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Wang JCK, Baddock HT, Mafi A, Foe IT, Bratkowski M, Lin TY, Jensvold ZD, Preciado López M, Stokoe D, Eaton D, Hao Q, Nile AH. Structure of the p53 degradation complex from HPV16. Nat Commun 2024; 15:1842. [PMID: 38418456 PMCID: PMC10902388 DOI: 10.1038/s41467-024-45920-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
Human papillomavirus (HPV) is a significant contributor to the global cancer burden, and its carcinogenic activity is facilitated in part by the HPV early protein 6 (E6), which interacts with the E3-ligase E6AP, also known as UBE3A, to promote degradation of the tumor suppressor, p53. In this study, we present a single-particle cryoEM structure of the full-length E6AP protein in complex with HPV16 E6 (16E6) and p53, determined at a resolution of ~3.3 Å. Our structure reveals extensive protein-protein interactions between 16E6 and E6AP, explaining their picomolar binding affinity. These findings shed light on the molecular basis of the ternary complex, which has been pursued as a potential therapeutic target for HPV-driven cervical, anal, and oropharyngeal cancers over the last two decades. Understanding the structural and mechanistic underpinnings of this complex is crucial for developing effective therapies to combat HPV-induced cancers. Our findings may help to explain why previous attempts to disrupt this complex have failed to generate therapeutic modalities and suggest that current strategies should be reevaluated.
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Affiliation(s)
- John C K Wang
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Hannah T Baddock
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Amirhossein Mafi
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Ian T Foe
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Matthew Bratkowski
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Ting-Yu Lin
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Zena D Jensvold
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | | | - David Stokoe
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Dan Eaton
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Qi Hao
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA.
| | - Aaron H Nile
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA.
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Sridar J, Mafi A, Judge RA, Xu J, Kong KA, Wang JCK, Stoll VS, Koukos G, Simon RJ, Eaton D, Bratkowski M, Hao Q. Cryo-EM structure of human PAPP-A2 and mechanism of substrate recognition. Commun Chem 2023; 6:234. [PMID: 37898658 PMCID: PMC10613257 DOI: 10.1038/s42004-023-01032-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Pregnancy-Associated Plasma Protein A isoforms, PAPP-A and PAPP-A2, are metalloproteases that cleave insulin-like growth factor binding proteins (IGFBPs) to modulate insulin-like growth factor signaling. The structures of homodimeric PAPP-A in complex with IGFBP5 anchor peptide, and inhibitor proteins STC2 and proMBP have been recently reported. Here, we present the single-particle cryo-EM structure of the monomeric, N-terminal LG, MP, and the M1 domains (with the exception of LNR1/2) of human PAPP-A2 to 3.13 Å resolution. Our structure together with functional studies provides insight into a previously reported patient mutation that inactivates PAPP-A2 in a distal region of the protein. Using a combinational approach, we suggest that PAPP-A2 recognizes IGFBP5 in a similar manner as PAPP-A and show that PAPP-A2 cleaves IGFBP5 less efficiently due to differences in the M2 domain. Overall, our studies characterize the cleavage mechanism of IGFBP5 by PAPP-A2 and shed light onto key differences with its paralog PAPP-A.
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Affiliation(s)
- Janani Sridar
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | | | | | - Jun Xu
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - Kailyn A Kong
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - John C K Wang
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | | | - Georgios Koukos
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - Reyna J Simon
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - Dan Eaton
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | | | - Qi Hao
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
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Bratkowski M, Burdett TC, Danao J, Wang X, Mathur P, Gu W, Beckstead JA, Talreja S, Yang YS, Danko G, Park JH, Walton M, Brown SP, Tegley CM, Joseph PRB, Reynolds CH, Sambashivan S. Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease. Neuron 2022; 110:3711-3726.e16. [PMID: 36087583 DOI: 10.1016/j.neuron.2022.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Axon degeneration is an early pathological event in many neurological diseases. The identification of the nicotinamide adenine dinucleotide (NAD) hydrolase SARM1 as a central metabolic sensor and axon executioner presents an exciting opportunity to develop novel neuroprotective therapies that can prevent or halt the degenerative process, yet limited progress has been made on advancing efficacious inhibitors. We describe a class of NAD-dependent active-site SARM1 inhibitors that function by intercepting NAD hydrolysis and undergoing covalent conjugation with the reaction product adenosine diphosphate ribose (ADPR). The resulting small-molecule ADPR adducts are highly potent and confer compelling neuroprotection in preclinical models of neurological injury and disease, validating this mode of inhibition as a viable therapeutic strategy. Additionally, we show that the most potent inhibitor of CD38, a related NAD hydrolase, also functions by the same mechanism, further underscoring the broader applicability of this mechanism in developing therapies against this class of enzymes.
