1
|
Gou Y, Li D, Zhao M, Li M, Zhang J, Zhou Y, Xiao F, Liu G, Ding H, Sun C, Ye C, Dong C, Gao J, Gao D, Bao Z, Huang L, Xu Z, Lian J. Intein-mediated temperature control for complete biosynthesis of sanguinarine and its halogenated derivatives in yeast. Nat Commun 2024; 15:5238. [PMID: 38898098 PMCID: PMC11186835 DOI: 10.1038/s41467-024-49554-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
While sanguinarine has gained recognition for antimicrobial and antineoplastic activities, its complex conjugated structure and low abundance in plants impede broad applications. Here, we demonstrate the complete biosynthesis of sanguinarine and halogenated derivatives using highly engineered yeast strains. To overcome sanguinarine cytotoxicity, we establish a splicing intein-mediated temperature-responsive gene expression system (SIMTeGES), a simple strategy that decouples cell growth from product synthesis without sacrificing protein activity. To debottleneck sanguinarine biosynthesis, we identify two reticuline oxidases and facilitated functional expression of flavoproteins and cytochrome P450 enzymes via protein molecular engineering. After comprehensive metabolic engineering, we report the production of sanguinarine at a titer of 448.64 mg L-1. Additionally, our engineered strain enables the biosynthesis of fluorinated sanguinarine, showcasing the biotransformation of halogenated derivatives through more than 15 biocatalytic steps. This work serves as a blueprint for utilizing yeast as a scalable platform for biomanufacturing diverse benzylisoquinoline alkaloids and derivatives.
Collapse
Affiliation(s)
- Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Dongfang Li
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Minghui Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiaojiao Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yilian Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Feng Xiao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Gaofei Liu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Haote Ding
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Chenfan Sun
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zehua Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
| |
Collapse
|
2
|
Didiasova M, Banning A, Tikkanen R. Development of precision therapies for rare inborn errors of metabolism: Functional investigations in cell culture models. J Inherit Metab Dis 2024; 47:509-516. [PMID: 37606592 DOI: 10.1002/jimd.12674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Due to the low number of patients, rare genetic diseases are a special challenge for the development of therapies, especially for diseases that result from numerous, patient-specific pathogenic variants. Precision medicine makes use of various kinds of molecular information about a specific variant, so that the possibilities for an effective therapy based on the molecular features of the variants can be elucidated. The attention to personalized precision therapies has increased among scientists and clinicians, since the "single drug for all patients" approach does not allow the classification of individuals in subgroups according to the differences in the disease genotype or phenotype. This review article summarizes some approaches of personalized precision medicine that can be used for a cost-effective and fast development of therapies, even for single patients. We have focused on specific examples on inborn errors of metabolism, with special attention on drug repurposing. Furthermore, we provide an overview of cell culture models that are suitable for precision medicine approaches.
Collapse
Affiliation(s)
- Miroslava Didiasova
- Medical Faculty, Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Antje Banning
- Medical Faculty, Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Ritva Tikkanen
- Medical Faculty, Institute of Biochemistry, University of Giessen, Giessen, Germany
| |
Collapse
|
3
|
Kuang M, Zhang Y, Lam TW, Ting HF. MLProbs: A Data-Centric Pipeline for Better Multiple Sequence Alignment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:524-533. [PMID: 35120007 DOI: 10.1109/tcbb.2022.3148382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this paper, we explore using the data-centric approach to tackle the Multiple Sequence Alignment (MSA) construction problem. Unlike the algorithm-centric approach, which reduces the construction problem to a combinatorial optimization problem based on an abstract mathematical model, the data-centric approach explores using classification models trained from existing benchmark data to guide the construction. We identified two simple classifications to help us choose a better alignment tool and determine whether and how much to carry out realignment. We show that shallow machine-learning algorithms suffice to train sensitive models for these classifications. Based on these models, we implemented a new multiple sequence alignment pipeline, called MLProbs. Compared with 10 other popular alignment tools over four benchmark databases (namely, BAliBASE, OXBench, OXBench-X and SABMark), MLProbs consistently gives the highest TC score. More importantly, MLProbs shows non-trivial improvement for protein families with low similarity; in particular, when evaluated against the 1,356 protein families with similarity ≤ 50%, MLProbs achieves a TC score of 56.93, while the next best three tools are in the range of [55.41, 55.91] (increased by more than 1.8%). We also compared the performance of MLProbs and other MSA tools in two real-life applications - Phylogenetic Tree Construction Analysis and Protein Secondary Structure Prediction - and MLProbs also had the best performance. In our study, we used only shallow machine-learning algorithms to train our models. It would be interesting to study whether deep-learning methods can help make further improvements, so we suggest some possible research directions in the conclusion section.
Collapse
|
4
|
Sreepada A, Tiwari M, Pal K. Adhesion G protein-coupled receptor gluing action guides tissue development and disease. J Mol Med (Berl) 2022; 100:1355-1372. [PMID: 35969283 DOI: 10.1007/s00109-022-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 10/15/2022]
Abstract
Phylogenetic analysis of human G protein-coupled receptors (GPCRs) divides these transmembrane signaling proteins into five groups: glutamate, rhodopsin, adhesion, frizzled, and secretin families, commonly abbreviated as the GRAFS classification system. The adhesion GPCR (aGPCR) sub-family comprises 33 different receptors in humans. Majority of the aGPCRs are orphan receptors with unknown ligands, structures, and tissue expression profiles. They have a long N-terminal extracellular domain (ECD) with several adhesion sites similar to integrin receptors. Many aGPCRs undergo autoproteolysis at the GPCR proteolysis site (GPS), enclosed within the larger GPCR autoproteolysis inducing (GAIN) domain. Recent breakthroughs in aGPCR research have created new paradigms for understanding their roles in organogenesis. They play crucial roles in multiple aspects of organ development through cell signaling, intercellular adhesion, and cell-matrix associations. They are involved in essential physiological processes like regulation of cell polarity, mitotic spindle orientation, cell adhesion, and migration. Multiple aGPCRs have been associated with the development of the brain, musculoskeletal system, kidneys, cardiovascular system, hormone secretion, and regulation of immune functions. Since aGPCRs have crucial roles in tissue patterning and organogenesis, mutations in these receptors are often associated with diseases with loss of tissue integrity. Thus, aGPCRs include a group of enigmatic receptors with untapped potential for elucidating novel signaling pathways leading to drug discovery. We summarized the current knowledge on how aGPCRs play critical roles in organ development and discussed how aGPCR mutations/genetic variants cause diseases.
Collapse
Affiliation(s)
- Abhijit Sreepada
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, 131029, India
| | - Mansi Tiwari
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, 131029, India
| | - Kasturi Pal
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, 131029, India.
| |
Collapse
|
5
|
Loch JI, Klonecka A, Kądziołka K, Bonarek P, Barciszewski J, Imiolczyk B, Brzezinski K, Gilski M, Jaskolski M. Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase. Acta Crystallogr D Struct Biol 2022; 78:911-926. [PMID: 35775990 PMCID: PMC9248843 DOI: 10.1107/s2059798322005691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
This work reports the results of random mutagenesis of the Escherichia coli class 2 L-asparaginase EcAIII belonging to the Ntn-hydrolase family. New variants of EcAIII were studied using structural, biophysical and bioinformatic methods. Activity tests revealed that the L-asparaginase activity is abolished in all analyzed mutants with the absence of Arg207, but some of them retained the ability to undergo the autoproteolytic maturation process. The results of spectroscopic studies and the determined crystal structures showed that the EcAIII fold is flexible enough to accept different types of mutations; however, these mutations may have a diverse impact on the thermal stability of the protein. The conclusions from the experiments are grouped into six lessons focused on (i) the adaptation of the EcAIII fold to new substitutions, (ii) the role of Arg207 in EcAIII activity, (iii) a network of residues necessary for autoprocessing, (iv) the complexity of the autoprocessing reaction, (v) the conformational changes observed in enzymatically inactive variants and (vi) the cooperativity of the EcAIII dimer subunits. Additionally, the structural requirements (pre-maturation checkpoints) that are necessary for the initiation of the autocleavage of Ntn-hydrolases have been classified. The findings reported in this work provide useful hints that should be considered before planning enzyme-engineering experiments aimed at the design of proteins for therapeutic applications. This is especially important for L-asparaginases that can be utilized in leukemia therapy, as alternative therapeutics are urgently needed to circumvent the severe side effects associated with the currently used enzymes.
Collapse
Affiliation(s)
- Joanna I. Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Agnieszka Klonecka
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Kinga Kądziołka
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jakub Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Imiolczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | - Mirosław Gilski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| |
Collapse
|
6
|
Nagaratnam N, Delker SL, Jernigan R, Edwards TE, Snider J, Thifault D, Williams D, Nannenga BL, Stofega M, Sambucetti L, Hsieh JJ, Flint AJ, Fromme P, Martin-Garcia JM. Structural insights into the function of the catalytically active human Taspase1. Structure 2021; 29:873-885.e5. [PMID: 33784495 DOI: 10.1016/j.str.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/07/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse models of glioblastoma. Taspase1 is synthesized as an inactive proenzyme, becoming active upon intramolecular cleavage. The activation process changes the conformation of a long fragment at the C-terminus of the α subunit, for which no full-length structural information exists and whose function is poorly understood. We present a cloning strategy to generate a circularly permuted form of Taspase1 to determine the crystallographic structure of active Taspase1. We discovered that this region forms a long helix and is indispensable for the catalytic activity of Taspase1. Our study highlights the importance of this element for the enzymatic activity of Ntn-hydrolases, suggesting that it could be a potential target for the design of inhibitors with potential to be developed into anticancer therapeutics.
