E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

RNF213 is a giant E3 ubiquitin ligase and a major susceptibility factor of Moyamoya disease, a cerebrovascular disorder that can result in stroke or death. In the cell, RNF213 is involved in lipid droplet formation, lipotoxicity, hypoxia, and NF-κB signaling, but its exact function in these processes is unclear. Structural characterization has revealed the presence of a dynein-like ATPase module and an unprecedented but poorly understood E3 module. Here, we demonstrate that RNF213 E3 activity is dependent on ATP binding, rather than ATP hydrolysis, and is particularly responsive to the ATP/ADP/AMP ratio. Biochemical and activity-based probe analyses identify a non-canonical zinc finger domain as the E3 active site, which utilizes the strictly conserved Cys4462, not involved in zinc coordination, as the reactive nucleophile. The cryo-EM structure of the trapped RNF213:E2~Ub intermediate reveals RNF213 C-terminal domain as the E2 docking site, which positions the ubiquitin-loaded E2 proximal to the catalytic zinc finger, facilitating nucleophilic attack of Cys4462 on the E2~Ub thioester. Our findings show that RNF213 represents an undescribed type of a transthiolation E3 enzyme and is regulated by adenine nucleotide concentration via its ATPase core, possibly allowing it to react to changing metabolic conditions in the cell.

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HELZ2 Promotes K63-Linked Polyubiquitination of c-Myc to Induce Retinoblastoma Tumorigenesis

10.21203/rs.3.rs-866845/v1 ◽

2021 ◽

Author(s):

Hanjun Dai ◽

wen ZENG ◽

WEIJUAN ZENG ◽

MING YAN ◽

ping jiang ◽

...

Keyword(s):

Cell Proliferation ◽

Zinc Finger ◽

Ubiquitin Ligase ◽

Critical Role ◽

E3 Ubiquitin Ligase ◽

Transcriptional Regulators ◽

Zinc Finger Domain ◽

Retinoblastoma Cell ◽

Animal Survival

Abstract Retinoblastoma is a rare ocular tumor in children that originates in the retina. Several core transcriptional regulators maintain the expansion of retinoblastoma tumors, including c-Myc. Here, we demonstrated that Helicase with zinc finger domain 2 (HELZ2) promoted retinoblastoma tumorigenesis by targeting c-Myc. HELZ2-deficient inhibited retinoblastoma cell proliferation, whereas overexpression of HELZ2 promoted retinoblastoma cell proliferation. In addition, high levels of HELZ2 promoted xenograft retinoblastoma tumorigenesis and inhibited animal survival. Mechanistically, HELZ2 interacted with c-Myc and promoted its K63-linked polyubiquitination. We indicated that HELZ2 promoted the interaction between E3 ubiquitin ligase HUWE1 and c-Myc, and HELZ2-mediated K63-linked polyubiquitination and activation of c-Myc were dependent on HUWE1. Taken together, HELZ2 plays a critical role in the regulation of retinoblastoma tumorigenesis by enhancing the activity of c-Myc.

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E3 ubiquitin ligase RNF2 interacts with the S6′ proteasomal ATPase subunit and increases the ATP hydrolysis activity of S6′

Biochemical Journal ◽

10.1042/bj20041982 ◽

2005 ◽

Vol 389 (2) ◽

pp. 457-463 ◽

Cited By ~ 12

Author(s):

Sun-Joo Lee ◽

Dongwon Choi ◽

Hyangshuk Rhim ◽

Seongman Kang

Keyword(s):

Ubiquitin Ligase ◽

Atp Hydrolysis ◽

E3 Ubiquitin Ligase ◽

Ring Finger ◽

Degradation Pathway ◽

Dual Function ◽

Atpase Subunit ◽

Regulatory Complex ◽

Ubiquitin Conjugating Enzyme ◽

Hydrolysis Activity

We reported previously that the human RNF2 (RING finger protein 2) protein is an E3 ubiquitin ligase that interacts with the human ubiquitin-conjugating enzyme Hip-2/hE2-25K. In the present study, we show that RNF2 interacts with S6′ ATPase, a subunit of the proteasomal 19 S regulatory complex. S6′ interacts with RNF2 through its N-terminal RING domain, and RNF2 interacts with S6′ through its C-terminal region. Interestingly, the RNF2-S6′ interaction increases the ATP hydrolysis activity of the S6′ protein. Moreover, S6′ ATPase activity is highly increased in the presence of ubiquitinated proteins. The present study suggests that the E3 ubiquitin ligase RNF2 might have a dual function: facilitating the ubiquitination of its target substrates and recruiting the substrates to the proteasome. Furthermore, ATP hydrolysis in the E3/proteasome complex might act as an important signal for the protein degradation pathway.

