1
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Yu L, Liu Q, Luo W, Zhao J, Alzan HF, He L. The Structural Basis of Babesia orientalis Lactate Dehydrogenase. Front Cell Infect Microbiol 2022; 11:790101. [PMID: 35071043 PMCID: PMC8766848 DOI: 10.3389/fcimb.2021.790101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Glycolytic enzymes play a crucial role in the anaerobic glycolysis of apicomplexan parasites for energy generation. Consequently, they are considered as potential targets for new drug development. Previous studies revealed that lactate dehydrogenase (LDH), a glycolytic enzyme, is a potential drug target in different parasites, such as Plasmodium, Toxoplasma, Cryptosporidium, and Piroplasma. Herein, in order to investigate the structural basis of LDH in Babesia spp., we determined the crystal structure of apo Babesia orientalis (Bo) LDH at 2.67-Å resolution in the space group P1. A five-peptide insertion appears in the active pocket loop of BoLDH to create a larger catalytic pocket, like other protozoa (except for Babesia microti LDH) and unlike its mammalian counterparts, and the absence of this extra insertion inactivates BoLDH. Without ligands, the apo BoLDH takes R-state (relaxed) with the active-site loop open. This feature is obviously different from that of allosteric LDHs in T-state (tense) with the active-site loop open. Compared with allosteric LDHs, the extra salt bridges and hydrogen bonds make the subunit interfaces of BoLDH more stable, and that results in the absence of T-state. Interestingly, BoLDH differs significantly from BmLDH, as it exhibits the ability to adapt quickly to the synthetic co-factor APAD+. In addition, the enzymatic activity of BoLDH was inhibited non-competitively by polyphenolic gossypol with a Ki value of 4.25 μM, indicating that BoLDH is sensitive to the inhibition of gossypol and possibly to its new derivative compounds. The current work provides the structural basis of BoLDH for the first time and suggests further investigation on the LDH structure of other Babesia spp. That knowledge would indeed facilitate the screening and designing of new LDH inhibitors to control the intracellular proliferation of Babesia spp.
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Affiliation(s)
- Long Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Qin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Wanxin Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Heba F Alzan
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.,Parasitology and Animal Diseases Department, National Research Center, Giza, Egypt.,Tick and Tick-Borne Disease Research Unit, National Research Center, Giza, Egypt
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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2
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Hodges M, Barahona M, Yaliraki SN. Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase. Sci Rep 2018; 8:11079. [PMID: 30038211 PMCID: PMC6056424 DOI: 10.1038/s41598-018-27992-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/13/2018] [Indexed: 11/08/2022] Open
Abstract
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicting allosteric sites in a wide range of proteins using an energy-weighted atomistic graph obtained from the protein structure and given knowledge only of the location of the active site. Bond-to-bond propensity establishes if energy fluctuations at given bonds have significant effects on any other bond in the protein, by considering their propagation through the protein graph. In this work, we use bond-to-bond propensity analysis to study different aspects of ATCase activity using three different protein structures and sources of fluctuations. First, we predict key residues and bonds involved in the transition between inactive (T) and active (R) states of ATCase by analysing allosteric substrate binding as a source of energy perturbations in the protein graph. Our computational results also indicate that the effect of multiple allosteric binding is non linear: a switching effect is observed after a particular number and arrangement of substrates is bound suggesting a form of long range communication between the distantly arranged allosteric sites. Second, cooperativity is explored by considering a bisubstrate analogue as the source of energy fluctuations at the active site, also leading to the identification of highly significant residues to the T ↔ R transition that enhance cooperativity across active sites. Finally, the inactive (T) structure is shown to exhibit a strong, non linear communication between the allosteric sites and the interface between catalytic subunits, rather than the active site. Bond-to-bond propensity thus offers an alternative route to explain allosteric and cooperative effects in terms of detailed atomistic changes to individual bonds within the protein, rather than through phenomenological, global thermodynamic arguments.