Collapse
Affiliation(s)
- Nirupa Nagaratnam
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Silvia L Delker
- Beryllium Discovery Corp., with present address of UCB Biosciences, Bedford, MA 01730, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., with present address of UCB Biosciences, Bedford, MA 01730, USA
| | - Janey Snider
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Darren Thifault
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Dewight Williams
- Eyring Materials Center, Arizona State University, Tempe, AZ 85257, USA
| | - Brent L Nannenga
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Mary Stofega
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Lidia Sambucetti
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - James J Hsieh
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Andrew J Flint
- Frederick National Lab for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", Spanish National Research Council (CSIC), Madrid 28006, Spain.
| |
Collapse
|
7
|
Abstract
The Ca2+-dependent clip-and-link activity of large repeat-in-toxin (RTX) proteins is an exceptional posttranslational process in which an internal domain called a self-processing module (SPM) mediates Ca2+-dependent processing of a highly specific aspartate-proline (Asp-Pro) peptide bond and covalent linkage of the released aspartyl to an adjacent lysine residue through an isopeptide bond. Here, we report the solution structures of the Ca2+-loaded SPM (Ca-SPM) defining the mechanism of the autocatalytic cleavage of the Asp414-Pro415 peptide bond of the Neisseria meningitidis FrpC exoprotein. Moreover, deletion of the SPM domain in the ApxIVA protein, the FrpC homolog of Actinobacillus pleuropneumoniae, resulted in attenuation of virulence of the bacterium in a pig infection model, indicating that the Ca2+-dependent clip-and-link activity plays a role in the virulence of Gram-negative pathogens. The posttranslational Ca2+-dependent “clip-and-link” activity of large repeat-in-toxin (RTX) proteins starts by Ca2+-dependent structural rearrangement of a highly conserved self-processing module (SPM). Subsequently, an internal aspartate-proline (Asp-Pro) peptide bond at the N-terminal end of SPM breaks, and the liberated C-terminal aspartyl residue can react with a free ε-amino group of an adjacent lysine residue to form a new isopeptide bond. Here, we report a solution structure of the calcium-loaded SPM (Ca-SPM) derived from the FrpC protein of Neisseria meningitidis. The Ca-SPM structure defines a unique protein architecture and provides structural insight into the autocatalytic cleavage of the Asp-Pro peptide bond through a “twisted-amide” activation. Furthermore, in-frame deletion of the SPM domain from the ApxIVA protein of Actinobacillus pleuropneumoniae attenuated the virulence of this porcine pathogen in a pig respiratory challenge model. We hypothesize that the Ca2+-dependent clip-and-link activity represents an unconventional strategy for Gram-negative pathogens to adhere to the host target cell surface.
Collapse
|
8
|
Noguera ME, Jakoncic J, Ermácora MR. High-resolution structure of intramolecularly proteolyzed human mucin-1 SEA domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140361. [PMID: 31923589 DOI: 10.1016/j.bbapap.2020.140361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 01/26/2023]
Abstract
SEA domains are ubiquitous in large proteins associated with highly glycosylated environments. Certain SEA domains undergo intramolecular proteolysis involving a nucleophilic attack of a serine hydroxyl group on the preceding glycine carbonyl. The mucin-1 (MUC1) SEA domain has been extensively investigated as a model of intramolecular proteolysis. Since neither a general base, a general acid, nor an oxyanion hole could be identified in MUC1 SEA, it has been suggested that proteolysis is accelerated by a non-planarity of the scissile peptide bond imposed by protein folding. A reactant distorted peptide bond has been also invoked to explain the autoproteolysis of several unrelated proteins. However, the only evidence of peptide distortion in MUC1 SEA stems from molecular dynamic simulations of the reactant modeled upon a single NMR structure of the cleaved product. We report the first high-resolution X-ray structure of cleaved MUC1 SEA. Structural comparison with uncleaved SEA domains suggests that the number of residues evolutionarily inserted in the cleaved loop of MUC1 SEA precludes the formation of a properly hydrogen-bonded beta turn. By sequence analysis, we show that this conformational frustration is shared by all known cleaved SEA domains. In addition, alternative conformations of the uncleaved precursor could be modeled in which the scissile peptide bond is planar. The implications of these structures for autoproteolysis are discussed in the light of the previous research on autoproteolysis.
Collapse
Affiliation(s)
- Martín E Noguera
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jean Jakoncic
- Photon Science Directorate, Brookhaven National Laboratory, Upton, New York, United States
| | - Mario R Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes,Argentina.
| |
Collapse
|
9
|
Mutational Analysis of a Highly Conserved PLSSMXP Sequence in the Small Subunit of Bacillus licheniformis γ-Glutamyltranspeptidase. Biomolecules 2019; 9:biom9090508. [PMID: 31546955 PMCID: PMC6769717 DOI: 10.3390/biom9090508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/13/2023] Open
Abstract
A highly conserved 458PLSSMXP464 sequence in the small subunit (S-subunit) of an industrially important Bacillus licheniformis γ-glutamyltranspeptidase (BlGGT) was identified by sequence alignment. Molecular structures of the precursor mimic and the mature form of BlGGT clearly reveal that this peptide sequence is in close spatial proximity to the self-processing and catalytic sites of the enzyme. To probe the role of this conserved sequence, ten mutant enzymes of BlGGT were created through a series of deletion and alanine-scanning mutagenesis. SDS-PAGE and densitometric analyses showed that the intrinsic ability of BlGGT to undergo autocatalytic processing was detrimentally affected by the deletion-associated mutations. However, loss of self-activating capacity was not obviously observed in most of the Ala-replacement mutants. The Ala-replacement mutants had a specific activity comparable to or greater than that of the wild-type enzyme; conversely, all deletion mutants completely lost their enzymatic activity. As compared with BlGGT, S460A and S461S showed greatly enhanced kcat/Km values by 2.73- and 2.67-fold, respectively. The intrinsic tryptophan fluorescence and circular dichroism spectral profiles of Ala-replacement and deletion mutants were typically similar to those of BlGGT. However, heat and guanidine hydrochloride-induced unfolding transitions of the deletion-associated mutant proteins were severely reduced as compared with the wild-type enzyme. The predictive mutant models suggest that the microenvironments required for both self-activation and catalytic reaction of BlGGT can be altered upon mutations.
Collapse
|
10
|
Gamage DG, Gunaratne A, Periyannan GR, Russell TG. Applicability of Instability Index for In vitro Protein Stability Prediction. Protein Pept Lett 2019; 26:339-347. [DOI: 10.2174/0929866526666190228144219] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/22/2019] [Accepted: 02/06/2019] [Indexed: 11/22/2022]
Abstract
Background:
The dipeptide composition-based Instability Index (II) is one of the protein
primary structure-dependent methods available for in vivo protein stability predictions. As per this
method, proteins with II value below 40 are stable proteins. Intracellular protein stability principles
guided the original development of the II method. However, the use of the II method for in vitro
protein stability predictions raises questions about the validity of applying the II method under
experimental conditions that are different from the in vivo setting.
Objective:
The aim of this study is to experimentally test the validity of the use of II as an in vitro
protein stability predictor.
Methods:
A representative protein CCM (CCM - Caulobacter crescentus metalloprotein) that
rapidly degrades under in vitro conditions was used to probe the dipeptide sequence-dependent
degradation properties of CCM by generating CCM mutants to represent stable and unstable II
values. A comparative degradation analysis was carried out under in vitro conditions using wildtype
CCM, CCM mutants and two other candidate proteins: metallo-β-lactamase L1 and α -S1-
casein representing stable, borderline stable/unstable, and unstable proteins as per the II predictions.
The effect of temperature and a protein stabilizing agent on CCM degradation was also tested.
Results:
Data support the dipeptide composition-dependent protein stability/instability in wt-CCM
and mutants as predicted by the II method under in vitro conditions. However, the II failed to
accurately represent the stability of other tested proteins. Data indicate the influence of protein
environmental factors on the autoproteolysis of proteins.
Conclusion:
Broader application of the II method for the prediction of protein stability under in
vitro conditions is questionable as the stability of the protein may be dependent not only on the
intrinsic nature of the protein but also on the conditions of the protein milieu.
