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Shergalis AG, Marin VL, Rhee DY, Senaweera S, McCloud RL, Ronau JA, Hutchins CW, McLoughlin S, Woller KR, Warder SE, Vasudevan A, Reitsma JM. CRISPR Screen Reveals BRD2/4 Molecular Glue-like Degrader via Recruitment of DCAF16. ACS Chem Biol 2023; 18:331-339. [PMID: 36656921 DOI: 10.1021/acschembio.2c00747] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecular glues (MGs) are monovalent small molecules that induce an interaction between proteins (native or non-native partners) by altering the protein-protein interaction (PPI) interface toward a higher-affinity state. Enhancing the PPI between a protein and E3 ubiquitin ligase can lead to degradation of the partnering protein. Over the past decade, retrospective studies of clinical drugs identified that immunomodulatory drugs (e.g., thalidomide and analogues) and indisulam exhibit a molecular glue effect by driving the interaction between non-native substrates to CRBN and DCAF15 ligases, respectively. Ensuing reports of phenotypic screens focused on MG discovery have suggested that these molecules may be more common than initially anticipated. However, prospective discovery of MGs remains challenging. Thus, expanding the repertoire of MGs will enhance our understanding of principles for prospective design. Herein, we report the results of a CRISPR/Cas9 knockout screen of over 1000 ligases and ubiquitin proteasome system components in a BRD4 degradation assay with a JQ1-based monovalent degrader, compound 1a. We identified DCAF16, a substrate recognition component of the Cul4 ligase complex, as essential for compound activity, and we demonstrate that compound 1a drives the interaction between DCAF16 and BRD2/4 to promote target degradation. Taken together, our data suggest that compound 1a functions as an MG degrader between BRD2/4 and DCAF16 and provides a foundation for further mechanistic dissection to advance prospective MG discovery.
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Affiliation(s)
- Andrea G Shergalis
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Violeta L Marin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - David Y Rhee
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Sameera Senaweera
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Rebecca L McCloud
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Judith A Ronau
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Shaun McLoughlin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Kevin R Woller
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Scott E Warder
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Justin M Reitsma
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
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2
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Berk JM, Lim C, Ronau JA, Chaudhuri A, Chen H, Beckmann JF, Loria JP, Xiong Y, Hochstrasser M. A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Nat Commun 2020; 11:2343. [PMID: 32393759 PMCID: PMC7214410 DOI: 10.1038/s41467-020-15985-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/02/2020] [Indexed: 01/07/2023] Open
Abstract
Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.
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Affiliation(s)
- Jason M Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Discovery, Research and Development, AbbVie, Inc., North Chicago, IL, 60064, USA
| | - Apala Chaudhuri
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Hongli Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36830, USA
| | - J Patrick Loria
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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3
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Chen H, Ronau JA, Beckmann JF, Hochstrasser M. A Wolbachia nuclease and its binding partner provide a distinct mechanism for cytoplasmic incompatibility. Proc Natl Acad Sci U S A 2019; 116:22314-22321. [PMID: 31615889 PMCID: PMC6825299 DOI: 10.1073/pnas.1914571116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are endosymbiotic bacteria that infect nearly half of all arthropod species. This pandemic is due in part to their ability to increase their transmission through the female germline, most commonly by a mechanism called cytoplasmic incompatibility (CI). The Wolbachia cid operon, encoding 2 proteins, CidA and CidB, the latter a deubiquitylating enzyme (DUB), recapitulates CI in transgenic Drosophila melanogaster However, some CI-inducing Wolbachia strains lack a DUB-encoding cid operon; it was therefore proposed that the related cin operon codes for an alternative CI system. Here we show that the Wolbachia cin operon encodes a nuclease, CinB, and a second protein, CinA, that tightly binds CinB. Recombinant CinB has nuclease activity against both single-stranded and double-stranded DNA but not RNA under the conditions tested. Expression of the cin operon in transgenic male flies induces male sterility and embryonic defects typical of CI. Importantly, transgenic CinA can rescue defects in egg-hatch rates when expressed in females. Expression of CinA also rescues CinB-induced growth defects in yeast. CinB has 2 PD-(D/E)xK nuclease domains, and both are required for nuclease activity and for toxicity in yeast and flies. Our data suggest a distinct mechanism for CI involving a nuclease toxin and highlight the central role of toxin-antidote operons in Wolbachia-induced cytoplasmic incompatibility.
