Table 1. E2s, E3s, and DUBs involved in... | Rockefeller University Press

Table 1.

E2s, E3s, and DUBs involved in the assembly or disassembly of branched ubiquitin chains

Branching E3s
Linkage type	Mechanism	E2s and E3s	Substrates	Function	Technology	References
K11/K48	A	APC/C + UBE2C +UBE2S	Cyclin A	Proteasomal degradation	Ub mutation	Meyer and Rape (2014)
			NEK2A		Bispecific antibody	Yau et al. (2017)
			Histone H2B		Bispecific antibody	Oh et al. (2020)
	B	UBR5 + K11-specific E2/E3	73Q-HTT	Proteasomal degradation	Bispecific antibody	Yau et al. (2017)
K29/K48	B	Ufd4 + Ufd2	Ub-V-GFP	Proteasomal degradation	Ub mutation	Liu et al. (2017)
	B	CRL2^VHL or CRL4^CRBN + TRIP12	BRD4	Targeted protein degradation	Mass spectrometry, Ub-Clipping	Kaiho-Soma et al. (2021)
	C	HECTD1	N/A	N/A	UbiCRest, Mass spectrometry	Harris et al. (2021)
	C	UBE3C	N/A VPS34	N/A Proteasomal degradation	Ub mutation, Mass spectrometry	Wang et al. (2006)
	C	UBE3C	N/A VPS34	N/A Proteasomal degradation	Ub mutation	Chen et al. (2021)
K6/K48	C	IpaH9.8	N/A	N/A	Mass spectrometry	Valkevich et al. (2014)
	C	Parkin	N/A	Mitophagy	Ub-clipping	Swatek et al. (2019)
	C	NlEL	N/A	N/A	UbiCRest	Hospenthal et al. (2013)
	C	NlEL	N/A	N/A	Mass spectrometry	Valkevich et al. (2014)
K48/K63	B	ITCH + UBR5	TXNIP	Proteasomal degradation	Ub mutation, Mass spectrometry	Ohtake et al. (2018)
	B	TRAF6 + HUWE1	TRAF6	NFkB signal activation	Mass spectrometry, Ub mutation	Ohtake et al. (2016)
	A?	Ubc1/UBE2K	N/A	N/A	Ub mutation	Pluska et al. (2021)
K11/K48/K63	C	WWP1	WBP2	N/A	Ub mutation	French et al. (2017)
K11/K48/K63	A	cIAP1 + UBE2D + UBE2N/UBE2V	cIAP1, ER-α	Targeted protein degradation	Mass spectrometry, UbiCRest	Akizuki et al. (2023)
K63/M1	B	TRAF6 + LUBAC	IRAK1	NFkB signal activation	UbiCRest	Emmerich et al. (2013)
K63/M1	B	TRAF6 + LUBAC	RIP1 and RIP2	NFkB signal activation	UbiCRest	Emmerich et al. (2016)
Multiple types	B	UBE2D + multiple RING E3s	Luciferase, troponin I	Inhibition of proteasomal degradation	Ub mutation	Kim et al. (2007)