Collapse
Affiliation(s)
- Dilani G. Gamage
- Department of Chemistry and Biochemistry, Eastern Illinois University, Charleston, IL, United States
| | - Ajith Gunaratne
- Department of Mathematics, Florida Agricultural and Mechanical University, Tallahassee, FL, United States
| | - Gopal R. Periyannan
- Department of Chemistry and Biochemistry, Eastern Illinois University, Charleston, IL, United States
| | - Timothy G. Russell
- Department of Chemistry and Biochemistry, Eastern Illinois University, Charleston, IL, United States
| |
Collapse
|
11
|
Pande S, Guo HC. The T99K variant of glycosylasparaginase shows a new structural mechanism of the genetic disease aspartylglucosaminuria. Protein Sci 2019; 28:1013-1023. [PMID: 30901125 DOI: 10.1002/pro.3607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022]
Abstract
Aspartylglucosaminuria (AGU) is an inherited disease caused by mutations in a lysosomal amidase called aspartylglucosaminidase (AGA) or glycosylasparaginase (GA). This disorder results in an accumulation of glycoasparagines in the lysosomes of virtually all cell types, with severe clinical symptoms affecting the central nervous system, skeletal abnormalities, and connective tissue lesions. GA is synthesized as a single-chain precursor that requires an intramolecular autoprocessing to form a mature amidase. Previously, we showed that a Canadian AGU mutation disrupts this obligatory intramolecular autoprocessing with the enzyme trapped as an inactive precursor. Here, we report biochemical and structural characterization of a model enzyme corresponding to a new American AGU allele, the T99K variant. Unlike other variants with known 3D structures, this T99K model enzyme still has autoprocessing capacity to generate a mature form. However, its amidase activity to digest glycoasparagines remains low, consistent with its association with AGU. We have determined a 1.5-Å-resolution structure of this new AGU model enzyme and built an enzyme-substrate complex to provide a structural basis to analyze the negative effects of the T99K point mutation on KM and kcat of the amidase. It appears that a "molecular clamp" capable of fixing local disorders at the dimer interface might be able to rescue the deficiency of this new AGU variant.
Collapse
Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854
| |
Collapse
|
12
|
Pande S, Bizilj W, Guo HC. Biochemical and structural insights into an allelic variant causing the lysosomal storage disorder - aspartylglucosaminuria. FEBS Lett 2018; 592:2550-2561. [PMID: 29993127 DOI: 10.1002/1873-3468.13190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/03/2023]
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by defects of the hydrolase glycosylasparaginase (GA). Previously, we showed that a Canadian AGU mutation disrupts an obligatory intramolecular autoprocessing with the enzyme trapped as an inactive precursor. Here, we report biochemical and structural characterizations of a model enzyme corresponding to a Finnish AGU allele, the T234I variant. Unlike the Canadian counterpart, the Finnish variant is capable of a slow autoprocessing to generate detectible hydrolyzation activity of the natural substrate of GA. We have determined a 1.6 Å-resolution structure of the Finnish AGU model and built an enzyme-substrate complex to provide a structural basis for analyzing the negative effects of the point mutation on KM and kcat of the mature enzyme. ENZYME Glycosylasparaginase or aspartylglucosaminidase, EC3.5.1.26.
Collapse
Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - William Bizilj
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| |
Collapse
|
13
|
Gordo V, Aparicio D, Pérez-Luque R, Benito A, Vilanova M, Usón I, Fita I, Ribó M. Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein. Cell Chem Biol 2018; 25:871-879.e2. [PMID: 29754955 DOI: 10.1016/j.chembiol.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/28/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
Abstract
Split inteins are expressed as two separated subunits (N-intein and C-intein) fused to the corresponding exteins. The specific association of both intein subunits precedes protein splicing, which results in excision of the intein subunits and in ligation, by a peptide bond, of the concomitant exteins. Catalytically active intein precursors are typically too reactive for crystallization or even isolation. Neq pol is the trans-intein of the B-type DNA polymerase I split gene from hyperthermophile Nanoarchaeum equitans. We have determined the crystal structures of both the isolated NeqN and the complex of NeqN and NeqC subunits carrying the wild-type sequences, including the essential catalytic residues Ser1 and Thr+1, in addition to seven and three residues of the N- and C-exteins, respectively. These structures provide detailed information on the unique oxyester chemistry of the splicing mechanism of Neq pol and of the extensive rearrangements that occur in NeqN during the association step.
Collapse
Affiliation(s)
- Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Antoni Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Maria Vilanova
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain; ICREA Lluís Companys 23, 08003 Barcelona, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain.
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain.
| |
Collapse
|
14
|
Gebai A, Gorelik A, Li Z, Illes K, Nagar B. Structural basis for the activation of acid ceramidase. Nat Commun 2018; 9:1621. [PMID: 29692406 PMCID: PMC5915598 DOI: 10.1038/s41467-018-03844-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/14/2018] [Indexed: 01/21/2023] Open
Abstract
Acid ceramidase (aCDase, ASAH1) hydrolyzes lysosomal membrane ceramide into sphingosine, the backbone of all sphingolipids, to regulate many cellular processes. Abnormal function of aCDase leads to Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, and is associated with Alzheimer’s, diabetes, and cancer. Here, we present crystal structures of mammalian aCDases in both proenzyme and autocleaved forms. In the proenzyme, the catalytic center is buried and protected from solvent. Autocleavage triggers a conformational change exposing a hydrophobic channel leading to the active site. Substrate modeling suggests distinct catalytic mechanisms for substrate hydrolysis versus autocleavage. A hydrophobic surface surrounding the substrate binding channel appears to be a site of membrane attachment where the enzyme accepts substrates facilitated by the accessory protein, saposin-D. Structural mapping of disease mutations reveals that most would destabilize the protein fold. These results will inform the rational design of aCDase inhibitors and recombinant aCDase for disease therapeutics. Acid ceramidase (aCDase) hydrolyzes lysosomal membrane ceramide into sphingosine and its dysfunction leads to a variety of disease phenotypes. Here, the authors present structures of aCDase in its proenzyme and autocleaved forms, which provides insight into its mechanism of action.
Collapse
Affiliation(s)
- Ahmad Gebai
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Alexei Gorelik
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Zixian Li
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Katalin Illes
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada.
| |
Collapse
|
15
|
Gα i-mediated TRPC4 activation by polycystin-1 contributes to endothelial function via STAT1 activation. Sci Rep 2018; 8:3480. [PMID: 29472562 PMCID: PMC5823873 DOI: 10.1038/s41598-018-21873-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Hypertension and aneurysm are frequently associated with autosomal dominant polycystic kidney disease (ADPKD) caused by polycystin-1 (PC1) mutations, which is closely related to endothelial dysfunction. PC1 is an atypical G-protein-coupled receptor that activates G-proteins by self-cleavage; currently, however, the molecular and cellular mechanisms of the associated intracellular signaling and ion channel activation remain poorly elucidated. Here, we report an activation mechanism of a calcium-permeable canonical transient receptor potential 4 (TRPC4) channel by PC1 and its endothelial function. We found that the inhibitory Gαi3 protein selectively bound to the G-protein-binding domain on the C-terminus of PC1. The dissociation of Gαi3 upon cleavage of PC1 increased TRPC4 activity. Calcium influx through TRPC4 activated the transcription factor STAT1 to regulate cell proliferation and death. The down-regulation of PC1/TRPC4/STAT1 disrupted migration of endothelial cell monolayers, leading to an increase in endothelial permeability. These findings contribute to greater understanding of the high risk of aneurysm in patients with ADPKD.
Collapse
|
16
|
Pande S, Lakshminarasimhan D, Guo HC. Crystal structure of a mutant glycosylasparaginase shedding light on aspartylglycosaminuria-causing mechanism as well as on hydrolysis of non-chitobiose substrate. Mol Genet Metab 2017; 121:150-156. [PMID: 28457719 PMCID: PMC5504686 DOI: 10.1016/j.ymgme.2017.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
Glycosylasparaginase (GA) is an amidase that cleaves Asn-linked glycoproteins in lysosomes. Deficiency of this enzyme causes accumulation of glycoasparagines in lysosomes of cells, resulting in a genetic condition called aspartylglycosaminuria (AGU). To better understand the mechanism of a disease-causing mutation with a single residue change from a glycine to an aspartic acid, we generated a model mutant enzyme at the corresponding position (named G172D mutant). Here we report a 1.8Å resolution crystal structure of mature G172D mutant and analyzed the reason behind its low hydrolase activity. Comparison of mature G172D and wildtype GA models reveals that the presence of Asp 172 near the catalytic site affects substrate catabolism in mature G172D, making it less efficient in substrate processing. Also recent studies suggest that GA is capable of processing substrates that lack a chitobiose (Glycan, N-acetylchiobios, NAcGlc) moiety, by its exo-hydrolase activity. The mechanism for this type of catalysis is not yet clear. l-Aspartic acid β-hydroxamate (β-AHA) is a non-chitobiose substrate that is known to interact with GA. To study the underlying mechanism of non-chitobiose substrate processing, we built a GA-β-AHA complex structure by comparing to a previously published G172D mutant precursor in complex with a β-AHA molecule. A hydrolysis mechanism of β-AHA by GA is proposed based on this complex model.
