ELM - Detail for DEG_SCF_FBXO31

Accession:	ELME000512
Functional site class:	SCF ubiquitin E3 ligase FBXO31 degron
Functional site description:	SCF E3 ligase FBXO31 has a phospho-independent degron recognition specificity in contrast to some other E3 ligases of the SCF group (FBW7, betaTrCP1, Skp2-Cks1). SCF-FBXO31 is composed of SKP1 bound by the F-box of FBXO31 with two β-barrel domains of FBXO31 attached by a helical linker. The second β-barrel of FBXO31 recognizes C-terminal degrons of cyclin Ds. The Ser/Thr phosphorylations N-terminal to these degrons do not contribute to the specificity of the recognition but regulate their nuclear export. D-type cyclins form complexes with CDK4/6 to phosphorylate and inactivate the retinoblastoma (pRb) tumour suppressor. This process is thought to be indispensable for transition from G1 to S phase, given that cells deficient in D-type cyclins or in CDK4/6 show significant defects in this step of cell cycle progression. Mutations of degron residues and the adjacent phosphosites are known to be present in solid tumours and blood cancers: Degron mutations cause overexpression of cyclin Ds.
ELM Description:	Ubiquitination of cyclin D1 (P24385) is believed to be triggered by its nuclear export that requires the phosphorylation of a single threonine residue (Thr286) near the C terminus of the protein (Diehl,1997; Santra,2009). The mutation Thr286Ala was shown to reduce cyclin D1 polyubiquitination and stabilize the protein in proliferating and quiescent fibroblasts (Diehl,1997), mostly likely by abrogating nuclear export. An in vitro biochemical study shows that the SCF-FBXO31 ubiquitin ligase (Q5XUX0) can ubiquitinate both unphosphorylated forms of cyclin D1 and its T286A mutant (Li,2018). The extreme C-terminal region of cyclin D1 binds to the second β-barrel domain of FBXO31 independently of the phosphorylation of Thr286. It is visible in the structure (5VZU) that the C-terminal carboxylate group of the peptide inserts into the open cavity in the β-barrel (Li,2018). The N-terminal half of the degron (residues 289−292) adopts a turn-like conformation so that the peptide chain stays on top of the barrel, whereas a 3/10 helix formed by residues 292−294 is tucked into the cavity. The degron motif was shown to be conserved across all three cyclin D paralogs (Li,2018). Sequence alignment reveals a highly conserved motif on the vertebrate level but more divergent in other clades and the C-terminus can be changed. The degron is located immediately downstream from the phosphorylated pThr residue at the extreme C-terminal region and composed mainly of hydrophobic and negatively charged residues. Proline seems to be incompatible with the bound helical structure observed in the co-crystal complex, confirmed by sequence alignment lacking this residue in any of the positions. Mutations in the first five positions of the degron motif have been strongly associated with both blood cancers and solid tumours but they might also affect CRM1 (O14980) binding and nuclear export, not just the degron function.
Pattern:	`D[LVIM].[DAEN][VILM][^P][ILF]$`
Pattern Probability:	`6.448e-08`
Present in taxon:	Eukaryota
Interaction Domain:	Cyclin_D1_bind (PF12014) Cyclin D1 binding domain (Stochiometry: 1 : 1)

SCF ubiquitin E3 ligase FBXO31 degron

SCF E3 ligase FBXO31 has a phospho-independent degron recognition specificity in contrast to some other E3 ligases of the SCF group (FBW7, betaTrCP1, Skp2-Cks1). SCF-FBXO31 is composed of SKP1 bound by the F-box of FBXO31 with two β-barrel domains of FBXO31 attached by a helical linker. The second β-barrel of FBXO31 recognizes C-terminal degrons of cyclin Ds. The Ser/Thr phosphorylations N-terminal to these degrons do not contribute to the specificity of the recognition but regulate their nuclear export. D-type cyclins form complexes with CDK4/6 to phosphorylate and inactivate the retinoblastoma (pRb) tumour suppressor. This process is thought to be indispensable for transition from G1 to S phase, given that cells deficient in D-type cyclins or in CDK4/6 show significant defects in this step of cell cycle progression. Mutations of degron residues and the adjacent phosphosites are known to be present in solid tumours and blood cancers: Degron mutations cause overexpression of cyclin Ds.

ELM Description:

Ubiquitination of cyclin D1 (P24385) is believed to be triggered by its nuclear export that requires the phosphorylation of a single threonine residue (Thr286) near the C terminus of the protein (Diehl,1997; Santra,2009). The mutation Thr286Ala was shown to reduce cyclin D1 polyubiquitination and stabilize the protein in proliferating and quiescent fibroblasts (Diehl,1997), mostly likely by abrogating nuclear export. An in vitro biochemical study shows that the SCF-FBXO31 ubiquitin ligase (Q5XUX0) can ubiquitinate both unphosphorylated forms of cyclin D1 and its T286A mutant (Li,2018).
The extreme C-terminal region of cyclin D1 binds to the second β-barrel domain of FBXO31 independently of the phosphorylation of Thr286. It is visible in the structure (5VZU) that the C-terminal carboxylate group of the peptide inserts into the open cavity in the β-barrel (Li,2018). The N-terminal half of the degron (residues 289−292) adopts a turn-like conformation so that the peptide chain stays on top of the barrel, whereas a 3/10 helix formed by residues 292−294 is tucked into the cavity.
The degron motif was shown to be conserved across all three cyclin D paralogs (Li,2018). Sequence alignment reveals a highly conserved motif on the vertebrate level but more divergent in other clades and the C-terminus can be changed. The degron is located immediately downstream from the phosphorylated pThr residue at the extreme C-terminal region and composed mainly of hydrophobic and negatively charged residues. Proline seems to be incompatible with the bound helical structure observed in the co-crystal complex, confirmed by sequence alignment lacking this residue in any of the positions. Mutations in the first five positions of the degron motif have been strongly associated with both blood cancers and solid tumours but they might also affect CRM1 (O14980) binding and nuclear export, not just the degron function.

