1
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Hupfeld E, Schlee S, Wurm JP, Rajendran C, Yehorova D, Vos E, Ravindra Raju D, Kamerlin SCL, Sprangers R, Sterner R. Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα) 8-Barrel Enzyme of Histidine Biosynthesis HisF. JACS AU 2024; 4:3258-3276. [PMID: 39211614 PMCID: PMC11350729 DOI: 10.1021/jacsau.4c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The overall significance of loop motions for enzymatic activity is generally accepted. However, it has largely remained unclear whether and how such motions can control different steps of catalysis. We have studied this problem on the example of the mobile active site β1α1-loop (loop1) of the (βα)8-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 variants containing single mutations of conserved amino acids showed drastically reduced rates for the turnover of the substrates N'-[(5'-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) and ammonia to the products imidazole glycerol phosphate (ImGP) and 5-aminoimidazole-4-carboxamide-ribotide (AICAR). A comprehensive mechanistic analysis including stopped-flow kinetics, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations detected three conformations of loop1 (open, detached, closed) whose populations differed between wild-type HisF and functionally affected loop1 variants. Transient stopped-flow kinetic experiments demonstrated that wt-HisF binds PrFAR by an induced-fit mechanism whereas catalytically impaired loop1 variants bind PrFAR by a simple two-state mechanism. Our findings suggest that PrFAR-induced formation of the closed conformation of loop1 brings active site residues in a productive orientation for chemical turnover, which we show to be the rate-limiting step of HisF catalysis. After the cyclase reaction, the closed loop conformation is destabilized, which favors the formation of detached and open conformations and hence facilitates the release of the products ImGP and AICAR. Our data demonstrate how different conformations of active site loops contribute to different catalytic steps, a finding that is presumably of broad relevance for the reaction mechanisms of (βα)8-barrel enzymes and beyond.
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Affiliation(s)
- Enrico Hupfeld
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Dariia Yehorova
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Eva Vos
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Dinesh Ravindra Raju
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Shina Caroline Lynn Kamerlin
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Remco Sprangers
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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2
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Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
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Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
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3
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Lenferink WB, Bakken LR, Jetten MSM, van Kessel MAHJ, Lücker S. Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification. SCIENCE ADVANCES 2024; 10:eadl3587. [PMID: 38848370 PMCID: PMC11160463 DOI: 10.1126/sciadv.adl3587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.
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Affiliation(s)
- Wouter B. Lenferink
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
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4
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Klem H, Alegre-Requena JV, Paton RS. Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase. ACS Catal 2023; 13:16249-16257. [PMID: 38125975 PMCID: PMC10729027 DOI: 10.1021/acscatal.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.
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Affiliation(s)
- Heidi Klem
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Juan V Alegre-Requena
- Dpto.de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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5
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Ballut L, Violot S, Kumar S, Aghajari N, Balaram H. GMP Synthetase: Allostery, Structure, and Function. Biomolecules 2023; 13:1379. [PMID: 37759779 PMCID: PMC10526850 DOI: 10.3390/biom13091379] [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: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Glutamine amidotransferases (GATs) catalyze the hydrolysis of glutamine and transfer the generated ammonia to diverse metabolites. The two catalytic activities, glutaminolysis and the subsequent amination of the acceptor substrate, happen in two distinct catalytic pockets connected by a channel that facilitates the movement of ammonia. The de novo pathway for the synthesis of guanosine monophosphate (GMP) from xanthosine monophosphate (XMP) is enabled by the GAT GMP synthetase (GMPS). In most available crystal structures of GATs, the ammonia channel is evident in their native state or upon ligand binding, providing molecular details of the conduit. In addition, conformational changes that enable the coordination of the two catalytic chemistries are also informed by the available structures. In contrast, despite the first structure of a GMPS being published in 1996, the understanding of catalysis in the acceptor domain and inter-domain crosstalk became possible only after the structure of a glutamine-bound mutant of Plasmodium falciparum GMPS was determined. In this review, we present the current status of our understanding of the molecular basis of catalysis in GMPS, becoming the first comprehensive assessment of the biochemical function of this intriguing enzyme.
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Affiliation(s)
- Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sanjeev Kumar
- Trivedi School of Biosciences, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India;
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur 560064, Bangalore, India
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6
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Hiefinger C, Mandl S, Wieland M, Kneuttinger A. Rational design, production and in vitro analysis of photoxenoproteins. Methods Enzymol 2023; 682:247-288. [PMID: 36948704 DOI: 10.1016/bs.mie.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In synthetic biology, the artificial control of proteins by light is of growing interest since it enables the spatio-temporal regulation of downstream molecular processes. This precise photocontrol can be established by the site-directed incorporation of photo-sensitive non-canonical amino acids (ncAAs) into proteins, which generates so-called photoxenoproteins. Photoxenoproteins can be engineered using ncAAs that facilitate the irreversible activation or reversible regulation of their activity upon irradiation. In this chapter, we provide a general outline of the engineering process based on the current methodological state-of-the-art to obtain artificial photocontrol in proteins using the ncAAs o-nitrobenzyl-O-tyrosine as example for photocaged ncAAs (irreversible), and phenylalanine-4'-azobenzene as example for photoswitchable ncAAs (reversible). We thereby focus on the initial design as well as the production and characterization of photoxenoproteins in vitro. Finally, we outline the analysis of photocontrol under steady-state and non-steady-state conditions using the allosteric enzyme complexes imidazole glycerol phosphate synthase and tryptophan synthase as examples.