Collapse
Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Damodharan Lakshminarasimhan
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.
| |
Collapse
|
17
|
Chand D, Avinash VS, Yadav Y, Pundle AV, Suresh CG, Ramasamy S. Molecular features of bile salt hydrolases and relevance in human health. Biochim Biophys Acta Gen Subj 2017; 1861:2981-2991. [DOI: 10.1016/j.bbagen.2016.09.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023]
|
18
|
Van Kerckhoven SH, de la Torre FN, Cañas RA, Avila C, Cantón FR, Cánovas FM. Characterization of Three L-Asparaginases from Maritime Pine ( Pinus pinaster Ait.). FRONTIERS IN PLANT SCIENCE 2017; 8:1075. [PMID: 28690619 PMCID: PMC5481357 DOI: 10.3389/fpls.2017.01075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/06/2017] [Indexed: 05/15/2023]
Abstract
Asparaginases (ASPG, EC 3.5.1.1) catalyze the hydrolysis of the amide group of L-asparagine producing L-aspartate and ammonium. Three ASPG, PpASPG1, PpASPG2, and PpASPG3, have been identified in the transcriptome of maritime pine (Pinus pinaster Ait.) that were transiently expressed in Nicotiana benthamiana by agroinfection. The three recombinant proteins were processed in planta to active enzymes and it was found that all mature forms exhibited double activity asparaginase/isoaspartyl dipeptidase but only PpASPG1 was able to catalyze efficiently L-asparagine hydrolysis. PpASPG1 contains a variable region of 77 amino acids that is critical for proteolytic processing of the precursor and is retained in the mature enzyme. Furthermore, the functional analysis of deletion mutants demonstrated that this protein fragment is required for specific recognition of the substrate and favors enzyme stability. Potassium has a limited effect on the activation of maritime pine ASPG what is consistent with the lack of a critical residue essential for interaction of cation. Taken together, the results presented here highlight the specific features of ASPG from conifers when compared to the enzymes from angiosperms.
Collapse
|
19
|
Identification of Small Molecule Compounds for Pharmacological Chaperone Therapy of Aspartylglucosaminuria. Sci Rep 2016; 6:37583. [PMID: 27876883 PMCID: PMC5120323 DOI: 10.1038/srep37583] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/02/2016] [Indexed: 12/16/2022] Open
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder that is caused by genetic deficiency of the enzyme aspartylglucosaminidase (AGA) which is involved in glycoprotein degradation. AGU is a progressive disorder that results in severe mental retardation in early adulthood. No curative therapy is currently available for AGU. We have here characterized the consequences of a novel AGU mutation that results in Thr122Lys exchange in AGA, and compared this mutant form to one carrying the worldwide most common AGU mutation, AGU-Fin. We show that T122K mutated AGA is expressed in normal amounts and localized in lysosomes, but exhibits low AGA activity due to impaired processing of the precursor molecule into subunits. Coexpression of T122K with wildtype AGA results in processing of the precursor into subunits, implicating that the mutation causes a local misfolding that prevents the precursor from becoming processed. Similar data were obtained for the AGU-Fin mutant polypeptide. We have here also identified small chemical compounds that function as chemical or pharmacological chaperones for the mutant AGA. Treatment of patient fibroblasts with these compounds results in increased AGA activity and processing, implicating that these substances may be suitable for chaperone mediated therapy for AGU.
Collapse
|
20
|
Matthews ML, He L, Horning BD, Olson EJ, Correia BE, Yates JR, Dawson PE, Cravatt BF. Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 2016; 9:234-243. [PMID: 28221344 PMCID: PMC5325178 DOI: 10.1038/nchem.2645] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. We show here that "reverse-polarity" (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells, including the pyruvoyl cofactor of S-adenosyl-l-methionine decarboxylase (AMD1), which we find is dynamically controlled by intracellular methionine concentrations, and a heretofore unknown modification – an N-terminally bound glyoxylyl group – in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells. A chemical proteomic strategy is described for the discovery of protein-bound electrophilic groups in human cells and used to characterize dynamic regulation of the pyruvoyl catalytic cofactor in S-adenosyl-l-methionine decarboxylase and to discover an N-terminal glyoxylyl modification on Secernin proteins.
Collapse
Affiliation(s)
- Megan L Matthews
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Lin He
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada
| | - Benjamin D Horning
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Erika J Olson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Bruno E Correia
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - John R Yates
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Philip E Dawson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Benjamin F Cravatt
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| |
Collapse
|
21
|
Trudel M, Yao Q, Qian F. The Role of G-Protein-Coupled Receptor Proteolysis Site Cleavage of Polycystin-1 in Renal Physiology and Polycystic Kidney Disease. Cells 2016; 5:cells5010003. [PMID: 26805887 PMCID: PMC4810088 DOI: 10.3390/cells5010003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
Polycystin-1 (PC1) plays an essential role in renal tubular morphogenesis, and PC1 dysfunction causes human autosomal dominant polycystic kidney disease. A fundamental characteristic of PC1 is post-translational modification via cleavage at the juxtamembrane GPCR proteolysis site (GPS) motif that is part of the larger GAIN domain. Given the considerable biochemical complexity of PC1 molecules generated in vivo by this process, GPS cleavage has several profound implications on the intracellular trafficking and localization in association with their particular function. The critical nature of GPS cleavage is further emphasized by the increasing numbers of PKD1 mutations that significantly affect this cleavage process. The GAIN domain with the GPS motif therefore represents the key structural element with fundamental importance for PC1 and might be polycystic kidney disease’s (PKD) Achilles’ heel in a large spectrum of PKD1 missense mutations. We highlight the central roles of PC1 cleavage for the regulation of its biogenesis, intracellular trafficking and function, as well as its significance in polycystic kidney disease.
Collapse
Affiliation(s)
- Marie Trudel
- Molecular Genetics and Development, Institut de Recherches Cliniques de Montreal, Universite de Montreal, Faculte de Medecine, Montréal, Québec H2W 1R7, Canada.
| | - Qin Yao
- Department of Medicine, Division of Nephrology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Feng Qian
- Department of Medicine, Division of Nephrology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| |
Collapse
|
22
|
Abstract
Proteolytic processing events in adhesion GPCRs. aGPCRs can undergo multiple autoproteolytic (red asterisks) and proteolytic processing events by exogenous proteases (yellow asterisks) that may be involved in signaling events of the receptors. Proteolytic processing is an unusual property of adhesion family G protein-coupled receptors (aGPCRs) that was observed upon their cloning and biochemical characterization.Ever since, much effort has been dedicated to delineate the mechanisms and requirements for cleavage events in the control of aGPCR function. Most notably, all aGPCRs possess a juxtamembrane protein fold, the GPCR autoproteolysis-inducing (GAIN) domain, which operates as an autoprotease for many aGPCR homologs investigated thus far. Analysis of its autoproteolytic reaction, the consequences for receptor fate and function, and the allocation of physiological effects to this peculiar feature of aGPCRs has occupied the experimental agenda of the aGPCR field and shaped our current understanding of the signaling properties and cell biological effects of aGPCRs. Interestingly, individual aGPCRs may undergo additional proteolytic steps, one of them resulting in shedding of the entire ectodomain that is secreted and can function independently. Here, we summarize the current state of knowledge on GAIN domain-mediated and GAIN domain-independent aGPCR cleavage events and their significance for the pharmacological and cellular actions of aGPCRs. Further, we compare and contrast the proteolytic profile of aGPCRs with known signaling routes that are governed through proteolysis of surface molecules such as the Notch and ephrin pathways.
Collapse
|
23
|
Taspase1: a 'misunderstood' protease with translational cancer relevance. Oncogene 2015; 35:3351-64. [PMID: 26657154 DOI: 10.1038/onc.2015.436] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/09/2015] [Accepted: 10/09/2015] [Indexed: 12/20/2022]
Abstract
Proteolysis is not only a critical requirement for life, but the executing enzymes also play important roles in numerous pathological conditions, including cancer. Therefore, targeting proteases is clearly relevant for improving cancer patient care. However, to effectively control proteases, a profound knowledge of their mechanistic function as well as their regulation and downstream signalling in health and disease is required. The highly conserved protease Threonine Aspartase1 (Taspase1) is overexpressed in numerous liquid and solid malignancies and was characterized as a 'non-oncogene addiction' protease. Although Taspase1 was shown to cleave various regulatory proteins in humans as well as leukaemia provoking mixed lineage leukaemia fusions, our knowledge on its detailed functions and the underlying mechanisms contributing to cancer is still incomplete. Despite superficial similarity to type 2 asparaginases as well as Ntn proteases, such as the proteasome, Taspase1-related research so far gives us the picture of a unique protease exhibiting special features. Moreover, neither effective genetic nor chemical inhibitors for this enzyme are available so far, thus hampering not only to further dissect Taspase1's pathobiological functions but also precluding the assessment of its clinical impact. Based on recent insights, we here critically review the current knowledge of Taspase1's structure-function relationship and its mechanistic relevance for tumorigenesis obtained from in vitro and in vivo cancer models. We provide a comprehensive overview of tumour entities for which Taspase1 might be of predictive and therapeutic value, and present the respective experimental evidence. To stimulate progress in the field, a comprehensive overview of Taspase1 targeting approaches is presented, including coverage of Taspase1-related patents. We conclude by discussing future inhibition strategies and relevant challenges, which need to be resolved by the field.