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Affiliation(s)
- Maxwell Hodges
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Sophia N Yaliraki
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
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3
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Pritišanac I, Würz JM, Güntert P. Fully automated assignment of methyl resonances of a 36 kDa protein dimer from sparse NOESY data. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1742-6596/1036/1/012008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Lin YR, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Sci 2017; 26:2187-2194. [PMID: 28801928 DOI: 10.1002/pro.3270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
We have previously shown that monomeric globular αβ-proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β-strand backbone interactions were structurally confirmed through x-ray crystallography and small-angle X-ray scattering (SAXS). In contrast, C3-C5 designed homo-oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo-oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.
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Affiliation(s)
- Yu-Ru Lin
- Department of Biochemistry, University of Washington, and Howard Hughes Medical Institute, Seattle, Washington 98195
| | - Nobuyasu Koga
- Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institute of Natural Sciences (NINS), Okazaki 444-8585, Japan.,JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Sergey M Vorobiev
- Department of Biological Science, Northeast Structural Genomics Consortium, Columbia University, New York, New York
| | - David Baker
- Department of Biochemistry, University of Washington, and Howard Hughes Medical Institute, Seattle, Washington 98195
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5
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Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, AB E, Siegal G, Baldwin AJ. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. J Am Chem Soc 2017; 139:9523-9533. [DOI: 10.1021/jacs.6b11358] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iva Pritišanac
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Matteo T. Degiacomi
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - T. Reid Alderson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Marta G. Carneiro
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Eiso AB
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Gregg Siegal
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Andrew J. Baldwin
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
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6
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Abstract
Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following Review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery.
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Affiliation(s)
- George P. Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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7
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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8
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Shi D, Allewell NM, Tuchman M. From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases. Int J Mol Sci 2015; 16:18836-64. [PMID: 26274952 PMCID: PMC4581275 DOI: 10.3390/ijms160818836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate. The two best-characterized members, aspartate transcarbamylase (ATCase) and ornithine transcarbamylase (OTCase), are present in most organisms from bacteria to humans. Recently, structures of four new transcarbamylase members, N-acetyl-l-ornithine transcarbamylase (AOTCase), N-succinyl-l-ornithine transcarbamylase (SOTCase), ygeW encoded transcarbamylase (YTCase) and putrescine transcarbamylase (PTCase) have also been determined. Crystal structures of these enzymes have shown that they have a common overall fold with a trimer as their basic biological unit. The monomer structures share a common CP binding site in their N-terminal domain, but have different second substrate binding sites in their C-terminal domain. The discovery of three new transcarbamylases, l-2,3-diaminopropionate transcarbamylase (DPTCase), l-2,4-diaminobutyrate transcarbamylase (DBTCase) and ureidoglycine transcarbamylase (UGTCase), demonstrates that our knowledge and understanding of the spectrum of the transcarbamylase family is still incomplete. In this review, we summarize studies on the structures and function of transcarbamylases demonstrating how structural information helps to define biological function and how small structural differences govern enzyme specificity. Such information is important for correctly annotating transcarbamylase sequences in the genome databases and for identifying new members of the transcarbamylase family.
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Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| | - Norma M Allewell
- Department of Cell Biology and Molecular Genetics, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
- Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
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9
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The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer. PLoS One 2014; 9:e96536. [PMID: 24787711 PMCID: PMC4008608 DOI: 10.1371/journal.pone.0096536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/08/2014] [Indexed: 11/24/2022] Open
Abstract
The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P) deaminase from Escherichia coli (EcGNPDA) as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P). We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the background of the known crystallographic structures of T and R EcGNPDA conformers. These results are consistent with the postulates of the Tertiary Two-States (TTS) model.