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Single subunit degradation of WIZ, a lenalidomide- and pomalidomide-dependent substrate of E3 ubiquitin ligase CRL4CRBN

10.1101/595389 ◽

2019 ◽

Cited By ~ 1

Author(s):

Helen H. Yu ◽

Justin M. Reitsma ◽

Mike J. Sweredoski ◽

Annie Moradian ◽

Sonja Hess ◽

...

Keyword(s):

Zinc Finger ◽

Ubiquitin Ligase ◽

Biological Effects ◽

E3 Ubiquitin Ligase ◽

Protein Targets ◽

Protein Levels ◽

Physical Association ◽

Zinc Finger Motifs ◽

Cullin 4A ◽

Transcriptional Complex

AbstractImmunomodulators (IMiDs) are an effective class of drugs used to treat blood cancers. IMiDs are believed to work by recruiting protein targets containing a β-hairpin motif for ubiquitination by E3 ubiquitin ligase complexes composed of cereblon (CRBN), Cullin-4a (CUL4a), DNA Damage Binding protein-1 (DDB1), and Ring Box-1 (RBX1). The ubiquitinated protein is subsequently degraded by the proteasome. By characterizing the repertoire of proteins that show an increased physical association with CRBN after IMiD treatment, we identified a novel IMiD substrate, Widely Interspaced Zinc Finger Motifs (WIZ). WIZ contains a C2H2 zinc finger domain, like several other substrates that were previously characterized. We demonstrate that IMiDs stabilize physical association of WIZ with CRBN, deplete WIZ steady state protein levels in a way that is dependent on E3 ligase activity, and enhance the rate of its degradation. Notably, proteins that assemble with WIZ are co-recruited to CRBN by IMiDs but are not degraded, illustrating the potential of targeted protein degradation to eliminate individual subunits of a protein complex. These findings suggest that systematic characterization of the full repertoire of proteins that are targeted for degradation by IMiD compounds will be required to better understand their biological effects.SynopsisProteolysis Targeting Chimeras (PROTACs) can be used to precisely target a subunit of a transcriptional complex for degradation in subpopulations of cells.

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ATL9, a RING Zinc Finger Protein with E3 Ubiquitin Ligase Activity Implicated in Chitin- and NADPH Oxidase-Mediated Defense Responses

PLoS ONE ◽

10.1371/journal.pone.0014426 ◽

2010 ◽

Vol 5 (12) ◽

pp. e14426 ◽

Cited By ~ 52

Author(s):

Marta Berrocal-Lobo ◽

Sophia Stone ◽

Xin Yang ◽

Jay Antico ◽

Judy Callis ◽

...

Keyword(s):

Nadph Oxidase ◽

Zinc Finger ◽

Ubiquitin Ligase ◽

Zinc Finger Protein ◽

E3 Ubiquitin Ligase ◽

Defense Responses ◽

Finger Protein ◽

Ubiquitin Ligase Activity ◽

Ring Zinc Finger ◽

Ring Zinc Finger Protein

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Structural Insight into the Human Immunodeficiency Virus Vif SOCS Box and Its Role in Human E3 Ubiquitin Ligase Assembly

Journal of Virology ◽

10.1128/jvi.00767-08 ◽

2008 ◽

Vol 82 (17) ◽

pp. 8656-8663 ◽

Cited By ~ 87

Author(s):

Bradford J. Stanley ◽

Elana S. Ehrlich ◽

Leslie Short ◽

Yunkai Yu ◽

Zuoxiang Xiao ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Zinc Finger ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

E3 Ligase ◽

Zinc Finger Motif ◽

Antiviral Protein ◽

Virion Infectivity Factor ◽

Human Ubiquitin ◽

Immunodeficiency Virus

ABSTRACT Human immunodeficiency virus (HIV) virion infectivity factor (Vif) causes the proteasome-mediated destruction of human antiviral protein APOBEC3G by tethering it to a cellular E3 ubiquitin ligase composed of ElonginB, ElonginC, Cullin5, and Rbx2. It has been proposed that HIV Vif hijacks the E3 ligase through two regions within its C-terminal domain: a BC box region that interacts with ElonginC and a novel zinc finger motif that interacts with Cullin5. We have determined the crystal structure of the HIV Vif BC box in complex with human ElonginB and ElonginC. This complex presents direct structural evidence of the recruitment of a human ubiquitin ligase by a viral BC box protein that mimics the conserved interactions of cellular ubiquitin ligases. We further mutated conserved hydrophobic residues in a region downstream of the Vif BC box. These mutations demonstrate that this region, the Vif Cullin box, composes a third E3-ligase recruiting site critical for interaction between Vif and Cullin5. Furthermore, our homology modeling reveals that the Vif Cullin box and zinc finger motif may be positioned adjacent to the N terminus of Cullin5 for interaction with loop regions in the first cullin repeat of Cullin5.

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