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Affiliation(s)
- Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sabrina Mandl
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Wieland
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Kneuttinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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7
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Shivakumaraswamy S, Kumar S, Bellur A, Polisetty SD, Balaram H. Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme. Biochemistry 2022; 61:1988-2006. [PMID: 36040251 DOI: 10.1021/acs.biochem.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine 5'-monophosphate (GMP) synthetases, enzymes that catalyze the conversion of xanthosine 5'-monophosphate (XMP) to GMP, are composed of two different catalytic units, which are either two domains of a polypeptide chain or two subunits that associate to form a complex. The glutamine amidotransferase (GATase) unit hydrolyzes glutamine generating ammonia, and the ATP pyrophosphatase (ATPPase) unit catalyzes the formation of an AMP-XMP intermediate. The substrate-bound ATPPase allosterically activates GATase, and the ammonia thus generated is tunneled to the ATPPase active site where it reacts with AMP-XMP generating GMP. In ammonia channeling enzymes reported thus far, a tight complex of the two subunits is observed, while the interaction of the two subunits of Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is transient with the underlying mechanism of allostery and substrate channeling largely unclear. Here, we present a mechanistic model encompassing the various steps in the catalytic cycle of MjGMPS based on biochemical experiments, crystal structure, and cross-linking mass spectrometry guided integrative modeling. pH dependence of enzyme kinetics establishes that ammonia is tunneled across the subunits with the lifetime of the complex being ≤0.5 s. The crystal structure of the XMP-bound ATPPase subunit reported herein highlights the role of conformationally dynamic loops in enabling catalysis. The structure of MjGMPS derived using restraints obtained from cross-linking mass spectrometry has enabled the visualization of subunit interactions that enable allostery under catalytic conditions. We integrate the results and propose a functional mechanism for MjGMPS detailing the various steps involved in catalysis.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Satya Dev Polisetty
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
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8
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Calvó-Tusell C, Maria-Solano MA, Osuna S, Feixas F. Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase. J Am Chem Soc 2022; 144:7146-7159. [PMID: 35412310 PMCID: PMC9052757 DOI: 10.1021/jacs.1c12629] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Deciphering the molecular
mechanisms of enzymatic allosteric regulation
requires the structural characterization of functional states and
also their time evolution toward the formation of the allosterically
activated ternary complex. The transient nature and usually slow millisecond
time scale interconversion between these functional states hamper
their experimental and computational characterization. Here, we combine
extensive molecular dynamics simulations, enhanced sampling techniques,
and dynamical networks to describe the allosteric activation of imidazole
glycerol phosphate synthase (IGPS) from the substrate-free form to
the active ternary complex. IGPS is a heterodimeric bienzyme complex
whose HisH subunit is responsible for hydrolyzing glutamine and delivering
ammonia for the cyclase activity in HisF. Despite significant advances
in understanding the underlying allosteric mechanism, essential molecular
details of the long-range millisecond allosteric activation of IGPS
remain hidden. Without using a priori information
of the active state, our simulations uncover how IGPS, with the allosteric
effector bound in HisF, spontaneously captures glutamine in a catalytically
inactive HisH conformation, subsequently attains a closed HisF:HisH
interface, and finally forms the oxyanion hole in HisH for efficient
glutamine hydrolysis. We show that the combined effector and substrate
binding dramatically decreases the conformational barrier associated
with oxyanion hole formation, in line with the experimentally observed
4500-fold activity increase in glutamine hydrolysis. The allosteric
activation is controlled by correlated time-evolving dynamic networks
connecting the effector and substrate binding sites. This computational
strategy tailored to describe millisecond events can be used to rationalize
the effect of mutations on the allosteric regulation and guide IGPS
engineering efforts.