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10
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Cockrell GM, Zheng Y, Guo W, Peterson AW, Truong JK, Kantrowitz ER. New paradigm for allosteric regulation of Escherichia coli aspartate transcarbamoylase. Biochemistry 2013; 52:8036-47. [PMID: 24138583 DOI: 10.1021/bi401205n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For nearly 60 years, the ATP activation and the CTP inhibition of Escherichia coli aspartate transcarbamoylase (ATCase) has been the textbook example of allosteric regulation. We present kinetic data and five X-ray structures determined in the absence and presence of a Mg(2+) concentration within the physiological range. In the presence of 2 mM divalent cations (Mg(2+), Ca(2+), Zn(2+)), CTP does not significantly inhibit the enzyme, while the allosteric activation by ATP is enhanced. The data suggest that the actual allosteric inhibitor of ATCase in vivo is the combination of CTP, UTP, and a divalent cation, and the actual allosteric activator is a divalent cation with ATP or ATP and GTP. The structural data reveals that two NTPs can bind to each allosteric site with a divalent cation acting as a bridge between the triphosphates. Thus, the regulation of ATCase is far more complex than previously believed and calls many previous studies into question. The X-ray structures reveal that the catalytic chains undergo essentially no alternations; however, several regions of the regulatory chains undergo significant structural changes. Most significant is that the N-terminal region of the regulatory chains exists in different conformations in the allosterically activated and inhibited forms of the enzyme. Here, a new model of allosteric regulation is proposed.
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Affiliation(s)
- Gregory M Cockrell
- Department of Chemistry, Boston College , Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467 U.S.A
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11
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Trapping and structure determination of an intermediate in the allosteric transition of aspartate transcarbamoylase. Proc Natl Acad Sci U S A 2012; 109:7741-6. [PMID: 22547808 DOI: 10.1073/pnas.1119683109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-ray crystallography and small-angle X-ray scattering (SAXS) in solution have been used to show that a mutant aspartate transcarbamoylase exists in an intermediate quaternary structure between the canonical T and R structures. Additionally, the SAXS data indicate a pH-dependent structural alteration consistent with either a pH-induced conformational change or a pH-induced alteration in the T to R equilibrium. These data indicate that this mutant is not a model for the R state, as has been proposed, but rather represents the enzyme trapped along the path of the allosteric transition between the T and R states.
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12
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Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase. Arch Biochem Biophys 2011; 519:81-90. [PMID: 22198283 DOI: 10.1016/j.abb.2011.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/20/2022]
Abstract
The allosteric enzyme aspartate transcarbamoylase (ATCase) from Escherichia coli has been the subject of investigations for approximately 50 years. This enzyme controls the rate of pyrimidine nucleotide biosynthesis by feedback inhibition, and helps to balance the pyrimidine and purine pools by competitive allosteric activation by ATP. The catalytic and regulatory components of the dodecameric enzyme can be separated and studied independently. Many of the properties of the enzyme follow the Monod, Wyman Changeux model of allosteric control thus E. coli ATCase has become the textbook example. This review will highlight kinetic, biophysical, and structural studies which have provided a molecular level understanding of how the allosteric nature of this enzyme regulates pyrimidine nucleotide biosynthesis.
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13
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Kay LE. Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:159-170. [PMID: 21458338 DOI: 10.1016/j.jmr.2011.03.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/03/2011] [Accepted: 03/03/2011] [Indexed: 05/30/2023]
Abstract
With the development of appropriate labeling schemes and the associated experiments that exploit them it has become possible to record high quality solution NMR spectra of supra-molecular complexes with molecular masses extending to 1MDa. One such approach involves selective (13)CH(3) methyl labeling in highly deuterated proteins using experiments that make use of a methyl-TROSY effect that significantly improves both resolution and sensitivity in spectra. The utility of this methodology has been demonstrated on a growing number of interesting particles. It seems appropriate at this juncture, therefore, to 'step back' and evaluate the role that solution NMR spectroscopy can play in what has traditionally been the domain of X-ray crystallography and more recently cryo-electron microscopy. It is argued here that solution NMR can make a critical contribution to our understanding of how dynamics regulate function in these high molecular weight systems. Several examples from work in my laboratory on the proteasome are presented as an illustration.
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Affiliation(s)
- Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8.
