Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1 DOI Creative Commons

Jonas Duering,

M. Wolter,

Julia J. Toplak

и другие.

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Дек. 13, 2023

Abstract Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct signals. Structure determination of underlying, specific E3-substrate complexes, however, has proven challenging due to their transient nature. In particular, it is incompletely understood how members catalytic cysteine-driven class HECT-type position substrate proteins for modification. Here we report a cryo-EM structure full-length human ligase HACE1, along solution-based conformational analyses small-angle X-ray scattering hydrogen-deuterium exchange mass spectrometry. Structure-based functional vitro cells reveal that activity HACE1 stringently regulated dimerization-induced autoinhibition. The inhibition occurs at first step cycle thus substrate-independent. We employ mechanism-based chemical crosslinking reconstitute complex activated, monomeric its major substrate, RAC1, visualize cryo-EM, validate binding mode analyses. Our findings explain achieves selectivity ubiquitinating active, GTP-loaded state RAC1 establish framework interpreting mutational alterations HACE1-RAC1 interplay disease. More broadly, this work illuminates central unexplored aspects architecture, dynamics, regulation, ligases.

Язык: Английский

Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5 DOI Creative Commons
Laura A. Hehl, Daniel Horn‐Ghetko, J. Rajan Prabu

и другие.

Nature Chemical Biology, Год журнала: 2023, Номер 20(2), С. 190 - 200

Опубликована: Авг. 24, 2023

Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) visualize stable mimics of intermediates along K48-linked Ub human E3, UBR5. The data reveal a ≈ 620 kDa UBR5 dimer as functional unit, comprising scaffold with flexibly tethered Ub-associated (UBA) domains, elaborately arranged HECT domains. Chains are forged UBA domain capturing an acceptor Ub, its K48 lured into active site numerous interactions between manifold elements donor Ub. cryo-EM reconstructions allow defining conserved conformations catalyzing transfer from E2 E3. Our show how full-length ubiquitins be adjoined, intermediary products guide feed-forward conformational cycle establishing highly efficient, broadly targeting, forging machine.

Язык: Английский

Процитировано

35
Orphan quality control shapes network dynamics and gene expression DOI Creative Commons
Kevin G. Mark,

SriDurgaDevi Kolla,

Jacob D. Aguirre

и другие.

Cell, Год журнала: 2023, Номер 186(16), С. 3460 - 3475.e23

Опубликована: Июль 20, 2023

All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex are established remains poorly understood. Here, we identify E3 ligase UBR5 as a signaling hub helps degrade unpaired subunits multiple transcriptional regulators act within centered on c-Myc oncoprotein. Biochemical structural analyses show binds motifs only become available upon dissociation. By rapidly turning over transcription factor subunits, establishes dynamic allow cells effectively execute gene expression while remaining receptive environmental signals. We conclude orphan quality control plays an essential role establishing networks, which may explain conserved need for degradation during offers opportunities modulate disease.

Язык: Английский

Процитировано

33
Cryo‐EM structure of the chain‐elongating E3 ubiquitin ligase UBR5 DOI Creative Commons
Zuzana Hodáková, Irina Grishkovskaya, Hanna L. Brunner

и другие.

The EMBO Journal, Год журнала: 2023, Номер 42(16)

Опубликована: Июль 6, 2023

UBR5 is a nuclear E3 ligase that ubiquitinates vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin has recently been identified as an important regulator oncogenes, e.g., MYC, but little known about its structure or mechanisms substrate engagement and ubiquitination. Here, we present the cryo-EM human UBR5, revealing α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into antiparallel dimer adopts further oligomeric states. Using processing tools, observe dynamic nature catalytic domain, which postulate enzymatic activity. We characterise import factor AKIRIN2 protein propose efficient chain elongator. preference ubiquitinated several distinct domains interactions may explain how linked to different signalling pathways cancers. Together, our data expand on limited knowledge function ligases.

Язык: Английский

Процитировано

23
Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1 DOI Creative Commons
Jonas Düring, M. Wolter,

Julia J. Toplak

и другие.

Nature Structural & Molecular Biology, Год журнала: 2024, Номер 31(2), С. 364 - 377

Опубликована: Фев. 1, 2024

Abstract Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct signals. However, structure determination of underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members catalytic cysteine-driven class HECT-type (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) full-length human HECT HACE1, along solution-based conformational analyses small-angle X-ray scattering hydrogen–deuterium exchange mass spectrometry. Structure-based functional vitro cells reveal that activity HACE1 stringently regulated dimerization-induced autoinhibition. The inhibition occurs at first step cycle thus substrate-independent. We use mechanism-based chemical crosslinking reconstitute complex activated, monomeric its major substrate, RAC1, determine cryo-EM validate binding mode analyses. Our findings explain achieves selectivity ubiquitinating active, GTP-loaded state RAC1 establish framework interpreting mutational alterations HACE1–RAC1 interplay disease. More broadly, this work illuminates central unexplored aspects architecture, dynamics, regulation HECTs.