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Affiliation(s)
- Carla Calvó-Tusell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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9
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Yao XQ, Hamelberg D. Residue–Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways. J Chem Theory Comput 2022; 18:1173-1187. [DOI: 10.1021/acs.jctc.1c00669] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
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10
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Maschietto F, Gheeraert A, Piazzi A, Batista VS, Rivalta I. Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria. Biophys J 2022; 121:119-130. [PMID: 34864045 PMCID: PMC8758406 DOI: 10.1016/j.bpj.2021.11.2888] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/17/2021] [Accepted: 11/29/2021] [Indexed: 01/07/2023] Open
Abstract
Understanding the relationship between protein structures and their function is still an open question that becomes very challenging when allostery plays an important functional role. Allosteric proteins, in fact, exploit different ranges of motions (from sidechain local fluctuations to long-range collective motions) to effectively couple distant binding sites, and of particular interest is whether allosteric proteins of the same families with similar functions and structures also necessarily share the same allosteric mechanisms. Here, we compared the early dynamics initiating the allosteric communication of a prototypical allosteric enzyme from two different organisms, i.e., the imidazole glycerol phosphate synthase (IGPS) enzymes from the thermophilic bacteria and the yeast, working at high and room temperatures, respectively. By combining molecular dynamics simulations and network models derived from graph theory, we found rather distinct early allosteric dynamics in the IGPS from the two organisms, involving significatively different allosteric pathways in terms of both local and collective motions. Given the successful prediction of key allosteric residues in the bacterial IGPS, whose mutation disrupts its allosteric communication, the outcome of this study paves the way for future experimental studies on the yeast IGPS that could foster therapeutic applications by exploiting the control of IGPS enzyme allostery.
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Affiliation(s)
| | - Aria Gheeraert
- Université de Lyon, CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Andrea Piazzi
- Dipartimento di Chimica Industriale “Toso Montanari”, Alma Mater Studiorum, Università di Bologna, Bologna, Italia
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, Connecticut,Corresponding author
| | - Ivan Rivalta
- Université de Lyon, CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, Lyon Cedex 07, France,Dipartimento di Chimica Industriale “Toso Montanari”, Alma Mater Studiorum, Università di Bologna, Bologna, Italia,Corresponding author
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11
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Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Top Catal 2021; 65:165-186. [DOI: 10.1007/s11244-021-01521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Wurm JP, Sung S, Kneuttinger AC, Hupfeld E, Sterner R, Wilmanns M, Sprangers R. Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex. Nat Commun 2021; 12:2748. [PMID: 33980881 PMCID: PMC8115485 DOI: 10.1038/s41467-021-22968-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/07/2021] [Indexed: 01/14/2023] Open
Abstract
Imidazole glycerol phosphate synthase (HisFH) is a heterodimeric bienzyme complex operating at a central branch point of metabolism. HisFH is responsible for the HisH-catalyzed hydrolysis of glutamine to glutamate and ammonia, which is then used for a cyclase reaction by HisF. The HisFH complex is allosterically regulated but the underlying mechanism is not well understood. Here, we elucidate the molecular basis of the long range, allosteric activation of HisFH. We establish that the catalytically active HisFH conformation is only formed when the substrates of both HisH and HisF are bound. We show that in this conformation an oxyanion hole in the HisH active site is established, which rationalizes the observed 4500-fold allosteric activation compared to the inactive conformation. In solution, the inactive and active conformations are in a dynamic equilibrium and the HisFH turnover rates correlate with the population of the active conformation, which is in accordance with the ensemble model of allostery. The allosteric regulation of the bienzyme complex imidazole glycerol phosphate synthase (HisFH) remains to be elucidated. Here, the authors provide structural insights into the dynamic allosteric mechanism by which ligand binding to the cyclase and glutaminase active sites of HisFH regulate enzyme activation.
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Affiliation(s)
- Jan Philip Wurm
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sihyun Sung
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Andrea Christa Kneuttinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Enrico Hupfeld
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. .,University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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13
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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14
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Chioccioli S, Del Duca S, Vassallo A, Castronovo LM, Fani R. Exploring the role of the histidine biosynthetic hisF gene in cellular metabolism and in the evolution of (ancestral) genes: from LUCA to the extant (micro)organisms. Microbiol Res 2020; 240:126555. [PMID: 32673985 DOI: 10.1016/j.micres.2020.126555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 01/14/2023]
Abstract
Histidine biosynthesis is an ancestral pathway that was assembled before the appearance of the Last Universal Common Ancestor; afterwards, it remained unaltered in all the extant histidine-synthesizing (micro)organisms. It is a metabolic cross-road interconnecting histidine biosynthesis to nitrogen metabolism and the de novo synthesis of purines. This interconnection is due to the reaction catalyzed by the products of hisH and hisF genes. The latter gene is an excellent model to study which trajectories have been followed by primordial cells to build the first metabolic routes, since its evolution is the result of different molecular rearrangement events, i.e. gene duplication, gene fusion, gene elongation, and domain shuffling. Additionally, this review summarizes data concerning the involvement of hisF and its product in other different cellular processes, revealing that HisF very likely plays a role also in cell division control and involvement in virulence and nodule development in different bacteria. From the metabolic viewpoint, these results suggest that HisF plays a central role in cellular metabolism, highlighting the interconnections of different metabolic pathways.