Branching E3s
Linkage type	Mechanism	E2s and E3s	Substrates	Function	Technology	References
K11/K48	A	APC/C + UBE2C +UBE2S	Cyclin A	Proteasomal degradation	Ub mutation	Meyer and Rape (2014)
			NEK2A		Bispecific antibody	Yau et al. (2017)
			Histone H2B		Bispecific antibody	Oh et al. (2020)
	B	UBR5 + K11-specific E2/E3	73Q-HTT	Proteasomal degradation	Bispecific antibody	Yau et al. (2017)
K29/K48	B	Ufd4 + Ufd2	Ub-V-GFP	Proteasomal degradation	Ub mutation	Liu et al. (2017)
	B	CRL2^VHL or CRL4^CRBN + TRIP12	BRD4	Targeted protein degradation	Mass spectrometry, Ub-Clipping	Kaiho-Soma et al. (2021)
	C	HECTD1	N/A	N/A	UbiCRest, Mass spectrometry	Harris et al. (2021)
	C	UBE3C	N/A VPS34	N/A Proteasomal degradation	Ub mutation, Mass spectrometry	Wang et al. (2006)
	C	UBE3C	N/A VPS34	N/A Proteasomal degradation	Ub mutation	Chen et al. (2021)
K6/K48	C	IpaH9.8	N/A	N/A	Mass spectrometry	Valkevich et al. (2014)
	C	Parkin	N/A	Mitophagy	Ub-clipping	Swatek et al. (2019)
	C	NlEL	N/A	N/A	UbiCRest	Hospenthal et al. (2013)
	C	NlEL	N/A	N/A	Mass spectrometry	Valkevich et al. (2014)
K48/K63	B	ITCH + UBR5	TXNIP	Proteasomal degradation	Ub mutation, Mass spectrometry	Ohtake et al. (2018)
	B	TRAF6 + HUWE1	TRAF6	NFkB signal activation	Mass spectrometry, Ub mutation	Ohtake et al. (2016)
	A?	Ubc1/UBE2K	N/A	N/A	Ub mutation	Pluska et al. (2021)
K11/K48/K63	C	WWP1	WBP2	N/A	Ub mutation	French et al. (2017)
K11/K48/K63	A	cIAP1 + UBE2D + UBE2N/UBE2V	cIAP1, ER-α	Targeted protein degradation	Mass spectrometry, UbiCRest	Akizuki et al. (2023)
K63/M1	B	TRAF6 + LUBAC	IRAK1	NFkB signal activation	UbiCRest	Emmerich et al. (2013)
K63/M1	B	TRAF6 + LUBAC	RIP1 and RIP2	NFkB signal activation	UbiCRest	Emmerich et al. (2016)
Multiple types	B	UBE2D + multiple RING E3s	Luciferase, troponin I	Inhibition of proteasomal degradation	Ub mutation	Kim et al. (2007)

DUBs
Target branched linkage	Effect of branched chains	DUB	Family	Linkage specificity	Substrate	Function	References
K29/K48	Retain	TRABID/ZRANB1	OTU	K29,K33>>K63	HECTD1	Protect from degradation	Harris et al. (2021)
K11/K48, K11/K63, M1/Oxyester		Cezanne	OTU	K11, Oxyester	APC/C substrates	Protect from degradation	Mevissen et al. (2016)
M1/Oxyester		Cezanne	OTU	K11, Oxyester	N/A	Inhibit NF-kB signal	Rodriguez Carvajal et al. (2021)
K6/K48		UPS30	USP	K6	Parkin	Inhibit mitophagy	Deol et al. (2020b)
K63/M1	Inhibition	A20	OTU	K63	RIPK-1	Inhibit NF-kB signal	Wertz et al. (2015)
K63/K48	Inhibition	CYLD	USP	K63, M1	TRAF6	Inhibit NF-kB signal	Ohtake et al. (2016)
K6/K48, K48/K63	Promotion	UCH37	UCH	K48	N/A	Promote proteasomal degradation	Deol et al. (2020b)

DUBs
Target branched linkage	Effect of branched chains	DUB	Family	Linkage specificity	Substrate	Function	References
K29/K48	Retain	TRABID/ZRANB1	OTU	K29,K33>>K63	HECTD1	Protect from degradation	Harris et al. (2021)
K11/K48, K11/K63, M1/Oxyester		Cezanne	OTU	K11, Oxyester	APC/C substrates	Protect from degradation	Mevissen et al. (2016)
M1/Oxyester		Cezanne	OTU	K11, Oxyester	N/A	Inhibit NF-kB signal	Rodriguez Carvajal et al. (2021)
K6/K48		UPS30	USP	K6	Parkin	Inhibit mitophagy	Deol et al. (2020b)
K63/M1	Inhibition	A20	OTU	K63	RIPK-1	Inhibit NF-kB signal	Wertz et al. (2015)
K63/K48	Inhibition	CYLD	USP	K63, M1	TRAF6	Inhibit NF-kB signal	Ohtake et al. (2016)
K6/K48, K48/K63	Promotion	UCH37	UCH	K48	N/A	Promote proteasomal degradation	Deol et al. (2020b)

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