low affinity of each CPD motif in Sic1 reflects structural discordance with one or more elements of the Cdc4 binding site. Reengineering of Cdc4 to reduce selection against Sic1 sequences allows ubiquitination of lower phosphorylated forms of Sic1. These features account for the observed phosphorylation threshold in Sic1 recognition and suggest an equilibrium binding mode between a single receptor site in Cdc4 and multiple low-affinity CPD sites in Sic1.

Selected figure(s)

Figure 3.
Figure 3. Substrate Orientation within the Skp1-Cdc4-CPD Complex(A) Comparison of the ScSkp1-ScCdc4-CPD complex and the hSkp1-hSkp2 complex. Complexes were superimposed through a least squares optimization of Skp1 β strands 1 to 3 and α helices 1 to 6 (RMSD Cα = 0.74Å). Skp1 and F box secondary structure elements that deviate significantly in size and position between the two structures are labeled.(B) Model of the ubiquitin-E2-SCF^Cdc4-CPD complex. The arrow indicates the 59 Å distance separating the phosphate group of the CPD and the active site cysteine of the E2.

Figure 4.
Figure 4. The CPD Binding Pocket of the WD40 Domain(A) Surface representation of the CPD binding pocket, indicating invariant and highly conserved residues. Basic (blue), hydrophobic (green), and small polar residues (orange) are shown. The bound CPD is in ball and stick representation with carbon (white), nitrogen (blue), oxygen (red), and phosphorous (yellow) atoms shown.(B) Surface representation of CPD binding region indicating electrostatic potential. Blue and red indicate regions of positive and negative potential, respectively, over the range 10 to −10 k[B]T.(C) Stereo ribbons representation of side chains and molecular interactions in the CPD binding pocket. Highly conserved and invariant side chains of Cdc4 and the CPD are displayed in ball and stick representation. Sites of mutation that give rise to severe and intermediate loss of function (see Figure 5) are colored red and blue, respectively; nonessential residues are colored green.(D) Schematic of CPD binding pocket interactions with the CPD peptide.

The above figures are reprinted by permission from Cell Press: Cell (2003, 112, 243-256) copyright 2003.

Figures were selected by the author.