Collapse
|
24
|
Stauber RH, Hahlbrock A, Knauer SK, Wünsch D. Cleaving for growth: threonine aspartase 1--a protease relevant for development and disease. FASEB J 2015; 30:1012-22. [PMID: 26578689 DOI: 10.1096/fj.15-270611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/28/2015] [Indexed: 12/15/2022]
Abstract
From the beginning of life, proteases are key to organismal development comprising morphogenesis, cellular differentiation, and cell growth. Regulated proteolytic activity is essential for the orchestration of multiple developmental pathways, and defects in protease activity can account for multiple disease patterns. The highly conserved protease threonine aspartase 1 is a member of such developmental proteases and critically involved in the regulation of complex processes, including segmental identity, head morphogenesis, spermatogenesis, and proliferation. Additionally, threonine aspartase 1 is overexpressed in numerous liquid as well as in solid malignancies. Although threonine aspartase 1 is able to cleave the master regulator mixed lineage leukemia protein as well as other regulatory proteins in humans, our knowledge of its detailed pathobiological function and the underlying molecular mechanisms contributing to development and disease is still incomplete. Moreover, neither effective genetic nor chemical inhibitors for this enzyme are available so far precluding the detailed dissection of the pathobiological functions of threonine aspartase 1. Here, we review the current knowledge of the structure-function relationship of threonine aspartase 1 and its mechanistic impact on substrate-mediated coordination of the cell cycle and development. We discuss threonine aspartase 1-mediated effects on cellular transformation and conclude by presenting a short overview of recent interference strategies.
Collapse
Affiliation(s)
- Roland H Stauber
- *Molecular and Cellular Oncology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of Mainz, Mainz, Germany; and Institute for Molecular Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Angelina Hahlbrock
- *Molecular and Cellular Oncology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of Mainz, Mainz, Germany; and Institute for Molecular Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Shirley K Knauer
- *Molecular and Cellular Oncology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of Mainz, Mainz, Germany; and Institute for Molecular Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Désirée Wünsch
- *Molecular and Cellular Oncology, Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of Mainz, Mainz, Germany; and Institute for Molecular Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
25
|
Pica A, Chi MC, Chen YY, d'Ischia M, Lin LL, Merlino A. The maturation mechanism of γ-glutamyl transpeptidases: Insights from the crystal structure of a precursor mimic of the enzyme from Bacillus licheniformis and from site-directed mutagenesis studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:195-203. [PMID: 26536828 DOI: 10.1016/j.bbapap.2015.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/20/2023]
Abstract
γ-Glutamyl transpeptidases (γ-GTs) are members of N-terminal nucleophile hydrolase superfamily. They are synthetized as single-chain precursors, which are then cleaved to form mature enzymes. Basic aspects of autocatalytic processing of these pro-enzymes are still unknown. Here we describe the X-ray structure of the precursor mimic of Bacillus licheniformis γ-GT (BlGT), obtained by mutating catalytically important threonine to alanine (T399A-BlGT), and report results of autoprocessing of mutants of His401, Thr415, Thr417, Glu419 and Arg571. Data suggest that Thr417 is in a competent position to activate the catalytic threonine (Thr399) for nucleophilic attack of the scissile peptide bond and that Thr415 plays a major role in assisting the process. On the basis of these new structural results, a possible mechanism of autoprocessing is proposed. This mechanism, which guesses the existence of a six-membered transition state involving one carbonyl and two hydroxyl groups, is in agreement with all the available experimental data collected on γ-GTs from different species and with our new Ala-scanning mutagenesis data.
Collapse
Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Marco d'Ischia
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy.
| |
Collapse
|
26
|
Bastiaansen KC, van Ulsen P, Wijtmans M, Bitter W, Llamas MA. Self-cleavage of the Pseudomonas aeruginosa Cell-surface Signaling Anti-sigma Factor FoxR Occurs through an N-O Acyl Rearrangement. J Biol Chem 2015; 290:12237-46. [PMID: 25809487 DOI: 10.1074/jbc.m115.643098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/06/2022] Open
Abstract
The Fox system of Pseudomonas aeruginosa is a cell-surface signaling (CSS) pathway employed by the bacterium to sense and respond to the presence of the heterologous siderophore ferrioxamine in the environment. This regulatory pathway controls the transcription of the foxA ferrioxamine receptor gene through the extracytoplasmic function sigma factor σ(FoxI). In the absence of ferrioxamine, the activity of σ(FoxI) is inhibited by the transmembrane anti-sigma factor FoxR. Upon binding of ferrioxamine by the FoxA receptor, FoxR is processed by a complex proteolytic cascade leading to the release and activation of σ(FoxI). Interestingly, we have recently shown that FoxR undergoes self-cleavage between the periplasmic Gly-191 and Thr-192 residues independent of the perception of ferrioxamine. This autoproteolytic event, which is widespread among CSS anti-sigma factors, produces two distinct domains that interact and function together to transduce the presence of the signal. In this work, we provide evidence that the self-cleavage of FoxR is not an enzyme-dependent process but is induced by an N-O acyl rearrangement. Mutation analysis showed that the nucleophilic side chain of the Thr-192 residue at +1 of the cleavage site is required for an attack on the preceding Gly-191, after which the resulting ester bond is likely hydrolyzed. Because the cleavage site is well preserved and the hydrolysis of periplasmic CSS anti-sigma factors is widely observed, we hypothesize that cleavage via an N-O acyl rearrangement is a conserved feature of these proteins.
Collapse
Affiliation(s)
- Karlijn C Bastiaansen
- From the Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada E-18008, Spain and Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - Peter van Ulsen
- Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - María A Llamas
- From the Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada E-18008, Spain and
| |
Collapse
|
27
|
Sui L, Lakshminarasimhan D, Pande S, Guo HC. Structural basis of a point mutation that causes the genetic disease aspartylglucosaminuria. Structure 2014; 22:1855-1861. [PMID: 25456816 DOI: 10.1016/j.str.2014.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/30/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disease caused by a metabolic disorder of lysosomes to digest Asn-linked glycoproteins. The specific enzyme linked to AGU is a lysosomal hydrolase called glycosylasparaginase. Crystallographic studies revealed that a surface loop blocks the catalytic center of the mature hydrolase. Autoproteolysis is therefore required to remove this P loop and open up the hydrolase center. Nonetheless, AGU mutations result in misprocessing of their precursors and are deficient in hydrolyzing glycoasparagines. To understand the catalytic and structural consequences of AGU mutations, we have characterized two AGU models, one corresponding to a Finnish allele and the other found in a Canadian family. We also report a 2.1 Å resolution structure of the latter AGU model. The current crystallographic study provides a high-resolution structure of an AGU mutant. It reveals substantial conformation changes at the defective autocleavage site of the AGU mutant, which is trapped as an inactive precursor.
Collapse
Affiliation(s)
- Lufei Sui
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Damodharan Lakshminarasimhan
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.
| |
Collapse
|
28
|
Lizak C, Gerber S, Michaud G, Schubert M, Fan YY, Bucher M, Darbre T, Aebi M, Reymond JL, Locher KP. Unexpected reactivity and mechanism of carboxamide activation in bacterial N-linked protein glycosylation. Nat Commun 2014; 4:2627. [PMID: 24149797 DOI: 10.1038/ncomms3627] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/16/2013] [Indexed: 11/09/2022] Open
Abstract
The initial glycan transfer in asparagine-linked protein glycosylation is catalysed by the integral membrane enzyme oligosaccharyltransferase (OST). Here we study the mechanism of the bacterial PglB protein, a single-subunit OST, using chemically synthesized acceptor peptide analogues. We find that PglB can glycosylate not only asparagine but also glutamine, homoserine and the hydroxamate Asp(NHOH), although at much lower rates. In contrast, N-methylated asparagine or 2,4-diaminobutanoic acid (Dab) are not glycosylated. We find that of the various peptide analogues, only asparagine- or Dab-containing peptides bind tightly to PglB. Glycopeptide products are unable to bind, providing the driving force of product release. We find no suitably positioned residues near the active site of PglB that can activate the acceptor asparagine by deprotonation, making a general base mechanism unlikely and leaving carboxamide twisting as the most likely mechanistic proposal for asparagine activation.
Collapse
Affiliation(s)
- Christian Lizak
- 1] Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland [2]
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Mihaylov TT, Parac-Vogt TN, Pierloot K. A computational study of the glycylserine hydrolysis at physiological pH: a zwitterionic versus anionic mechanism. Org Biomol Chem 2014; 12:1395-404. [PMID: 24430931 DOI: 10.1039/c3ob42372g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The hydrolysis of GlySer at physiological pH was investigated by modeling the most feasible reaction mechanisms in aqueous phase at the MP2/6-311+(2df,2p)//SMD-M06/6-311+(2df,2p) level of the theory. To refine the energies of the most relevant transition states along the reaction paths the cluster-continuum concept was adopted. The hydrolytic process could proceed through two competitive mechanisms involving either the zwitterionic or the anionic form of GlySer. The calculations suggest that at physiological pH the actual mechanism is most probably mixed, anionic-zwitterionic. In this reaction scheme the first stage of N→O acyl transfer involves the anionic form whereas the second stage, during which the resultant ester is hydrolyzed, most likely involves the zwitterionic ester form of GlySer. The energy requirement for the first reaction stage is estimated to be slightly lower than for the second one. The calculated activation parameters (e.g. ΔG(#) = 27.8 kcal mol(-1)) for the nucleophilic addition of a water molecule to the ester carbonyl group of the zwitterionic ester are in good agreement with the experimentally determined values at pD 7.4 (ΔG(#) = 28.7 kcal mol(-1)).