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Affiliation(s)
- Sofia Chioccioli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Alberto Vassallo
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | | | - Renato Fani
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
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15
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Kneuttinger AC, Rajendran C, Simeth NA, Bruckmann A, König B, Sterner R. Significance of the Protein Interface Configuration for Allostery in Imidazole Glycerol Phosphate Synthase. Biochemistry 2020; 59:2729-2742. [DOI: 10.1021/acs.biochem.0c00332] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea C. Kneuttinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Nadja A. Simeth
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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16
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Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. SCIENCE ADVANCES 2020; 6:eaay7919. [PMID: 32284973 PMCID: PMC7124931 DOI: 10.1126/sciadv.aay7919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/08/2020] [Indexed: 06/11/2023]
Abstract
Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.
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Affiliation(s)
- Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Navjeet Ahalawat
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Padmani Sandhu
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Jagannath Mondal
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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17
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Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction. Proc Natl Acad Sci U S A 2019; 117:346-354. [PMID: 31871208 DOI: 10.1073/pnas.1912132117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tryptophan synthase (TS) is a heterotetrameric αββα complex. It is characterized by the channeling of the reaction intermediate indole and the mutual activation of the α-subunit TrpA and the β-subunit TrpB via a complex allosteric network. We have analyzed this allosteric network by means of ancestral sequence reconstruction (ASR), which is an in silico method to resurrect extinct ancestors of modern proteins. Previously, the sequences of TrpA and TrpB from the last bacterial common ancestor (LBCA) have been computed by means of ASR and characterized. LBCA-TS is similar to modern TS by forming a αββα complex with indole channeling taking place. However, LBCA-TrpA allosterically decreases the activity of LBCA-TrpB, whereas, for example, the modern ncTrpA from Neptuniibacter caesariensis allosterically increases the activity of ncTrpB. To identify amino acid residues that are responsible for this inversion of the allosteric effect, all 6 evolutionary TrpA and TrpB intermediates that stepwise link LBCA-TS with ncTS were characterized. Remarkably, the switching from TrpB inhibition to TrpB activation by TrpA occurred between 2 successive TS intermediates. Sequence comparison of these 2 intermediates and iterative rounds of site-directed mutagenesis allowed us to identify 4 of 413 residues from TrpB that are crucial for its allosteric activation by TrpA. The effect of our mutational studies was rationalized by a community analysis based on molecular dynamics simulations. Our findings demonstrate that ancestral sequence reconstruction can efficiently identify residues contributing to allosteric signal propagation in multienzyme complexes.
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18
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Kneuttinger AC, Straub K, Bittner P, Simeth NA, Bruckmann A, Busch F, Rajendran C, Hupfeld E, Wysocki VH, Horinek D, König B, Merkl R, Sterner R. Light Regulation of Enzyme Allostery through Photo-responsive Unnatural Amino Acids. Cell Chem Biol 2019; 26:1501-1514.e9. [PMID: 31495713 DOI: 10.1016/j.chembiol.2019.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/31/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
Imidazole glycerol phosphate synthase (ImGPS) is an allosteric bienzyme complex in which substrate binding to the synthase subunit HisF stimulates the glutaminase subunit HisH. To control this stimulation with light, we have incorporated the photo-responsive unnatural amino acids phenylalanine-4'-azobenzene (AzoF), o-nitropiperonyl-O-tyrosine (NPY), and methyl-o-nitropiperonyllysine (mNPK) at strategic positions of HisF. The light-mediated isomerization of AzoF at position 55 (fS55AzoFE ↔ fS55AzoFZ) resulted in a reversible 10-fold regulation of HisH activity. The light-mediated decaging of NPY at position 39 (fY39NPY → fY39) and of mNPK at position 99 (fK99mNPK → fK99) led to a 4- to 6-fold increase of HisH activity. Molecular dynamics simulations explained how the unnatural amino acids interfere with the allosteric machinery of ImGPS and revealed additional aspects of HisH stimulation in wild-type ImGPS. Our findings show that unnatural amino acids can be used as a powerful tool for the spatiotemporal control of a central metabolic enzyme complex by light.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Philipp Bittner
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Nadja A Simeth
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany; Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Enrico Hupfeld
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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19
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Wang Y, Zhang F, Nie Y, Shang G, Zhang H. Structural analysis of Shigella flexneri bi-functional enzyme HisIE in histidine biosynthesis. Biochem Biophys Res Commun 2019; 516:540-545. [PMID: 31235255 DOI: 10.1016/j.bbrc.2019.06.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022]
Abstract
Histidine biosynthesis, which is absent in animals, was shown to be highly conserved among gram-negative bacteria, thus making it an attractive target for antibiotic design. There are many fusion forms of enzymes in the histidine biosynthetic pathway and people still have limited knowledge about their domain organizations and catalytic mechanisms, due to the lack of structural information. Here we report the first crystal structure of Shigella flexneri bi-functional enzyme HisIE (SfHisIE) that functions in the 2nd and 3rd steps in the histidine biosynthetic pathway. This structure shows that HisIE exists as dimers with two loops (fusion loop) connecting the individual dimer of HisE and HisI in its N-terminus and C-terminus respectively. Our mutagenesis study shows mutations in this fusion loop are lethal for bacteria indicating the advantage of gene fusion in Histidine biosynthesis. Structural analysis revealed several highly conserved residues in the putative ligand binding grooves of HisE and HisI, showing an evolutionarily conserved catalytic mechanism shared among gram negative-bacteria.