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14
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Tolonen E, Bueno B, Kulshreshta S, Cieplak P, Argáez M, Velázquez L, Stec B. Allosteric transition and binding of small molecule effectors causes curvature change in central β-sheets of selected enzymes. J Mol Model 2011; 17:899-911. [PMID: 20602244 PMCID: PMC4127431 DOI: 10.1007/s00894-010-0784-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 06/14/2010] [Indexed: 10/19/2022]
Abstract
A quantitative description of allosteric transition remains a significant science challenge. Many allosteric enzymes contain a central β-sheet in their catalytic domain. When an allosteric protein undergoes the transition between T (tense) and R (relaxed) allosteric states, this central β-sheet undergoes a conformational change. A traditional method of measuring this change, the root mean square deviation (RMSD), appears to be inadequate to describe such changes in meaningful quantitative manner. We designed a novel quantitative method to demonstrate this conformational transition by measuring the change in curvature of the central β-sheet when enzymes transition between allosteric states. The curvature was established by calculating the semiaxes of a 3-D hyperboloid fitted by least squares to the Cα atomic positions of the β-sheet. The two enzymes selected for this study, fructose 1,6-bisphosphatase (FBPase) from pig kidney and aspartate carbamoyltransferase (ATCase) from E. coli, showed while transitioning between the allosteric states (T ⇔ R) a notable change in β-sheet curvature (∼5%) that results in a large lateral shift at the sheet's edge, which is necessary to convey the signal. The results suggest that the β-sheet participates in storing elastic energy associated with the transition. Establishing a tentative link between the energetics of the β-sheet in different allosteric states provides a more objective basis for the naming convention of allosteric states (tense or relaxed), and provides insight into the hysteretic nature of the transition. The approach presented here allows for a better understanding of the internal dynamics of allosteric enzymes by defining the domains that directly participate in the transition.
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Affiliation(s)
- Ellen Tolonen
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Brenda Bueno
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sanjeev Kulshreshta
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Piotr Cieplak
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Miguel Argáez
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Leticia Velázquez
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
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15
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Mendes KR, Kantrowitz ER. A cooperative Escherichia coli aspartate transcarbamoylase without regulatory subunits . Biochemistry 2010; 49:7694-703. [PMID: 20681545 DOI: 10.1021/bi1010333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we report the isolation, kinetic characterization, and X-ray structure determination of a cooperative Escherichia coli aspartate transcarbamoylase (ATCase) without regulatory subunits. The native ATCase holoenzyme consists of six catalytic chains organized as two trimers bridged noncovalently by six regulatory chains organized as three dimers, c(6)r(6). Dissociation of the native holoenzyme produces catalytically active trimers, c(3), and nucleotide-binding regulatory dimers, r(2). By introducing specific disulfide bonds linking the catalytic chains from the upper trimer site specifically to their corresponding chains in the lower trimer prior to dissociation, a new catalytic unit, c(6), was isolated consisting of two catalytic trimers linked by disulfide bonds. Not only does the c(6) species display enhanced enzymatic activity compared to the wild-type enzyme, but the disulfide bonds also impart homotropic cooperativity, never observed in the wild-type c(3). The c(6) ATCase was crystallized in the presence of phosphate and its X-ray structure determined to 2.10 A resolution. The structure of c(6) ATCase liganded with phosphate exists in a nearly identical conformation as other R-state structures with similar values calculated for the vertical separation and planar angles. The disulfide bonds linking upper and lower catalytic trimers predispose the active site into a more active conformation by locking the 240s loop into the position characteristic of the high-affinity R state. Furthermore, the elimination of the structural constraints imposed by the regulatory subunits within the holoenzyme provides increased flexibility to the c(6) enzyme, enhancing its activity over the wild-type holoenzyme (c(6)r(6)) and c(3). The covalent linkage between upper and lower catalytic trimers restores homotropic cooperativity so that a binding event at one or so active sites stimulates binding at the other sites. Reduction of the disulfide bonds in the c(6) ATCase results in c(3) catalytic subunits that display kinetic parameters similar to those of wild-type c(3). This is the first report of an active c(6) catalytic unit that displays enhanced activity and homotropic cooperativity.