Pattern:

D[LVIM].[DAEN][VILM][^P][ILF]$

Pattern Probability:

6.448e-08

Present in taxon:

Eukaryota

Interaction Domain:

Cyclin_D1_bind (PF12014) Cyclin D1 binding domain (Stochiometry: 1 : 1)

FBXO31 (F-box only protein 31) is a DNA damage-induced checkpoint protein that promotes cyclin D degradation and subsequent G1 cell-cycle arrest in response to genotoxic stress (Santra,2009). FBXO31 (Q5XUX0) was first identified as a candidate tumor suppressor gene in several cancers, and its expression can be down-regulated in breast cancer cell lines and primary breast tumors as well as in hepatocellular carcinoma (Kumar,2005; Huang,2010).

Ubiquitination of cyclin D1 (P24385) is believed to be triggered by phosphorylation of a single threonine residue (Thr286) near the C-terminus of the protein (Diehl,1997) by either DYRK1B (Q9Y463; Ashford,2014) or the phospho-primed kinase glycogen synthase kinase 3-beta (GSK3beta) (P49841; Diehl,1998) and through the MAPK pathway (Santra,2009). Mutation of Thr286 to alanine (T286A) was shown to reduce cyclin D1 polyubiquitination and stabilize the protein in proliferating and quiescent fibroblasts (Diehl,1997). The highly stable cyclin D1 T286A mutant remains in the nucleus throughout the cell cycle (Diehl,1998). Wildtype cyclin D1 (P24385) accumulates in the nucleus during G1 phase and exits into the cytoplasm as cells proceed into S phase – and it is reported that phosphorylated cyclin D1 at Thr286 is targeted for nuclear export for subsequent degradation in the cytoplasm (Benzeno,2006) and that mutation of adjacent residues abrogates binding to the nuclear exportin CRM1 (O14980; Benzeno,2004).

An in vitro biochemical study shows that the SCF-FBXO31 ubiquitin ligase can bind both unphosphorylated forms of cyclin D1 (P24385) and its T286A mutant (Li,2018). It provides fundamental insights into the FBXO31–cyclin D1 interaction and delineates a mechanism for SCF-FBXO31-mediated binding of cyclin D1 in a phosphorylation-independent manner. This is consistent with phosphorylation of Thr286 directing the nuclear export of cyclin D1 (Diehl,1998) for subsequent ubiquitination and degradation by SCF-FBXO31 (Li,2018).

In addition to cyclin D proteins, some other FBXO31 substrates have been reported (Vadhvani,2013; Liu,2014; Malonia,2015; Jeffery,2017) but the degrons have not yet been identified. Despite FBXO31 having clear roles in different cellular processes, the mechanism whereby it renders substrate specificity to the SCF complex had remained largely unknown until the degron was defined in cyclin Ds.

The degron binding site of FBXO31 (Q5XUX0) and the corresponding degron motif for the cyclin D family has been revealed by crystallography (Li,2018; 5VZU). The structure of the Skp1–FBXO31–cyclin D1 complex reveals that the extreme C-terminal region of cyclin D1 (P24385) binds to the second β-barrel domain of FBXO31, in which the C-terminal carboxylate group of the peptide inserts into the open cavity in the β-barrel (Li,2018).

In addition to its cell cycle progression role in cancer, FBXO31 truncation can cause recessively inherited mental retardation (Mir,2014) while the mutation D334N has been shown to cause cerebral palsy (Jin,2020; Dzinovic,2021).

Biological Process:
Protein Polyubiquitination (also annotated in these classes: )
Regulation Of Protein Ubiquitination (also annotated in these classes: )
Ubiquitin-Dependent Protein Catabolism (also annotated in these classes: )
Mitotic Cell Cycle G1/S Transition Checkpoint (also annotated in these classes: DEG_SCF_SKP2-CKS1_1 )
Cellular Compartment:
Cytosol (also annotated in these classes: )
Nucleus (also annotated in these classes: )
Scf Ubiquitin Ligase Complex (also annotated in these classes: )
Molecular Function:
Ubiquitin-Protein Ligase Activity (also annotated in these classes: )
Protein Binding (also annotated in these classes: )

Acc., Gene-, Name	Start	End	Subsequence	Logic	#Ev.	Organism	Notes
P30281 CCND3 CCND3_HUMAN	286	292	SSSQGPSQTSTPTDVTAIHL	TP	1	Homo sapiens (Human)	1
P30279 CCND2 CCND2_HUMAN	283	289	KSEDELDQASTPTDVRDIDL	TP	1	Homo sapiens (Human)	1
P24385 CCND1 CCND1_HUMAN	289	295	EEEEEVDLACTPTDVRDVDI	TP	4	Homo sapiens (Human)	5VZU 5VZU 1

Acc., Gene-, Name

Start

End

Subsequence

Logic

#Ev.

Organism

Notes

P30281 CCND3
CCND3_HUMAN

286

292

SSSQGPSQTSTPTDVTAIHL