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Affiliation(s)
- Hongli Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 26849
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511
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4
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Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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5
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Bueno AN, Shrestha RK, Ronau JA, Babar A, Sheedlo MJ, Fuchs JE, Paul LN, Das C. Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase. Biochemistry 2016; 54:6038-51. [PMID: 26368668 DOI: 10.1021/acs.biochem.5b00631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The endosome-associated deubiquitinase (DUB) AMSH is a member of the JAMM family of zinc-dependent metallo isopeptidases with high selectivity for Lys63-linked polyubiquitin chains, which play a key role in endosomal-lysosomal sorting of activated cell surface receptors. The catalytic domain of the enzyme features a flexible flap near the active site that opens and closes during its catalytic cycle. Structural analysis of its homologues, AMSH-LP (AMSH-like protein) and the fission yeast counterpart, Sst2, suggests that a conserved Phe residue in the flap may be critical for substrate binding and/or catalysis. To gain insight into the contribution of this flap in substrate recognition and catalysis, we generated mutants of Sst2 and characterized them using a combination of enzyme kinetics, X-ray crystallography, molecular dynamics simulations, and isothermal titration calorimetry (ITC). Our analysis shows that the Phe residue in the flap contributes key interactions during the rate-limiting step but not to substrate binding, since mutants of Phe403 exhibit a defect only in kcat but not in KM. Moreover, ITC studies show Phe403 mutants have similar KD for ubiquitin compared to the wild-type enzyme. The X-ray structures of both Phe403Ala and the Phe403Trp, in both the free and ubiquitin bound form, reveal no appreciable structural change that might impair substrate or alter product binding. We observed that the side chain of the Trp residue is oriented identically with respect to the isopeptide moiety of the substrate as the Phe residue in the wild-type enzyme, so the loss of activity seen in this mutant cannot be explained by the absence of a group with the ability to provide van der Waals interactions that facilitate the hyrdolysis of the Lys63-linked diubiquitin. Molecular dynamics simulations indicate that the flap in the Trp mutant is quite flexible, allowing almost free rotation of the indole side chain. Therefore, it is possible that these different dynamic properties of the flap in the Trp mutant, compared to the wild-type enzyme, manifest as a defect in interactions that facilitate the rate-limiting step. Consistent with this notion, the Trp mutant was able to cleave Lys48-linked and Lys11-linked diubiquitin better than the wild-type enzyme, indicating altered mobility and hence reduced selectivity.
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Affiliation(s)
- Amy N Bueno
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Rashmi K Shrestha
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Judith A Ronau
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Aditya Babar
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Michael J Sheedlo
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Julian E Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Lake N Paul
- Bindley Biosciences Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
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6
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Shrestha RK, Ronau JA, Davies CW, Guenette RG, Strieter ER, Paul LN, Das C. Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product. Biochemistry 2014; 53:3199-217. [PMID: 24787148 PMCID: PMC4033627 DOI: 10.1021/bi5003162] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [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] [Indexed: 11/28/2022]
Abstract
![]()
AMSH, a conserved zinc metallo deubiquitinase,
controls downregulation
and degradation of cell-surface receptors mediated by the endosomal
sorting complexes required for transport (ESCRT) machinery. It displays
high specificity toward the Lys63-linked polyubiquitin chain, which
is used as a signal for ESCRT-mediated endosomal–lysosomal
sorting of receptors. Herein, we report the crystal structures of
the catalytic domain of AMSH orthologue Sst2 from fission yeast, its
ubiquitin (product)-bound form, and its Lys63-linked diubiquitin (substrate)-bound
form at 1.45, 1.7, and 2.3 Å, respectively. The structures reveal
that the P-side product fragment maintains nearly all the contacts
with the enzyme as seen with the P portion (distal ubiquitin) of the
Lys63-linked diubiquitin substrate, with additional coordination of
the Gly76 carboxylate group of the product with the active-site Zn2+. One of the product-bound structures described herein is
the result of an attempt to cocrystallize the diubiquitin substrate
bound to an active site mutant presumed to render the enzyme inactive,
instead yielding a cocrystal structure of the enzyme bound to the
P-side ubiquitin fragment of the substrate (distal ubiquitin). This
fragment was generated in situ from the residual
activity of the mutant enzyme. In this structure, the catalytic water
is seen placed between the active-site Zn2+ and the carboxylate
group of Gly76 of ubiquitin, providing what appears to be a snapshot
of the active site when the product is about to depart. Comparison
of this structure with that of the substrate-bound form suggests the
importance of dynamics of a flexible flap near the active site in
catalysis. The crystal structure of the Thr319Ile mutant of the catalytic
domain of Sst2 provides insight into structural basis of microcephaly
capillary malformation syndrome. Isothermal titration calorimetry
yields a dissociation constant (KD) of
10.2 ± 0.6 μM for the binding of ubiquitin to the enzyme,
a value comparable to the KM of the enzyme
catalyzing hydrolysis of the Lys63-linked diubiquitin substrate (∼20
μM). These results, together with the previously reported observation
that the intracellular concentration of free ubiquitin (∼20
μM) exceeds that of Lys63-linked polyubiquitin chains, imply
that the free, cytosolic form of the enzyme remains inhibited by being
tightly bound to free ubiquitin. We propose that when AMSH associates
with endosomes, inhibition would be relieved because of ubiquitin
binding domains present on its endosomal binding partners that would
shift the balance toward better recognition of polyubiquitin chains
via the avidity effect.