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Affiliation(s)
- Kimberly R Mendes
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, USA
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16
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Mendes KR, Kantrowitz ER. The pathway of product release from the R state of aspartate transcarbamoylase. J Mol Biol 2010; 401:940-8. [PMID: 20620149 DOI: 10.1016/j.jmb.2010.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/24/2010] [Accepted: 07/02/2010] [Indexed: 11/25/2022]
Abstract
The pathway of product release from the R state of aspartate transcarbamoylase (ATCase; EC 2.1.3.2, aspartate carbamoyltransferase) has been determined here by solving the crystal structure of Escherichia coli ATCase locked in the R quaternary structure by specific introduction of disulfide bonds. ATCase displays ordered substrate binding and product release, remaining in the R state until substrates are exhausted. The structure reported here represents ATCase in the R state bound to the final product molecule, phosphate. This structure has been difficult to obtain previously because the enzyme relaxes back to the T state after the substrates are exhausted. Hence, cocrystallizing the wild-type enzyme with phosphate results in a T-state structure. In this structure of the enzyme trapped in the R state with specific disulfide bonds, we observe two phosphate molecules per active site. The position of the first phosphate corresponds to the position of the phosphate of carbamoyl phosphate (CP) and the position of the phosphonate of N-phosphonacetyl-l-aspartate. However, the second, more weakly bound phosphate is bound in a positively charged pocket that is more accessible to the surface than the other phosphate. The second phosphate appears to be on the path that phosphate would have to take to exit the active site. Our results suggest that phosphate dissociation and CP binding can occur simultaneously and that the dissociation of phosphate may actually promote the binding of CP for more efficient catalysis.
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Affiliation(s)
- Kimberly R Mendes
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467-3807, USA
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17
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Velyvis A, Schachman HK, Kay LE. Assignment of Ile, Leu, and Val methyl correlations in supra-molecular systems: an application to aspartate transcarbamoylase. J Am Chem Soc 2010; 131:16534-43. [PMID: 19860411 DOI: 10.1021/ja906978r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A number of complementary approaches for the assignment of Ile, Leu, and Val methyl groups in Methyl-TROSY spectra of supra-molecular protein complexes are presented and compared. This includes the transfer of assignments from smaller fragments to the complex using a "divide-and-conquer" approach, assignment transfer via exchange spectroscopy, or, alternatively, generating assignments of the complex through the measurement of pseudocontact shifts, facilitated by the introduction of paramagnetic probes. The methodology is applied to the assignment of the regulatory chains in the 300 kDa enzyme aspartate transcarbamoylase, ATCase. The "divide-and-conquer" method that has proven to be very powerful in applications to other systems produced assignments for approximately 60% of the observed methyl groups in TROSY maps of ATCase. By contrast, the combination of all approaches led to assignments for 86% of the methyls, providing a large number of probes of structure and dynamics. The derived assignments were used to interpret chemical shift changes of ATCase upon titration with the nucleotide ATP. Large shift changes in the N-terminal tails of the regulatory chain provide the first evidence for structural perturbations in a region that is known to play a critical role on the effect of nucleotide binding on distal catalytic sites of this allosteric enzyme.
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Affiliation(s)
- Algirdas Velyvis
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
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18
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Stieglitz KA, Xia J, Kantrowitz E. The first high pH structure of Escherichia coli aspartate transcarbamoylase. Proteins 2009; 74:318-27. [PMID: 18618694 PMCID: PMC2920061 DOI: 10.1002/prot.22162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The activity and cooperativity of Escherichia coli aspartate transcarbamoylase (ATCase) vary as a function of pH, with a maximum of both parameters at approximately pH 8.3. Here we report the first X-ray structure of unliganded ATCase at pH 8.5, to establish a structural basis for the observed Bohr effect. The overall conformation of the active site at pH 8.5 more closely resembles the active site of the enzyme in the R-state structure than other T-state structures. In the structure of the enzyme at pH 8.5 the 80's loop is closer to its position in R-state structures. A unique electropositive channel, comprised of residues from the 50's region, is observed in this structure, with Arg54 positioned in the center of the channel. The planar angle between the carbamoyl phosphate and aspartate domains of the catalytic chain is more open at pH 8.5 than in ATCase structures determined at lower pH values. The structure of the enzyme at pH 8.5 also exhibits lengthening of a number of interactions in the interface between the catalytic and regulatory chains, whereas a number of interactions between the two catalytic trimers are shortened. These alterations in the interface between the upper and lower trimers may directly shift the allosteric equilibrium and thus the cooperativity of the enzyme. Alterations in the electropositive environment of the active site and alterations in the position of the catalytic chain domains may be responsible for the enhanced activity of the enzyme at pH 8.5.