Collapse
Affiliation(s)
- Tzvetan T Mihaylov
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001, Leuven, Belgium.
| | | | | |
Collapse
|
30
|
Mihaylov TT, Parac-Vogt TN, Pierloot K. A Mechanistic Study of the Spontaneous Hydrolysis of Glycylserine as the Simplest Model for Protein Self-Cleavage. Chemistry 2013; 20:456-66. [DOI: 10.1002/chem.201303564] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Indexed: 11/05/2022]
|
31
|
Su Y, Karamitros CS, Nomme J, McSorley T, Konrad M, Lavie A. Free glycine accelerates the autoproteolytic activation of human asparaginase. ACTA ACUST UNITED AC 2013; 20:533-40. [PMID: 23601642 DOI: 10.1016/j.chembiol.2013.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/25/2013] [Accepted: 03/04/2013] [Indexed: 12/21/2022]
Abstract
Human asparaginase 3 (hASNase3), which belongs to the N-terminal nucleophile hydrolase superfamily, is synthesized as a single polypeptide that is devoid of asparaginase activity. Intramolecular autoproteolytic processing releases the amino group of Thr168, a moiety required for catalyzing asparagine hydrolysis. Recombinant hASNase3 purifies as the uncleaved, asparaginase-inactive form and undergoes self-cleavage to the active form at a very slow rate. Here, we show that the free amino acid glycine selectively acts to accelerate hASNase3 cleavage both in vitro and in human cells. Other small amino acids such as alanine, serine, or the substrate asparagine are not capable of promoting autoproteolysis. Crystal structures of hASNase3 in complex with glycine in the uncleaved and cleaved enzyme states reveal the mechanism of glycine-accelerated posttranslational processing and explain why no other amino acid can substitute for glycine.
Collapse
Affiliation(s)
- Ying Su
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | | | | | | | | |
Collapse
|
32
|
Nayak S, Kundu SC. Sericin-carboxymethyl cellulose porous matrices as cellular wound dressing material. J Biomed Mater Res A 2013; 102:1928-40. [PMID: 23853114 DOI: 10.1002/jbm.a.34865] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/22/2013] [Accepted: 06/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Sunita Nayak
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 7213 02 West Bengal India
| | - S. C. Kundu
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 7213 02 West Bengal India
| |
Collapse
|
33
|
Dearden AK, Callahan B, Roey PV, Li Z, Kumar U, Belfort M, Nayak SK. A conserved threonine spring-loads precursor for intein splicing. Protein Sci 2013; 22:557-63. [PMID: 23423655 DOI: 10.1002/pro.2236] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 11/12/2022]
Abstract
Protein splicing is an autocatalytic process where an "intein" self-cleaves from a precursor and ligates the flanking N- and C-"extein" polypeptides. Inteins occur in all domains of life and have myriad uses in biotechnology. Although the reaction steps of protein splicing are known, mechanistic details remain incomplete, particularly the initial peptide rearrangement at the N-terminal extein/intein junction. Recently, we proposed that this transformation, an N-S acyl shift, is accelerated by a localized conformational strain, between the intein's catalytic cysteine (Cys1) and the neighboring glycine (Gly-1) in the N-extein. That proposal was based on the crystal structure of a catalytically competent trapped precursor. Here, we define the structural origins and mechanistic relevance of the conformational strain using a combination of quantum mechanical simulations, mutational analysis, and X-ray crystallography. Our results implicate a conserved, but largely unstudied, threonine residue of the Ssp DnaE intein (Thr69) as the mediator of conformational strain through hydrogen bonding. Further, the strain imposed by this residue is shown to position the splice junction in a manner that enhances the rate of the N-S acyl shift substantially. Taken together, our results not only provide fundamental understanding of the control of the first step of protein splicing but also have important implications in various biotechnological applications that require precursor manipulation.
Collapse
Affiliation(s)
- Albert K Dearden
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Chaipayang S, Heamatorn N, Keha L, Daduang S, Songsiriritthigul C, Swatsitang P, Dhiravisit A, Thammasirirak S. Purification and Characterization of Ovotransferrin from Crocodylus siamensis. Protein J 2013; 32:89-96. [DOI: 10.1007/s10930-012-9461-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
35
|
Heck T, Geueke B, Kohler HPE. Bacterialβ-Aminopeptidases: Structural Insights and Applications for Biocatalysis. Chem Biodivers 2012; 9:2388-409. [DOI: 10.1002/cbdv.201200305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Indexed: 12/12/2022]
|
36
|
Li W, Cantor JR, Yogesha S, Yang S, Chantranupong L, Liu JQ, Agnello G, Georgiou G, Stone EM, Zhang Y. Uncoupling intramolecular processing and substrate hydrolysis in the N-terminal nucleophile hydrolase hASRGL1 by circular permutation. ACS Chem Biol 2012; 7:1840-7. [PMID: 22891768 PMCID: PMC3514461 DOI: 10.1021/cb300232n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The human asparaginase-like protein 1 (hASRGL1) catalyzes the hydrolysis of l-asparagine and isoaspartyl-dipeptides. As an N-terminal nucleophile (Ntn) hydrolase superfamily member, the active form of hASRGL1 is generated by an intramolecular cleavage step with Thr168 as the catalytic residue. However, in vitro, autoprocessing is incomplete (~50%), fettering the biophysical characterization of hASRGL1. We circumvented this obstacle by constructing a circularly permuted hASRGL1 that uncoupled the autoprocessing reaction, allowing us to kinetically and structurally characterize this enzyme and the precursor-like hASRGL1-Thr168Ala variant. Crystallographic and biochemical evidence suggest an activation mechanism where a torsional restraint on the Thr168 side chain helps drive the intramolecular processing reaction. Cleavage and formation of the active site releases the torsional restriction on Thr168, which is facilitated by a small conserved Gly-rich loop near the active site that allows the conformational changes necessary for activation.
Collapse
Affiliation(s)
- Wenzong Li
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
| | - Jason R Cantor
- Departments of Biomedical and Chemical Engineering, University of Texas, Austin, Texas 78712
| | - S.D. Yogesha
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
| | - Shirley Yang
- Departments of Biomedical and Chemical Engineering, University of Texas, Austin, Texas 78712
| | - Lynne Chantranupong
- Departments of Biomedical and Chemical Engineering, University of Texas, Austin, Texas 78712
| | - June Qingxia Liu
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
| | - Giulia Agnello
- Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - George Georgiou
- Departments of Biomedical and Chemical Engineering, University of Texas, Austin, Texas 78712
,Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712
,Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Everett M Stone
- Departments of Biomedical and Chemical Engineering, University of Texas, Austin, Texas 78712
,Address correspondence to: Yan Zhang: 1 University Station A5300, Austin, TX 78712. Phone: (512)-471-8645. Fax: 512-471-9469. or Everett Stone: 1 University Station C0800, Austin, TX 78712. Phone: (512) 512-232-4105. stonesci@.utexas.edu
| | - Yan Zhang
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
,Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
,Address correspondence to: Yan Zhang: 1 University Station A5300, Austin, TX 78712. Phone: (512)-471-8645. Fax: 512-471-9469. or Everett Stone: 1 University Station C0800, Austin, TX 78712. Phone: (512) 512-232-4105. stonesci@.utexas.edu
| |
Collapse
|
37
|
Autoproteolytic and Catalytic Mechanisms for the β-Aminopeptidase BapA—A Member of the Ntn Hydrolase Family. Structure 2012; 20:1850-60. [DOI: 10.1016/j.str.2012.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/14/2012] [Accepted: 07/15/2012] [Indexed: 11/23/2022]
|
38
|
Chi MC, Chen YY, Lo HF, Lin LL. Experimental evidence for the involvement of amino acid residue Glu398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase. FEBS Open Bio 2012; 2:298-304. [PMID: 23772362 PMCID: PMC3678132 DOI: 10.1016/j.fob.2012.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 09/25/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
The role of glutamate 398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase (BlGGT) was explored by site-directed mutagenesis. This glutamate was substituted by either alanine, aspartate, arginine or glutamine and the expressed mutant enzymes were purified to apparent homogeneity with metal-affinity chromatography. SDS–PAGE analysis showed that E398A, E398D and E398K were unable to process themselves into a large and a small subunit. However, E398Q was not only able to process itself, but also had a catalytic activity comparable to that of BlGGT. As compared with the wild-type enzyme, no significant change in circular dichroism spectra was observed for the mutant proteins. Thermal unfolding of BlGGT, E398A, E398D, E398K and E398Q followed the two-state unfolding process with a transition point (Tm) of 47.7–69.4 °C. Tryptophan fluorescence spectra of the mutant enzymes were different from the wild-type protein in terms of fluorescence intensity. Native BlGGT started to unfold beyond ∼1.92 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl]0.5, N–U, at 3.07 M equivalent to free energy change (ΔGN−UH2O) of 14.53 kcal/mol for the N → U process, whereas the denaturation midpoints for the mutant enzymes were 1.31–2.99 M equivalent to ΔGN−UH2O of 3.29–12.05 kcal/mol. Taken together, these results strongly suggest that the explored glutamate residue is indeed important for the autocatalytic processing of BlGGT.