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Affiliation(s)
- Rashmi K Shrestha
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
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7
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Ronau JA, Paul LN, Fuchs JE, Corn IR, Wagner KT, Liedl KR, Abu-Omar MM, Das C. An additional substrate binding site in a bacterial phenylalanine hydroxylase. Eur Biophys J 2013; 42:691-708. [PMID: 23860686 PMCID: PMC3972754 DOI: 10.1007/s00249-013-0919-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/20/2013] [Accepted: 06/26/2013] [Indexed: 01/07/2023]
Abstract
Phenylalanine hydroxylase (PAH) is a non-heme iron enzyme that catalyzes oxidation of phenylalanine to tyrosine, a reaction that must be kept under tight regulatory control. Mammalian PAH has a regulatory domain in which binding of the substrate leads to allosteric activation of the enzyme. However, the existence of PAH regulation in evolutionarily distant organisms, for example some bacteria in which it occurs, has so far been underappreciated. In an attempt to crystallographically characterize substrate binding by PAH from Chromobacterium violaceum, a single-domain monomeric enzyme, electron density for phenylalanine was observed at a distal site 15.7 Å from the active site. Isothermal titration calorimetry (ITC) experiments revealed a dissociation constant of 24 ± 1.1 μM for phenylalanine. Under the same conditions, ITC revealed no detectable binding for alanine, tyrosine, or isoleucine, indicating the distal site may be selective for phenylalanine. Point mutations of amino acid residues in the distal site that contact phenylalanine (F258A, Y155A, T254A) led to impaired binding, consistent with the presence of distal site binding in solution. Although kinetic analysis revealed that the distal site mutants suffer discernible loss of their catalytic activity, X-ray crystallographic analysis of Y155A and F258A, the two mutants with the most noticeable decrease in activity, revealed no discernible change in the structure of their active sites, suggesting that the effect of distal binding may result from protein dynamics in solution.
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Affiliation(s)
- Judith A. Ronau
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Lake N. Paul
- Bindley Biosciences Center, Purdue University, West Lafayette, IN 47907, USA
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Isaac R. Corn
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Kyle T. Wagner
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Mahdi M. Abu-Omar
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA
| | - Chittaranjan Das
- Brown Laboratory of Chemistry, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN-47907, USA,To whom correspondence should be addressed: Chittaranjan Das, Brown Laboratory of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907, (765)-494-5478, Fax: (765)-494-0239,
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Madden JT, Toth SJ, Dettmar CM, Newman JA, Oglesbee RA, Hedderich HG, Everly RM, Becker M, Ronau JA, Buchanan SK, Cherezov V, Morrow ME, Xu S, Ferguson D, Makarov O, Das C, Fischetti R, Simpson GJ. Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline. J Synchrotron Radiat 2013; 20:531-40. [PMID: 23765294 PMCID: PMC3682636 DOI: 10.1107/s0909049513007942] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/22/2013] [Indexed: 05/22/2023]
Abstract
Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer. Both instruments enabled protein crystal identification with integration times between 80 and 150 µs per pixel, representing a ∼10(3)-10(4)-fold reduction in the per-pixel exposure time relative to X-ray raster scanning. Quantitative centering and analysis of phenylalanine hydroxylase from Chromobacterium violaceum cPAH, Trichinella spiralis deubiquitinating enzyme TsUCH37, human κ-opioid receptor complex kOR-T4L produced in lipidic cubic phase (LCP), intimin prepared in LCP, and α-cellulose samples were performed by collecting multiple NLO images. The crystalline samples were characterized by single-crystal diffraction patterns, while α-cellulose was characterized by fiber diffraction. Good agreement was observed between the sample positions identified by NLO and XRD raster measurements for all samples studied.