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Affiliation(s)
- Kimberly A. Stieglitz
- Department of Chemistry, University of Massachusetts, Boston, MA 02125, USA,Correspondence to Kimberly A. Stieglitz, Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA 02125,
| | - Jiarong Xia
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
| | - Evan Kantrowitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
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19
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Cardia JP, Eldo J, Xia J, O'Day EM, Tsuruta H, Gryncel KR, Kantrowitz ER. Use of L-asparagine and N-phosphonacetyl-L-asparagine to investigate the linkage of catalysis and homotropic cooperativity in E. coli aspartate transcarbomoylase. Proteins 2008; 71:1088-96. [PMID: 18004787 DOI: 10.1002/prot.21760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mechanism of domain closure and the allosteric transition of Escherichia coli aspartate transcarbamoylase (ATCase) are investigated using L-Asn, in the presence of carbamoyl phosphate (CP), and N-phosphonacetyl-L-asparagine (PASN). ATCase was found to catalyze the carbamoylation of L-Asn with a K(m) of 122 mM and a maximal velocity 10-fold lower than observed with the natural substrate, L-Asp. As opposed to L-Asp, no cooperativity was observed with respect to L-Asn. Time-resolved small-angle X-ray scattering (SAXS) and fluorescence experiments revealed that the combination of CP and L-Asn did not convert the enzyme from the T to the R state. PASN was found to be a potent inhibitor of ATCase exhibiting a K(D) of 8.8 microM. SAXS experiments showed that PASN was able to convert the entire population of molecules to the R state. Analysis of the crystal structure of the enzyme in the presence of PASN revealed that the binding of PASN was similar to that of the R-state complex of ATCase with N-phosphonaceyl-L-aspartate, another potent inhibitor of the enzyme. The linking of CP and L-Asn into one molecule, PASN, correctly orients the asparagine moiety in the active site to induce domain closure and the allosteric transition. This entropic effect allows for the high affinity binding of PASN. However, the binding of L-Asn, in the presence of a saturating concentration of CP, does not induce the closure of the two domains of the catalytic chain, nor does the enzyme undergo the transition to the high-activity high- affinity R structure. These results imply that Arg229, which interacts with the beta-carboxylate of L-Asp, plays a critical role in the orientation of L-Asp in the active site and demonstrates the requirement of the beta-carboxylate of L-Asp in the mechanism of domain closure and the allosteric transition in E. coli ATCase.
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Affiliation(s)
- James P Cardia
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3807, USA
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20
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Vitali J, Colaneri MJ, Kantrowitz E. Crystal structure of the catalytic trimer ofMethanococcus jannaschiiaspartate transcarbamoylase. Proteins 2007; 71:1324-34. [PMID: 18058907 DOI: 10.1002/prot.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jacqueline Vitali
- Department of Physics, Cleveland State University, Euclid Avenue at East 24th Street, Cleveland, Ohio 44115, USA.