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Affiliation(s)
- Yannan Wang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Fan Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.
| | - Heqiao Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.
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20
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Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase. J Mol Biol 2019; 431:2718-2728. [DOI: 10.1016/j.jmb.2019.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/31/2023]
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21
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Semmelmann F, Hupfeld E, Heizinger L, Merkl R, Sterner R. A Fold-Independent Interface Residue Is Crucial for Complex Formation and Allosteric Signaling in Class I Glutamine Amidotransferases. Biochemistry 2019; 58:2584-2588. [DOI: 10.1021/acs.biochem.9b00286] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Enrico Hupfeld
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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22
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Straub K, Merkl R. Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation. Methods Mol Biol 2019; 1851:171-182. [PMID: 30298397 DOI: 10.1007/978-1-4939-8736-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ancestral sequence reconstruction (ASR) is a powerful tool to infer primordial sequences from contemporary, i.e., extant ones. An essential element of ASR is the computation of a phylogenetic tree whose leaves are the chosen extant sequences. Most often, the reconstructed sequence related to the root of this tree is of greatest interest: It represents the common ancestor (CA) of the sequences under study. If this sequence encodes a protein, one can "resurrect" the CA by means of gene synthesis technology and study biochemical properties of this extinct predecessor with the help of wet-lab experiments.However, ASR deduces also sequences for all internal nodes of the tree, and the well-considered analysis of these "intermediates" can help to elucidate evolutionary processes. Moreover, one can identify key mutations that alter proteins or protein complexes and are responsible for the differing properties of extant proteins. As an illustrative example, we describe the protocol for the rapid identification of hotspots determining the binding of the two subunits within the heteromeric complex imidazole glycerol phosphate synthase.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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23
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Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Håvarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun 2018; 9:3180. [PMID: 30093673 PMCID: PMC6085368 DOI: 10.1038/s41467-018-05602-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.
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Affiliation(s)
- Cécile Morlot
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Nolwenn Simon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Anne-Marie Villard
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | | | - Francisco Leisico
- Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands
| | - Christine Gravier-Pelletier
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Laurent Le Corre
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Nicolas Pietrancosta
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Leiv Sigve Håvarstein
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - André Zapun
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.
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24
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Kneuttinger AC, Winter M, Simeth NA, Heyn K, Merkl R, König B, Sterner R. Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand. Chembiochem 2018; 19:1750-1757. [PMID: 29808949 DOI: 10.1002/cbic.201800219] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/07/2023]
Abstract
The artificial regulation of proteins by light is an emerging subdiscipline of synthetic biology. Here, we used this concept to photocontrol both catalysis and allostery within the heterodimeric enzyme complex imidazole glycerol phosphate synthase (ImGP-S). ImGP-S consists of the cyclase subunit HisF and the glutaminase subunit HisH, which is allosterically stimulated by substrate binding to HisF. We show that a light-sensitive diarylethene (1,2-dithienylethene, DTE)-based competitive inhibitor in its ring-open state binds with low micromolar affinity to the cyclase subunit and displaces its substrate from the active site. As a consequence, catalysis by HisF and allosteric stimulation of HisH are impaired. Following UV-light irradiation, the DTE ligand adopts its ring-closed state and loses affinity for HisF, restoring activity and allostery. Our approach allows for the switching of ImGP-S activity and allostery during catalysis and appears to be generally applicable for the light regulation of other multienzyme complexes.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Martin Winter
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Nadja A Simeth
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
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25
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Leisico F, V Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trincão J, Romão MJ, de Lencastre H, Santos-Silva T. First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD. Sci Rep 2018; 8:5313. [PMID: 29593310 PMCID: PMC5871853 DOI: 10.1038/s41598-018-22986-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/27/2018] [Indexed: 12/05/2022] Open
Abstract
Gram-positive bacteria homeostasis and antibiotic resistance mechanisms are dependent on the intricate architecture of the cell wall, where amidated peptidoglycan plays an important role. The amidation reaction is carried out by the bi-enzymatic complex MurT-GatD, for which biochemical and structural information is very scarce. In this work, we report the first crystal structure of the glutamine amidotransferase member of this complex, GatD from Staphylococcus aureus, at 1.85 Å resolution. A glutamine molecule is found close to the active site funnel, hydrogen-bonded to the conserved R128. In vitro functional studies using 1H-NMR spectroscopy showed that S. aureus MurT-GatD complex has glutaminase activity even in the absence of lipid II, the MurT substrate. In addition, we produced R128A, C94A and H189A mutants, which were totally inactive for glutamine deamidation, revealing their essential role in substrate sequestration and catalytic reaction. GatD from S. aureus and other pathogenic bacteria share high identity to enzymes involved in cobalamin biosynthesis, which can be grouped in a new sub-family of glutamine amidotransferases. Given the ubiquitous presence of GatD, these results provide significant insights into the molecular basis of the so far undisclosed amidation mechanism, contributing to the development of alternative therapeutics to fight infections.