Collapse
Affiliation(s)
- Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Taiwan
| | | | | | | |
Collapse
|
39
|
Buller AR, Labonte JW, Freeman MF, Wright NT, Schildbach JF, Townsend CA. Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis. J Mol Biol 2012; 422:508-18. [PMID: 22706025 PMCID: PMC3428426 DOI: 10.1016/j.jmb.2012.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/02/2012] [Accepted: 06/08/2012] [Indexed: 11/01/2022]
Abstract
cis-Autoproteolysis is a post-translational modification necessary for the function of ThnT, an enzyme involved in the biosynthesis of the β-lactam antibiotic thienamycin. This modification generates an N-terminal threonine nucleophile that is used to hydrolyze the pantetheinyl moiety of its natural substrate. We determined the crystal structure of autoactivated ThnT to 1.8Å through X-ray crystallography. Comparison to a mutationally inactivated precursor structure revealed several large conformational rearrangements near the active site. To probe the relevance of these transitions, we designed a pantetheine-like chloromethyl ketone inactivator and co-crystallized it with ThnT. Although this class of inhibitor has been in use for several decades, the mode of inactivation had not been determined for an enzyme that uses an N-terminal nucleophile. The co-crystal structure revealed the chloromethyl ketone bound to the N-terminal nucleophile of ThnT through an ether linkage, and analysis suggests inactivation through a direct displacement mechanism. More importantly, this inactivated complex shows that three regions of ThnT that are critical to the formation of the substrate binding pocket undergo rearrangement upon autoproteolysis. Comparison of ThnT with other autoproteolytic enzymes of disparate evolutionary lineage revealed a high degree of similarity within the proenzyme active site, reflecting shared chemical constraints. However, after autoproteolysis, many enzymes, like ThnT, are observed to rearrange in order to accommodate their specific substrate. We propose that this is a general phenomenon, whereby autoprocessing systems with shared chemistry may possess similar structural features that dissipate upon rearrangement into a mature state.
Collapse
Affiliation(s)
- Andrew R. Buller
- Department of Biophysics, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jason W. Labonte
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael F. Freeman
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nathan T. Wright
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joel F. Schildbach
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Craig A. Townsend
- Department of Biophysics, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
40
|
Nomme J, Su Y, Konrad M, Lavie A. Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis. Biochemistry 2012; 51:6816-26. [PMID: 22861376 DOI: 10.1021/bi300870g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asparaginases catalyze the hydrolysis of the amino acid asparagine to aspartate and ammonia. Bacterial asparaginases are used in cancer chemotherapy to deplete asparagine from the blood, because several hematological malignancies depend on extracellular asparagine for growth. To avoid the immune response against the bacterial enzymes, it would be beneficial to replace them with human asparaginases. However, unlike the bacterial asparaginases, the human enzymes have a millimolar K(m) value for asparagine, making them inefficient in depleting the amino acid from blood. To facilitate the development of human variants suitable for therapeutic use, we determined the structure of human l-asparaginase (hASNase3). This asparaginase is an N-terminal nucleophile (Ntn) family member that requires autocleavage between Gly167 and Thr168 to become catalytically competent. For most Ntn hydrolases, this autoproteolytic activation occurs efficiently. In contrast, hASNas3 is relatively stable in its uncleaved state, and this allowed us to observe the structure of the enzyme prior to cleavage. To determine the structure of the cleaved state, we exploited our discovery that the free amino acid glycine promotes complete cleavage of hASNase3. Both enzyme states were elucidated in the absence and presence of the product aspartate. Together, these structures provide insight into the conformational changes required for cleavage and the precise enzyme-substrate interactions. The new understanding of hASNase3 will serve to guide the design of variants that possess a decreased K(m) value for asparagine, making the human enzyme a suitable replacement for the bacterial asparaginases in cancer therapy.
Collapse
Affiliation(s)
- Julian Nomme
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | | | | |
Collapse
|
41
|
Insights into cis-autoproteolysis reveal a reactive state formed through conformational rearrangement. Proc Natl Acad Sci U S A 2012; 109:2308-13. [PMID: 22308359 DOI: 10.1073/pnas.1113633109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ThnT is a pantetheine hydrolase from the DmpA/OAT superfamily involved in the biosynthesis of the β-lactam antibiotic thienamycin. We performed a structural and mechanistic investigation into the cis-autoproteolytic activation of ThnT, a process that has not previously been subject to analysis within this superfamily of enzymes. Removal of the γ-methyl of the threonine nucleophile resulted in a rate deceleration that we attribute to a reduction in the population of the reactive rotamer. This phenomenon is broadly applicable and constitutes a rationale for the evolutionary selection of threonine nucleophiles in autoproteolytic systems. Conservative substitution of the nucleophile (T282C) allowed determination of a 1.6-Å proenzyme ThnT crystal structure, which revealed a level of structural flexibility not previously observed within an autoprocessing active site. We assigned the major conformer as a nonreactive state that is unable to populate a reactive rotamer. Our analysis shows the system is activated by a structural rearrangement that places the scissile amide into an oxyanion hole and forces the nucleophilic residue into a forbidden region of Ramachandran space. We propose that conformational strain may drive autoprocessing through the destabilization of nonproductive states. Comparison of our data with previous reports uncovered evidence that many inactivated structures display nonreactive conformations. For penicillin and cephalosporin acylases, this discrepancy between structure and function may be resolved by invoking the presence of a hidden conformational state, similar to that reported here for ThnT.
Collapse
|
42
|
Dembek M, Reynolds CB, Fairweather NF. Clostridium difficile cell wall protein CwpV undergoes enzyme-independent intramolecular autoproteolysis. J Biol Chem 2012; 287:1538-44. [PMID: 22128177 PMCID: PMC3256870 DOI: 10.1074/jbc.m111.302463] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/15/2011] [Indexed: 02/04/2023] Open
Abstract
Clostridium difficile infection is a leading cause of antibiotic-associated diarrhea, placing considerable economic pressure on healthcare systems and resulting in significant morbidity and mortality. The pathogen produces a proteinaceous array on its cell surface known as the S-layer, consisting primarily of the major S-layer protein SlpA and a family of SlpA homologs. CwpV is the largest member of this family and is expressed in a phase-variable manner. The protein is post-translationally processed into two fragments that form a noncovalent, heterodimeric complex. To date, no specific proteases capable of cleaving CwpV have been identified. Using site-directed mutagenesis we show that CwpV undergoes intramolecular autoproteolysis, most likely facilitated by a N-O acyl shift, with Thr-413 acting as the source of a nucleophile driving this rearrangement. We demonstrate that neighboring residues are also important for correct processing of CwpV. Based on protein structural predictions and analogy to the glycosylasparaginase family of proteins, it appears likely that these residues play key roles in determining the correct protein fold and interact directly with Thr-413 to promote nucleophilic attack. Furthermore, using a cell-free protein synthesis assay we show that CwpV maturation requires neither cofactors nor auxiliary enzymes.
Collapse
Affiliation(s)
- Marcin Dembek
- From the Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Catherine B. Reynolds
- From the Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Neil F. Fairweather
- From the Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
43
|
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A 2011; 109:449-53. [PMID: 22198840 DOI: 10.1073/pnas.1107115108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The planarity of peptide bonds is an assumption that underlies decades of theoretical modeling of proteins. Peptide bonds strongly deviating from planarity are considered very rare features of protein structure that occur for functional reasons. Here, empirical analyses of atomic-resolution protein structures reveal that trans peptide groups can vary by more than 25° from planarity and that the true extent of nonplanarity is underestimated even in 1.2 Å resolution structures. Analyses as a function of the ϕ,ψ-backbone dihedral angles show that the expected value deviates by ± 8° from planar as a systematic function of conformation, but that the large majority of variation in planarity depends on tertiary effects. Furthermore, we show that those peptide bonds in proteins that are most nonplanar, deviating by over 20° from planarity, are not strongly associated with active sites. Instead, highly nonplanar peptides are simply integral components of protein structure related to local and tertiary structural features that tend to be conserved among homologs. To account for the systematic ϕ,ψ-dependent component of nonplanarity, we present a conformation-dependent library that can be used in crystallographic refinement and predictive protein modeling.
Collapse
|
44
|
Chen DY, Lee Y, Van Tine BA, Searleman AC, Westergard TD, Liu H, Tu HC, Takeda S, Dong Y, Piwnica-Worms DR, Oh KJ, Korsmeyer SJ, Hermone A, Gussio R, Shoemaker RH, Cheng EHY, Hsieh JJD. A pharmacologic inhibitor of the protease Taspase1 effectively inhibits breast and brain tumor growth. Cancer Res 2011; 72:736-46. [PMID: 22166309 DOI: 10.1158/0008-5472.can-11-2584] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The threonine endopeptidase Taspase1 has a critical role in cancer cell proliferation and apoptosis. In this study, we developed and evaluated small molecule inhibitors of Taspase1 as a new candidate class of therapeutic modalities. Genetic deletion of Taspase1 in the mouse produced no overt deficiencies, suggesting the possibility of a wide therapeutic index for use of Taspase1 inhibitors in cancers. We defined the peptidyl motifs recognized by Taspase1 and conducted a cell-based dual-fluorescent proteolytic screen of the National Cancer Institute diversity library to identify Taspase1 inhibitors (TASPIN). On the basis of secondary and tertiary screens the 4-[(4-arsonophenyl)methyl]phenyl] arsonic acid NSC48300 was determined to be the most specific active compound. Structure-activity relationship studies indicated a crucial role for the arsenic acid moiety in mediating Taspase1 inhibition. Additional fluorescence resonance energy transfer-based kinetic analysis characterized NSC48300 as a reversible, noncompetitive inhibitor of Taspase1 (K(i) = 4.22 μmol/L). In the MMTV-neu mouse model of breast cancer and the U251 xenograft model of brain cancer, NSC48300 produced effective tumor growth inhibition. Our results offer an initial preclinical proof-of-concept to develop TASPINs for cancer therapy.