Язык: Английский

Процитировано

7
UBR5 in Tumor Biology: Exploring Mechanisms of Immune Regulation and Possible Therapeutic Implications in MPNST DOI Open Access
Diana Odhiambo, Shuangyi Fan, Angela C. Hirbe

и другие.

Cancers, Год журнала: 2025, Номер 17(2), С. 161 - 161

Опубликована: Янв. 7, 2025

Malignant peripheral nerve sheath tumor (MPNST) is a rare but aggressive soft-tissue sarcoma characterized by poor response to therapy. The primary treatment remains surgical resection with negative margins. Nonetheless, in the setting of neurofibromatosis type 1 (NF1), five-year survival rate at 20-50%, recurrence occurring up 50% individuals. For patients metastatic and unresectable disease, current options include cytotoxic chemotherapy, which offers minimal benefit, most die within five years diagnosis. Despite advances targeted therapy focusing on inhibiting Ras signaling its downstream effectors, clinical trials report highlighting need explore alternative pathways MPNST pathogenesis. Here, we discuss role E3 ubiquitin ligase, UBR5, cancer progression immune modulation across various malignancies, including breast, lung, ovarian cancer. We focus mechanisms UBR5 contributes tumorigenesis, influence microenvironment modulation. Additionally, UBR5's roles normal tissue function, DNA damage response, metastasis, therapeutic resistance, illustrating multifaceted contribution biology. evidence implicating evasion highlight potential as target enhance efficacy checkpoint blockade (ICB) MPNST, typically an cold microenvironment. outline immune-based strategies challenges management, ongoing efforts shift landscape ultimately, suggest that targeting could be novel strategy potentiate ICB therapy-mediated anti-tumor outcomes, particularly inoperable or disease.

Язык: Английский

Процитировано

0
Convergence of orphan quality control pathways at a ubiquitin chain-elongating ligase DOI Creative Commons

Sara Carrillo Roas,

Yuichi Yagita,

Paul V. Murphy

и другие.

Molecular Cell, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
Revisiting the structure of UBR box from human UBR6 DOI
Bokyung Kim, Sang Hyun Lee,

Bong Heon Kim

и другие.

Protein Science, Год журнала: 2025, Номер 34(4)

Опубликована: Март 18, 2025

Abstract Eukaryotic N‐degron pathways are proteolytic systems with the ability to recognize specific N‐terminal residues of substrate proteins, which essential parts their degradation signals. Domains, referred as UBR boxes, several E3 ubiquitin ligases can basic N‐degrons. UBR6 is among seven mammalian family proteins containing box domain. However, recognition type‐1 N‐degrons by still not well understood. The crystal structure from human revealed zinc‐mediated dimerization, a structural feature distinct other monomeric boxes. Furthermore, its folding pattern differed that fold, although sequences aligned those In this study, we re‐determined investigate whether unusual domain‐swapped dimer was structurally relevant. newly determined at 1.5 Å resolution monomer classical fold. Our compared previously reported structures and features were further analyzed using binding assays.

Язык: Английский

Процитировано

0
Harnessing UBR5 for targeted protein degradation of key transcriptional regulators DOI Creative Commons
Asad M. Taherbhoy, Danette L. Daniels

Trends in Pharmacological Sciences, Год журнала: 2023, Номер 44(11), С. 758 - 761

Опубликована: Сен. 26, 2023

Targeted protein degradation (TPD) has opened the door for drugging transcriptional regulators, yet number of proteins targeted and E3 ligases utilized remain limited. Here, we highlight UBR5 propose multiple strategies by which this ligase could be modulated to drive key targets implicated in disease.

Язык: Английский

Процитировано

9
The role of UBR5 in tumor proliferation and oncotherapy DOI

Bin Hu,

Shiyuan Chen

Gene, Год журнала: 2024, Номер 906, С. 148258 - 148258

Опубликована: Фев. 6, 2024

Язык: Английский

Процитировано

3
Noncanonical assembly, neddylation and chimeric cullin–RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex DOI Creative Commons
Daniel Horn‐Ghetko, Linus V. M. Hopf,

Ishita Tripathi‐Giesgen

и другие.

Nature Structural & Molecular Biology, Год журнала: 2024, Номер 31(7), С. 1083 - 1094

Опубликована: Апрель 11, 2024

Abstract Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, ‘cullin–RING’ and ‘RBR’, are individually found in several hundred human ligases, collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex RBX1 (also called ROC1), of interest due its tumor suppressive interaction TP53, uniquely encompasses both cullin–RING RBR Here, cryo-EM, biochemistry cellular assays elucidate a 1.8-MDa hexameric CUL9–RBX1 assembly. Within one dimeric subcomplex, an E2-bound domain activated neddylation own cullin positioning from adjacent trans . Our data show as unique among RBX1-bound cullins dependence on metazoan-specific UBE2F enzyme, while protects it deneddylation. Substrates recruited various upstream ubiquitylation relies CUL9’s neddylated domains achieving self-assembled chimeric cullin–RING/RBR ligase activity.

Язык: Английский

Процитировано

3