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21
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Wang J, Eldo J, Kantrowitz ER. Structural model of the R state of Escherichia coli aspartate transcarbamoylase with substrates bound. J Mol Biol 2007; 371:1261-73. [PMID: 17603076 PMCID: PMC2720131 DOI: 10.1016/j.jmb.2007.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 06/01/2007] [Accepted: 06/05/2007] [Indexed: 01/07/2023]
Abstract
The allosteric enzyme aspartate transcarbamoylase (ATCase) exists in two conformational states. The enzyme, in the absence of substrates is primarily in the low-activity T state, is converted to the high-activity R state upon substrate binding, and remains in the R state until substrates are exhausted. These conformational changes have made it difficult to obtain structural data on R-state active-site complexes. Here we report the R-state structure of ATCase with the substrate Asp and the substrate analog phosphonoactamide (PAM) bound. This R-state structure represents the stage in the catalytic mechanism immediately before the formation of the covalent bond between the nitrogen of the amino group of Asp and the carbonyl carbon of carbamoyl phosphate. The binding mode of the PAM is similar to the binding mode of the phosphonate moiety of N-(phosphonoacetyl)-l-aspartate (PALA), the carboxylates of Asp interact with the same residues that interact with the carboxylates of PALA, although the position and orientations are shifted. The amino group of Asp is 2.9 A away from the carbonyl oxygen of PAM, positioned correctly for the nucleophilic attack. Arg105 and Leu267 in the catalytic chain interact with PAM and Asp and help to position the substrates correctly for catalysis. This structure fills a key gap in the structural determination of each of the steps in the catalytic cycle. By combining these data with previously determined structures we can now visualize the allosteric transition through detailed atomic motions that underlie the molecular mechanism.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
| | - Joby Eldo
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
- E-mail address of corresponding author:
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22
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Eldo J, Cardia JP, O’Day EM, Xia J, Tsurata H, Kantrowitz ER. N-phosphonacetyl-L-isoasparagine a potent and specific inhibitor of Escherichia coli aspartate transcarbamoylase. J Med Chem 2006; 49:5932-8. [PMID: 17004708 PMCID: PMC2538380 DOI: 10.1021/jm0607294] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of a new inhibitor, N-phosphonacetyl-L-isoasparagine (PALI), of Escherichia coli aspartate transcarbamoylase (ATCase) is reported, as well as structural studies of the enzyme.PALI complex. PALI was synthesized in 7 steps from beta-benzyl L-aspartate. The KD of PALI was 2 microM. Kinetics and small-angle X-ray scattering experiments showed that PALI can induce the cooperative transition of ATCase from the T to the R state. The X-ray structure of the enzyme.PALI complex showed 22 hydrogen-bonding interactions between the enzyme and PALI. The kinetic characterization and crystal structure of the ATCase.PALI complex also provides detailed information regarding the importance of the alpha-carboxylate for the binding of the substrate aspartate.
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Affiliation(s)
| | | | | | | | | | - Evan R. Kantrowitz
- To whom correspondence should be addressed: Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467-3808, E-mail, ; tel, 617-552-4558; fax, 617-552-2705
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23
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Kapustina M, Carter CW. Computational studies of tryptophanyl-tRNA synthetase: activation of ATP by induced-fit. J Mol Biol 2006; 362:1159-80. [PMID: 16949606 DOI: 10.1016/j.jmb.2006.06.078] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 05/24/2006] [Accepted: 06/30/2006] [Indexed: 11/21/2022]
Abstract
Catalysis of amino acid activation by Bacillus stearothermophilus tryptophanyl-tRNA synthetase involves three allosteric states: (1) Open; (2) closed pre-transition state (PreTS); and (3) closed products (Product). The interconversions of these states entail significant domain motions driven by ligand binding. We explore the application of molecular dynamics simulations to investigate ligand-linked conformational stability changes associated with this catalytic cycle. Multiple molecular dynamics trajectories (5 ns) for 11 distinct liganded and unliganded monomer configurations show that the PreTS conformation is unstable in the absence of ATP, reverting within approximately 600 ps nearly to the Open conformation. In contrast, Open and Product state trajectories were stable, even without ligands, confirming the previous suggestion that catalysis entails destabilization of the protein conformation, driven by ATP-binding energies developed as the PreTS state assembles during induced-fit. The simulations suggest novel mechanistic details associated with both induced-fit (Open-PreTS) and catalysis (PreTS-Product). Notably, Mg2+ -ATP interactions are coupled to interactions between ATP and active-site lysine side-chains via mechanisms that cannot be captured under the molecular mechanics approximations, and which therefore require restraining potentials for stable simulation. Simulations of Mg2+. ATP-bound PreTS complexes with restraining potentials and with a virtual K111A mutant confirm that these coupling interactions are necessary to sustain the PreTS conformation and, in turn, provide a new model for how the PreTS conformation activates ATP for catalysis. These results emphasize the central role of the PreTS state as a high-energy intermediate structure along the catalytic pathway and suggest that Mg2+ and the KMSKS loop function cooperatively during catalysis.