Collapse
Affiliation(s)
- David Y Chen
- Department of Medicine, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, Missouri, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Witte MD, van der Marel GA, Aerts JMFG, Overkleeft HS. Irreversible inhibitors and activity-based probes as research tools in chemical glycobiology. Org Biomol Chem 2011; 9:5908-26. [DOI: 10.1039/c1ob05531c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
46
|
Chang HP, Liang WC, Lyu RC, Chi MC, Wang TF, Su KL, Hung HC, Lin LL. Effects of C-terminal truncation on autocatalytic processing of Bacillus licheniformis gamma-glutamyl transpeptidase. BIOCHEMISTRY (MOSCOW) 2010; 75:919-29. [PMID: 20673217 DOI: 10.1134/s0006297910070151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of the C-terminal region of Bacillus licheniformis gamma-glutamyl transpeptidase (BlGGT) was investigated by deletion analysis. Seven C-terminally truncated BlGGTs lacking 581-585, 577-585, 576-585, 566-585, 558-585, 523-585, and 479-585 amino acids, respectively, were generated by site-directed mutagenesis. Deletion of the last nine amino acids had no appreciable effect on the autocatalytic processing of the enzyme, and the engineered protein was active towards the synthetic substrate L-gamma-glutamyl-p-nitroanilide. However, a further deletion to Val576 impaired the autocatalytic processing. In vitro maturation experiments showed that the truncated BlGGT precursors, pro-Delta(576-585), pro-Delta(566-585), and pro-Delta(558-585), could partially precede a time-dependent autocatalytic process to generate the L- and S-subunits, and these proteins showed a dramatic decrease in catalytic activity with respect to the wild-type enzyme. The parental enzyme (BlGGT-4aa) and BlGGT were unfolded biphasically by guanidine hydrochloride (GdnCl), but Delta(577-585), Delta(576-585), Delta(566-585), Delta(558-585), Delta(523-585), and Delta(479-585) followed a monophasic unfolding process and showed a sequential reduction in the GdnCl concentration corresponding to half effect and DeltaG(0) for the unfolding. BlGGT-4aa and BlGGT sedimented at ~4.85 S and had a heterodimeric structure of approximately 65.23 kDa in solution, and this structure was conserved in all of the truncated proteins. The frictional ratio (f/f(o)) of BlGGT-4aa, BlGGT, Delta(581-585), and Delta(577-585) was 1.58, 1.57, 1.46, and 1.39, respectively, whereas the remaining enzymes existed exclusively as precursor form with a ratio of less than 1.18. Taken together, these results provide direct evidence for the functional role of the C-terminal region in the autocatalytic processing of BlGGT.
Collapse
Affiliation(s)
- Hui-Ping Chang
- Department of Applied Chemistry, National Chiayi University, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Wang Y, Guo HC. Crystallographic snapshot of glycosylasparaginase precursor poised for autoprocessing. J Mol Biol 2010; 403:120-130. [PMID: 20800597 DOI: 10.1016/j.jmb.2010.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/19/2010] [Accepted: 08/19/2010] [Indexed: 10/19/2022]
Abstract
Glycosylasparaginase belongs to a family of N-terminal nucleophile hydrolases that autoproteolytically generate their mature enzymes from single-chain protein precursors. Previously, based on a precursor structure paused at pre-autoproteolysis stage by a reversible inhibitor (glycine), we proposed a mechanism of intramolecular autoproteolysis. A key structural feature, a highly strained conformation at the scissile peptide bond, had been identified and was hypothesized to be critical for driving autoproteolysis through an N-O acyl shift. To examine this "twist-and-break" hypothesis, we report here a 1. 9-Å-resolution structure of an autoproteolysis-active precursor (a T152C mutant) that is free of inhibitor or ligand and is poised to undergo autoproteolysis. The current crystallographic study has provided direct evidence for the natural conformation of the glycosylasparaginase autocatalytic site without influence from any inhibitor or ligand. This finding has confirmed our previous proposal that conformational strain is an intrinsic feature of an active precursor.
Collapse
Affiliation(s)
- Yeming Wang
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2526, USA
| | - Hwai-Chen Guo
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2526, USA.
| |
Collapse
|
48
|
Bokhove M, Yoshida H, Hensgens CMH, van der Laan JM, Sutherland JD, Dijkstra BW. Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme. Structure 2010; 18:301-8. [PMID: 20223213 DOI: 10.1016/j.str.2010.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/06/2010] [Accepted: 01/18/2010] [Indexed: 10/19/2022]
Abstract
Penicillium chrysogenum Acyl coenzyme A:isopenicillin N acyltransferase (AT) performs the last step in the biosynthesis of hydrophobic penicillins, exchanging the hydrophilic side chain of a precursor for various hydrophobic side chains. Like other N-terminal nucleophile hydrolases AT is produced as an inactive precursor that matures upon posttranslational cleavage. The structure of a Cys103Ala precursor mutant shows that maturation is autoproteolytic, initiated by Cys103 cleaving its preceding peptide bond. The crystal structure of the mature enzyme shows that after autoproteolysis residues 92-102 fold outwards, exposing a buried pocket. This pocket is structurally and chemically flexible and can accommodate substrates of different size and polarity. Modeling of a substrate-bound state indicates the residues important for catalysis. Comparison of the proposed autoproteolytic and substrate hydrolysis mechanisms shows that in both events the same catalytic residues are used, but that they perform different roles in catalysis.
Collapse
Affiliation(s)
- Marcel Bokhove
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, Groningen, Netherlands
| | | | | | | | | | | |
Collapse
|
49
|
Rafiqi M, Gan PH, Ravensdale M, Lawrence GJ, Ellis JG, Jones DA, Hardham AR, Dodds PN. Internalization of flax rust avirulence proteins into flax and tobacco cells can occur in the absence of the pathogen. THE PLANT CELL 2010; 22:2017-32. [PMID: 20525849 PMCID: PMC2910983 DOI: 10.1105/tpc.109.072983] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 04/16/2010] [Accepted: 05/20/2010] [Indexed: 05/18/2023]
Abstract
Translocation of pathogen effector proteins into the host cell cytoplasm is a key determinant for the pathogenicity of many bacterial and oomycete plant pathogens. A number of secreted fungal avirulence (Avr) proteins are also inferred to be delivered into host cells, based on their intracellular recognition by host resistance proteins, including those of flax rust (Melampsora lini). Here, we show by immunolocalization that the flax rust AvrM protein is secreted from haustoria during infection and accumulates in the haustorial wall. Five days after inoculation, the AvrM protein was also detected within the cytoplasm of a proportion of plant cells containing haustoria, confirming its delivery into host cells during infection. Transient expression of secreted AvrL567 and AvrM proteins fused to cerulean fluorescent protein in tobacco (Nicotiana tabacum) and flax cells resulted in intracellular accumulation of the fusion proteins. The rust Avr protein signal peptides were functional in plants and efficiently directed fused cerulean into the secretory pathway. Thus, these secreted effectors are internalized into the plant cell cytosol in the absence of the pathogen, suggesting that they do not require a pathogen-encoded transport mechanism. Uptake of these proteins is dependent on signals in their N-terminal regions, but the primary sequence features of these uptake regions are not conserved between different rust effectors.
Collapse
Affiliation(s)
- Maryam Rafiqi
- Division of Plant Science, Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Pamela H.P. Gan
- Division of Plant Science, Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Michael Ravensdale
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - Gregory J. Lawrence
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - Jeffrey G. Ellis
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - David A. Jones
- Division of Plant Science, Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Adrienne R. Hardham
- Division of Plant Science, Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Peter N. Dodds
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
50
|
Branched intermediate formation stimulates peptide bond cleavage in protein splicing. Nat Chem Biol 2010; 6:527-33. [PMID: 20495572 PMCID: PMC2889191 DOI: 10.1038/nchembio.371] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/01/2010] [Indexed: 11/12/2022]
Abstract
Protein splicing is a posttranslational modification in which an intein domain excises itself out of a host protein. Here, we investigate how the steps in the splicing process are coordinated so as to maximize the production of the final splice products and minimize the generation of undesired cleavage products. Our approach has been to prepare a branched intermediate (and analogs thereof) of the Mxe GyrA intein using protein semi-synthesis. Kinetic analysis of these molecules indicates that the high fidelity of this protein splicing reaction results from the penultimate step in the process (intein-succinimide formation) being rate-limiting. NMR experiments indicate that formation of the branched intermediate affects the local structure around the amide bond cleaved during succinimide formation. We propose that this structural change reflects a re-organization of the catalytic apparatus to accelerate succinimide formation at the C-terminal splice junction.
Collapse
|