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The SCF ubiquitin ligase: insights into a molecular machine

Key Points

  • The SCF complex is a multi-subunit ubiquitin ligase that specifically transfers activated ubiquitin to target-protein substrates. SCF is named after Skp1–Cullin–F-box-protein, which are the three main proteins of the complex. A RING-domain-containing protein of the Roc1/Rbx1 family is the final component of the ligase.

  • The F-box-protein (FBP) component of SCF is the element that specifically binds to substrates. The FBP is therefore the main specificity determinant of the SCF, and a wide variety of cellular and developmental processes have been attributed to FBP function.

  • The post-translational nature of ubiquitin-mediated proteolytic degradation indicates that ubiquitin ligases such as SCF are well suited to regulate multi-component molecular machines like the DNA-synthesis and mitotic machinery, and transition points like the cell-cycle checkpoints.

  • The regulation of p27, p21, cyclin E, Cdc25a and Wee1 by SCF, along with SCF interregulation with the APC/C ubiquitin ligase, can be unified in a view of SCF ligases that modulate the cell cycle through the degradation of CDK subunits and their regulators.

  • The three-dimensional structure of SCF-component proteins reveals that the SCF might operate through a unique and flexible 'super-enzymatic' mechanism, which might be amenable to therapeutic intervention in diseases of cellular proliferation.

Abstract

Ubiquitin ligases are well suited to regulate molecular networks that operate on a post-translational timescale. The F-box family of proteins — which are the substrate-recognition components of the Skp1–Cul1–F-box-protein (SCF) ubiquitin ligase — are important players in many mammalian functions. Here we explore a unifying and structurally detailed view of SCF-mediated proteolytic control of cellular processes that has been revealed by recent studies.

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Figure 1: The interface between the F-box domain of Skp2 and Skp1.
Figure 2: Models of the complete SCF-ligase complexes with their substrate targets.

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Acknowledgements

We thank T. Hunter and N. Watanabe for communicating results prior to publication. We apologize to colleagues whose work could not be mentioned due to space limitations. M.P. is grateful to T. M. Thor for continuous support. Molecular graphics were produced by ICM software (Molsoft Limited Liability Corporation, La Jolla, California, USA). Work in the Pagano laboratory is supported by grants from the National Institutes of Health.

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Correspondence to Michele Pagano.

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DATABASES

Entrez

CCNF

InterPro

F-box domain

HECT domain

LRR

RING-finger domain

OMIM

split hand–foot malformation

Saccharomyces genome database

Cdc4

Cdc20

Sic1

Swiss-Prot

Cul1

Fbw1

Fbw4

Fbw7

Fbx2

Fbx3

Fbx4

Fbx5

Fbx6

Fbx32

Nedd8

p21

p27

Rbx1

Skp1

Skp2

Ubc3

VHL

FURTHER INFORMATION

HGNC F-box gene family nomenclature

Pfam database

InterPro database

Michele Pagano's laboratory

Glossary

CYCLIN-DEPENDENT KINASE

(CDK). A protein kinase that controls cell-cycle progression in all eukaryotes and requires physical association with cyclins to achieve full enzymatic activity.

F-BOX PROTEIN

(FBP). A component of the machinery for the ubiquitin-dependent degradation of proteins. F-box proteins recognize specific substrates and, with the help of other subunits of the E3 ubiquitin ligase, deliver them to the E2 ubiquitin-conjugating enzyme.

RING-FINGER

A protein-sequence motif corresponding to a particular folded protein domain that binds Zn2+ through a four-point arrangement of cysteine and histidine amino acids. In the E3 ubiquitin ligases, this domain seems to be responsible for binding the E2 ubiquitin-conjugating enzymes.

SCF UBIQUITIN LIGASE

A multisubunit ubiquitin ligase that contains Skp1, a member of the cullin family (Cul1), and an F-box protein, as well as a RING-finger-containing protein (Roc1/Rbx1).

UBIQUITIN-CONJUGATING ENZYME

(UBC). An enzyme (also known as E2) that accepts ubiquitin from a ubiquitin-activating enzyme (E1) and, together with a ubiquitin ligase (E3), transfers it to a substrate protein.

β-PROPELLER

A compact structural domain, or protein-folding pattern, in which similarly sized β-sheets are stacked and offset into a complete cylinder, so that they resemble the blades of a propeller.

LEUCINE-RICH REPEAT

(LRR). A protein-sequence motif that contains regular occurrences of the amino acid Leu, which are present as tandem arrays in certain proteins. The back-to-back set of motifs was found to correspond to a small subdomain structure in the protein that stacks next to adjacent repeats to form a parallel, β-sheet, arc-like structure.

ANAPHASE-PROMOTING COMPLEX/CYCLOSOME

(APC/C). Anaphase is the phase of mitosis during which condensed chromosomes separate into sister chromatids and move along the mitotic spindles to opposite poles of the cell. The APC/C is a multi-subunit E3 ubiquitin ligase with at least two alternative forms, which are activated by two different proteins (Cdc20 or Cdh1) and are necessary for the transition into anaphase, as well as the exit from mitosis and the maintenance of the G1 state.

SPINDLE CHECKPOINT

The molecular process that specifically controls the assembly of the kinetochore on the chromosomal centromere and the timing of kinetochore dissociation. Dissociation involves the movement of the kinetochores, along with their attached sister chromatids, to opposite poles of the mitotic spindle during anaphase.

KINETOCHORE

The complicated protein assembly that links the specialized areas of condensed chromosomes that are known as centromeres to the microtubule-based mitotic spindle.

APC/CCDC20

According to the convention for multi-subunit E3 ligases, the presumed activator, or substrate-targeting, subunit is shown in superscript text. So, the E3 ligase that is formed by the APC/C subunits and Cdc20 is written as shown, and the SCF ligase formed by Skp1, Cul1, Roc1 and the F-box protein Skp2 is known as SCFSkp2.

ALLOSTERIC SITE

A site on an enzyme, which, on binding of a modulator, causes the protein to undergo a conformational change that might alter the catalytic or binding properties of the enzyme.

DEGRON

A protein element, usually a sequence motif, that targets the protein for proteolytic degradation.

PHOSPHORECOGNITION

The process by which a specific binding site on one protein recognizes a specifically constructed site on another protein that has been post-translationally modified by the addition of a phosphate group to amenable side chains such as Ser or Thr.

COP9 SIGNALOSOME

An eight-subunit protein complex that regulates protein ubiquitylation and turnover in a variety of developmental and physiological contexts. Extensively characterized in plants but fundamental to all eukaryotes, this complex post-translationally modifies the cullin subunit of E3-ubiquitin ligases by cleaving off the covalently coupled peptide, Nedd8.

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Cardozo, T., Pagano, M. The SCF ubiquitin ligase: insights into a molecular machine. Nat Rev Mol Cell Biol 5, 739–751 (2004). https://doi.org/10.1038/nrm1471

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