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Affiliation(s)
| | - Thomas C Burdett
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Jean Danao
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Xidao Wang
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Prakhyat Mathur
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Weijing Gu
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | | | - Santosh Talreja
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Yu-San Yang
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Gregory Danko
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Jae Hong Park
- Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Mary Walton
- Chemistry Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | - Sean P Brown
- Chemistry Department, Nura Bio Inc., South San Francisco, CA 94080, USA
| | | | - Prem Raj B Joseph
- WuXi AppTec, Research Services Division, 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
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Bratkowski M, Yang X, Liu X. An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors. Sci Rep 2018; 8:9092. [PMID: 29904056 PMCID: PMC6002473 DOI: 10.1038/s41598-018-27175-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/25/2018] [Indexed: 01/08/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) mediates trimethylation of histone H3K27 (H3K27me3), an epigenetic hallmark for repressed chromatin. Overactive mutants of the histone lysine methyltransferase subunit of PRC2, Ezh2, are found in various types of cancers. Pyridone-containing inhibitors such as GSK126 compete with S-adenosylmethionine (SAM) for Ezh2 binding and effectively inhibit PRC2 activity. PRC2 from the thermophilic fungus Chaetomium thermophilum (ct) is functionally similar to the human version in several regards and has the added advantage of producing high-resolution crystal structures, although inhibitor-bound structures of human or human/chameleon PRC2 are also available at up to 2.6 Å resolution. We solved crystal structures of both human and ctPRC2 bound to GSK126 and the structurally similar inhibitor GSK343. While the two organisms feature a disparate degree of inhibitor potency, surprisingly, GSK126 binds in a similar manner in both structures. Structure-guided protein engineering of the drug binding pocket allowed us to introduce humanizing mutations into ctEzh2 to produce a ctPRC2 variant that is more susceptible to GSK126 inhibition. Additional analysis indicated that an evolutionarily conserved structural platform dictates a unique mode of GSK126 binding, suggesting a mechanism of drug selectivity. The existing drug scaffold may thus be used to probe the function and cellular regulation of PRC2 in a wide spectrum of organisms, ranging from fungi to humans.
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Affiliation(s)
- Matthew Bratkowski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xin Yang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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Bratkowski M, Unarta IC, Zhu L, Shubbar M, Huang X, Liu X. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk. J Biol Chem 2017; 293:1651-1665. [PMID: 29158257 DOI: 10.1074/jbc.m117.811521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/10/2017] [Indexed: 11/06/2022] Open
Abstract
Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that the TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. We propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk.
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Affiliation(s)
- Matthew Bratkowski
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Ilona Christy Unarta
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Lizhe Zhu
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Murtada Shubbar
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Xuhui Huang
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xin Liu
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and .,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
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Abstract
Polycomb-group proteins control many fundamental biological processes, such as anatomical development in mammals and vernalization in plants. Polycomb repressive complex 2 (PRC2) is responsible for methylation of histone H3 lysine 27 (H3K27), and trimethylated H3K27 (H3K27me3) is implicated in epigenetic gene silencing. Recent genomic, biochemical, and structural data indicate that PRC2 is broadly conserved from yeast to human in many aspects. Here, we determined the crystal structure of an apo-PRC2 from the fungus Chaetomium thermophilum captured in a bona fide autoinhibited state, which represents a novel conformation of PRC2 associated with enzyme regulation in light of the basal and stimulated states that we reported previously. We found that binding by the cofactor S-adenosylmethionine mitigates this autoinhibited structural state. Using steady-state enzyme kinetics, we also demonstrated that disrupting the autoinhibition results in a vastly activated enzyme complex. Autoinhibition provides a novel structural platform that may enable control of PRC2 activity in response to diverse transcriptional states and chromatin contexts and set a ground state to allow PRC2 activation by other cellular mechanisms as well.
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Affiliation(s)
- Matthew Bratkowski
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Xin Yang
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Xin Liu
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
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Lee G, Bratkowski M, Ding F, Ke A, Ha T. Single Molecule Analysis of Yeast Rrp44 Exonuclease Reveals a Spring-Loaded Mechanism of RNA Unwinding. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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