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Affiliation(s)
- Francisco Leisico
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diana V Vieira
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Oxford Protein Production Facility, Research Complex at Harwell, Didcot, United Kingdom
| | - Teresa A Figueiredo
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal
| | - Micael Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita G Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Madalena Ludovice
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Maria João Romão
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal.
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA.
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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26
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Lisi GP, Loria JP. Allostery in enzyme catalysis. Curr Opin Struct Biol 2017; 47:123-130. [DOI: 10.1016/j.sbi.2017.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/27/2017] [Accepted: 08/08/2017] [Indexed: 01/29/2023]
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27
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Altering the allosteric pathway in IGPS suppresses millisecond motions and catalytic activity. Proc Natl Acad Sci U S A 2017; 114:E3414-E3423. [PMID: 28396388 DOI: 10.1073/pnas.1700448114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Imidazole glycerol phosphate synthase (IGPS) is a V-type allosteric enzyme, meaning that its catalytic rate is critically dependent on activation by its allosteric ligand, N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR). The allosteric mechanism of IGPS is reliant on millisecond conformational motions for efficient catalysis. We engineered four mutants of IGPS designed to disrupt millisecond motions and allosteric coupling to identify regions that are critical to IGPS function. Multiple-quantum Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments and NMR chemical shift titrations reveal diminished enzyme flexibility and a reshaping of the allosteric connectivity in each mutant construct, respectively. The functional relevance of the observed motional quenching is confirmed by significant reductions in glutaminase kinetic activity and allosteric ligand binding affinity. This work presents relevant conclusions toward the control of protein allostery and design of unique allosteric sites for potential enzyme inhibitors with regulatory or therapeutic benefit.
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Holinski A, Heyn K, Merkl R, Sterner R. Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 2017; 85:312-321. [PMID: 27936490 DOI: 10.1002/prot.25225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 01/20/2023]
Abstract
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Holinski
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
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Zhao L, Rathnayake UM, Dewage SW, Wood WN, Veltri AJ, Cisneros GA, Hendrickson TL. Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase. FEBS Lett 2016; 590:3122-32. [DOI: 10.1002/1873-3468.12347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Liangjun Zhao
- Department of Chemistry; Wayne State University; Detroit MI USA
| | | | | | - Whitney N. Wood
- Department of Chemistry; Wayne State University; Detroit MI USA
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Lisi GP, Manley GA, Hendrickson H, Rivalta I, Batista VS, Loria JP. Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators. Structure 2016; 24:1155-66. [PMID: 27238967 PMCID: PMC4938718 DOI: 10.1016/j.str.2016.04.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 01/26/2023]
Abstract
The allosteric mechanism of the heterodimeric enzyme imidazole glycerol phosphate synthase was studied in detail with solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. We studied IGPS in complex with a series of allosteric activators corresponding to a large range of catalytic rate enhancements (26- to 4,900-fold), in which ligand binding is entropically driven. Conformational flexibility on the millisecond timescale plays a crucial role in intersubunit communication. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments probing Ile, Leu, and Val methyl groups reveal that the apo- and glutamine-mimicked complexes are static on the millisecond timescale. Domain-wide motions are stimulated in the presence of the allosteric activators. These studies, in conjunction with ligand titrations, demonstrate that the allosteric network is widely dispersed and varies with the identity of the effector. Furthermore, we find that stronger allosteric ligands create more conformational flexibility on the millisecond timescale throughout HisF. This domain-wide loosening leads to maximum catalytic activity.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Gregory A Manley
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Ivan Rivalta
- École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
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31
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Abstract
Protein deamidation has been considered a nonenzymatic process associated with protein functional decay or "aging." Recent studies implicate protein deamidation in regulating signal transduction in fundamental biological processes, such as innate immune responses. Work investigating gammaherpesviruses and bacterial pathogens indicates that microbial pathogens deploy deamidases or enzyme-deficient homologues (pseudoenzymes) to induce deamidation of key signaling components and evade host immune responses. Here, we review studies on protein deamidation in innate immune signaling and present several imminent questions concerning the roles of protein deamidation in infection and immunity.