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Affiliation(s)
- Jeremy T. Madden
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Scott J. Toth
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Christopher M. Dettmar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Justin A. Newman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Robert A. Oglesbee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Hartmut G. Hedderich
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - R. Michael Everly
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Michael Becker
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Susan K. Buchanan
- NIDDK, National Institutes of Health, Building 50, Room 4503, 50 South Drive, Bethesda, MD 20814, USA
| | - Vadim Cherezov
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marie E. Morrow
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Shenglan Xu
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Dale Ferguson
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Oleg Makarov
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Robert Fischetti
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
- Correspondence e-mail:
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9
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Morrow ME, Kim MI, Ronau JA, Sheedlo MJ, White RR, Chaney J, Paul LN, Lill MA, Artavanis-Tsakonas K, Das C. Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity. Biochemistry 2013; 52:3564-78. [PMID: 23617878 PMCID: PMC3898853 DOI: 10.1021/bi4003106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ubiquitination is countered by a group of enzymes collectively called deubiquitinases (DUBs); ∼100 of them can be found in the human genome. One of the most interesting aspects of these enzymes is the ability of some members to selectively recognize specific linkage types between ubiquitin in polyubiquitin chains and their endo and exo specificity. The structural basis of exo-specific deubiquitination catalyzed by a DUB is poorly understood. UCH37, a cysteine DUB conserved from fungi to humans, is a proteasome-associated factor that regulates the proteasome by sequentially cleaving polyubiquitin chains from their distal ends, i.e., by exo-specific deubiquitination. In addition to the catalytic domain, the DUB features a functionally uncharacterized UCH37-like domain (ULD), presumed to keep the enzyme in an inhibited state in its proteasome-free form. Herein we report the crystal structure of two constructs of UCH37 from Trichinella spiralis in complex with a ubiquitin-based suicide inhibitor, ubiquitin vinyl methyl ester (UbVME). These structures show that the ULD makes direct contact with ubiquitin stabilizing a highly unusual intramolecular salt bridge between Lys48 and Glu51 of ubiquitin, an interaction that would be favored only with the distal ubiquitin but not with the internal ones in a Lys48-linked polyubiquitin chain. An inspection of 39 DUB-ubiquitin structures in the Protein Data Bank reveals the uniqueness of the salt bridge in ubiquitin bound to UCH37, an interaction that disappears when the ULD is deleted, as revealed in the structure of the catalytic domain alone bound to UbVME. The structural data are consistent with previously reported mutational data on the mammalian enzyme, which, together with the fact that the ULD residues that bind to ubiquitin are conserved, points to a similar mechanism behind the exo specificity of the human enzyme. To the best of our knowledge, these data provide the only structural example so far of how the exo specificity of a DUB can be determined by its noncatalytic domain. Thus, our data show that, contrary to its proposed inhibitory role, the ULD actually contributes to substrate recognition and could be a major determinant of the proteasome-associated function of UCH37. Moreover, our structures show that the unproductively oriented catalytic cysteine in the free enzyme is aligned correctly when ubiquitin binds, suggesting a mechanism for ubiquitin selectivity.
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Affiliation(s)
- Marie E. Morrow
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Myung-Il Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Michael J. Sheedlo
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Rhiannon R. White
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Bldg, Imperial College Road, London, SW7 2AZ, UK
| | - Joseph Chaney
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Lake N. Paul
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN, 47907, USA
| | - Katerina Artavanis-Tsakonas
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Bldg, Imperial College Road, London, SW7 2AZ, UK
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA,To whom correspondence should be addressed: Chittaranjan Das, Brown Laboratory of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907, (765)-494-5478, Fax: (765)-494-0239,
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DeWalt EL, Begue VJ, Ronau JA, Sullivan SZ, Das C, Simpson GJ. Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains. Acta Crystallogr D Biol Crystallogr 2013; 69:74-81. [PMID: 23275165 PMCID: PMC3532131 DOI: 10.1107/s0907444912042503] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/10/2012] [Indexed: 11/11/2022]
Abstract
Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals.
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Affiliation(s)
- Emma L. DeWalt
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Victoria J. Begue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Shane Z. Sullivan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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Loaiza A, Ronau JA, Ribbe A, Stanciu L, Burgner JW, Paul LN, Abu-Omar MM. Folding dynamics of phenylalanine hydroxylase depends on the enzyme’s metallation state: the native metal, iron, protects against aggregate intermediates. Eur Biophys J 2011; 40:959-68. [DOI: 10.1007/s00249-011-0711-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/07/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022]
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