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32
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Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation. Nat Commun 2015; 6:8930. [PMID: 26592566 PMCID: PMC4673825 DOI: 10.1038/ncomms9930] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022] Open
Abstract
GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the GATase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. We suggest that conformational changes in helix 371–375 holding catalytic residues and in loop 376–401 along the rotation trajectory trigger the different steps of catalysis, and establish the central role of Glu374 in allostery and inter-domain crosstalk. These studies reveal the mechanism of domain rotation and inter-domain communication, providing a molecular framework for the function of all single polypeptide GMPSs and form a solid basis for rational drug design targeting this therapeutically important enzyme. GMP synthetase, a key enzyme in purine biosynthesis, is of interest for understanding purine metabolism processes and for developing therapeutic applications. Here, the authors propose a molecular mechanism and the structural basis for the catalytic activity of this enzyme.
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Wang H, Liu W, Cai Y, Ma L, Ma C, Luo A, Huang Y. Glutaminase 1 is a potential biomarker for chronic post-surgical pain in the rat dorsal spinal cord using differential proteomics. Amino Acids 2015; 48:337-48. [PMID: 26427714 DOI: 10.1007/s00726-015-2085-z] [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: 03/06/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022]
Abstract
Chronic post-surgical pain (CPSP) is a normal and significant symptom in clinical surgery, such as breast operation, biliary tract operation, cesarean operation, uterectomy and thoracic operation. Severe chronic post-surgical pain could increase post-surgical complications, including myocardial ischemia, respiratory insufficiency, pneumonia and thromboembolism. However, the underlying mechanism is still unknown. Herein, a rat CPSP model was produced via thoracotomy. After surgery, in an initial study, 5 out of 12 rats after surgery showed a significant decrease in mechanical withdrawal threshold and/or increase in the number of acetone-evoked responses, and therefore classified as the CPSP group. The remaining seven animals were classified as non-CPSP. Subsequently, open-chest operation was performed on another 30 rats and divided into CPSP and non-CPSP groups after 21-day observation. Protein expression levels in the dorsal spinal cord tissue were determined by 12.5 % SDS-PAGE. Finally, differently expressed proteins were identified by LC MS/MS and analyzed by MASCOT software, followed by Gene Ontology cluster analysis using PANTHER software. Compared with the non-CPSP group, 24 proteins were only expressed in the CPSP group and another 23 proteins expressed differentially between CPSP and non-CPSP group. Western blot further confirmed that the expression of glutaminase 1 (GLS1) was significantly higher in the CPSP than in the non-CPSP group. This study provided a new strategy to identify the spinal proteins, which may contribute to the development of chronic pain using differential proteomics, and suggested that GLS1 may serve as a potential biomarker for CPSP.
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Affiliation(s)
- Haitang Wang
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Wei Liu
- Department of Anesthesiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medicine Science, Beijing, China
| | - Yehua Cai
- Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lulu Ma
- Department of Anesthesiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medicine Science, Beijing, China
| | - Chao Ma
- Department of Anatomy, Histology and Embryology, Peking Union Medical College, School of Basic Medicine, Chinese Academy of Medical Sciences, Institute of Basic Medical Sciences, Beijing, China
| | - Ailun Luo
- Department of Anesthesiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medicine Science, Beijing, China
| | - Yuguang Huang
- Department of Anesthesiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medicine Science, Beijing, China.
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34
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Tanwar AS, Sindhikara DJ, Hirata F, Anand R. Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment. ACS Chem Biol 2015; 10:698-704. [PMID: 25551173 DOI: 10.1021/cb501015r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular tunnels in enzyme systems possess variable architecture and are therefore difficult to predict. In this work, we design and apply an algorithm to resolve the pathway followed by ammonia using the bifunctional enzyme formylglycinamide ribonucleotide amidotransferase (FGAR-AT) as a model system. Though its crystal structure has been determined, an ammonia pathway connecting the glutaminase domain to the 30 Å distal FGAR/ATP binding site remains elusive. Crystallography suggested two purported paths: an N-terminal-adjacent path (path 1) and an auxiliary ADP-adjacent path (path 2). The algorithm presented here, RismPath, which enables fast and accurate determination of solvent distribution inside a protein channel, predicted path 2 as the preferred mode of ammonia transfer. Supporting experimental studies validate the identity of the path, and results lead to the conclusion that the residues in the middle of the channel do not partake in catalytic coupling and serve only as channel walls facilitating ammonia transfer.
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Affiliation(s)
- Ajay S. Tanwar
- Department
of Chemistry, Indian Institute of Technology, IIT-Bombay, Mumbai 400076, India
| | - Daniel J. Sindhikara
- College
of Life Sciences, Ritsumeikan University and Molecular Design Frontier Co. Ltd., Kyoto, Japan
| | - Fumio Hirata
- College
of Life Sciences, Ritsumeikan University and Molecular Design Frontier Co. Ltd., Kyoto, Japan
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology, IIT-Bombay, Mumbai 400076, India
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35
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Oliver JC, Gudihal R, Burgner JW, Pedley AM, Zwierko AT, Davisson VJ, Linger RS. Conformational changes involving ammonia tunnel formation and allosteric control in GMP synthetase. Arch Biochem Biophys 2014; 545:22-32. [PMID: 24434004 DOI: 10.1016/j.abb.2014.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/27/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022]
Abstract
GMP synthetase is the glutamine amidotransferase that catalyzes the final step in the guanylate branch of de novo purine biosynthesis. Conformational changes are required to efficiently couple distal active sites in the protein; however, the nature of these changes has remained elusive. Structural information derived from both limited proteolysis and sedimentation velocity experiments support the hypothesis of nucleotide-induced loop- and domain-closure in the protein. These results were combined with information from sequence conservation and precedents from other glutamine amidotransferases to develop the first structural model of GMPS in a closed, active state. In analyzing this Catalytic model, an interdomain salt bridge was identified residing in the same location as seen in other triad glutamine amidotransferases. Using mutagenesis and kinetic analysis, the salt bridge between H186 and E383 was shown to function as a connection between the two active sites. Mutations at these residues uncoupled the two half-reactions of the enzyme. The chemical events of nucleotide binding initiate a series of conformational changes that culminate in the establishment of a tunnel for ammonia as well as an activated glutaminase catalytic site. The results of this study provide a clearer understanding of the allostery of GMPS, where, for the first time, key substrate binding and interdomain contacts are modeled and analyzed.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Ravidra Gudihal
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - John W Burgner
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, United States
| | - Anthony M Pedley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Alexander T Zwierko
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Rebecca S Linger
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States.
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36
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Reisinger B, Sperl J, Holinski A, Schmid V, Rajendran C, Carstensen L, Schlee S, Blanquart S, Merkl R, Sterner R. Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era. J Am Chem Soc 2013; 136:122-9. [DOI: 10.1021/ja4115677] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bernd Reisinger
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Josef Sperl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Alexandra Holinski
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Veronika Schmid
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Linn Carstensen
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Samuel Blanquart
- Equipe
Bonsai,
Institut National de Recherche en Informatique et en Automatique, INRIA Lille Nord Europe, 40 avenue Halley, 59650 Villeneuve d’Ascq, France
| | - Rainer Merkl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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37
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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38
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Tanwar AS, Goyal VD, Choudhary D, Panjikar S, Anand R. Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. PLoS One 2013; 8:e77781. [PMID: 24223728 PMCID: PMC3815217 DOI: 10.1371/journal.pone.0077781] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) is a 140 kDa bi-functional enzyme involved in a coupled reaction, where the glutaminase active site produces ammonia that is subsequently utilized to convert FGAR to its corresponding amidine in an ATP assisted fashion. The structure of FGAR-AT has been previously determined in an inactive state and the mechanism of activation remains largely unknown. In the current study, hydrophobic cavities were used as markers to identify regions involved in domain movements that facilitate catalytic coupling and subsequent activation of the enzyme. Three internal hydrophobic cavities were located by xenon trapping experiments on FGAR-AT crystals and further, these cavities were perturbed via site-directed mutagenesis. Biophysical characterization of the mutants demonstrated that two of these three voids are crucial for stability and function of the protein, although being ∼20 Å from the active centers. Interestingly, correlation analysis corroborated the experimental findings, and revealed that amino acids lining the functionally important cavities form correlated sets (co-evolving residues) that connect these regions to the amidotransferase active center. It was further proposed that the first cavity is transient and allows for breathing motion to occur and thereby serves as an allosteric hotspot. In contrast, the third cavity which lacks correlated residues was found to be highly plastic and accommodated steric congestion by local adjustment of the structure without affecting either stability or activity.
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Affiliation(s)
- Ajay Singh Tanwar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Venuka Durani Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepanshu Choudhary
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail:
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39
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Ali R, Kumar S, Balaram H, Sarma SP. Solution nuclear magnetic resonance structure of the GATase subunit and structural basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from Methanocaldococcus jannaschii. Biochemistry 2013; 52:4308-23. [PMID: 23724776 DOI: 10.1021/bi400472e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and ¹⁵N backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 ± 0.06 Å for backbone atoms and 0.8 ± 0.06 Å for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed β-sheet that is fenced by five α-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg(2+) interaction has been found to be ∼1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.
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Affiliation(s)
- Rustam Ali
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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