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Affiliation(s)
- Maryna Kapustina
- Department of Biochemistry and Biophysics, CB 7260, University of North Carolina, Chapel Hill, NC 27599-7260, USA
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24
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Heng S, Stieglitz KA, Eldo J, Xia J, Cardia JP, Kantrowitz ER. T-state Inhibitors of E. coli Aspartate Transcarbamoylase that Prevent the Allosteric Transition,. Biochemistry 2006; 45:10062-71. [PMID: 16906764 DOI: 10.1021/bi0601095] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli aspartate transcarbamoylase (ATCase) catalyzes the committed step in pyrimidine nucleotide biosynthesis, the reaction between carbamoyl phosphate (CP) and l-aspartate to form N-carbamoyl-l-aspartate and inorganic phosphate. The enzyme exhibits homotropic cooperativity and is allosterically regulated. Upon binding l-aspartate in the presence of a saturating concentration of CP, the enzyme is converted from the low-activity low-affinity T state to the high-activity high-affinity R state. The potent inhibitor N-phosphonacetyl-l-aspartate (PALA), which combines the binding features of Asp and CP into one molecule, has been shown to induce the allosteric transition to the R state. In the presence of only CP, the enzyme is the T structure with the active site primed for the binding of aspartate. In a structure of the enzyme-CP complex (T(CP)), two CP molecules were observed in the active site approximately 7A apart, one with high occupancy and one with low occupancy. The high occupancy site corresponds to the position for CP observed in the structure of the enzyme with CP and the aspartate analogue succinate bound. The position of the second CP is in a unique site and does not overlap with the aspartate binding site. As a means to generate a new class of inhibitors for ATCase, the domain-open T state of the enzyme was targeted. We designed, synthesized, and characterized three inhibitors that were composed of two phosphonacetamide groups linked together. These two phosphonacetamide groups mimic the positions of the two CP molecules in the T(CP) structure. X-ray crystal structures of ATCase-inhibitor complexes revealed that each of these inhibitors bind to the T state of the enzyme and occupy the active site area. As opposed to the binding of Asp in the presence of CP or PALA, these inhibitors are unable to initiate the global T to R conformational change. Although the best of these T-state inhibitors only has a K(i) value in the micromolar range, the structural information with respect to their mode of binding provides important information for the design of second generation inhibitors that will have even higher affinity for the active site of the T state of the enzyme.
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Affiliation(s)
- Sabrina Heng
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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25
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Spyrakis F, Raboni S, Cozzini P, Bettati S, Mozzarelli A. Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1102-9. [PMID: 16737856 DOI: 10.1016/j.bbapap.2006.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 03/16/2006] [Accepted: 03/16/2006] [Indexed: 12/12/2022]
Abstract
Ligand binding to the alpha-subunit of the alpha2beta2 complex of tryptophan synthase induces the alphaloop6 closure over the alpha-active site. This conformational change is associated with the formation of a hydrogen bond between alphaGly181 NH group and betaSer178 carbonyl oxygen, a key event for the triggering of intersubunit allosteric signals. Mutation of betaSer178 to Pro and alphaGly181 to Pro, Ala, Phe and Val abolishes the ligand-induced intersubunit communication. Molecular dynamics methods were applied to simulate the conformation of the highly flexible and crystallographically undetectable open state of alphaloop6 in the wild type and in the alpha181 mutants. The open conformation of alphaloop6 is favoured in the wild type enzyme in the absence of alpha-ligands, and in the alpha181 mutants both in the presence and absence of bound ligands. A very good correlation was found between the extent of limited tryptic proteolysis and both the hydrogen bond distance between alphaX181 and betaSer178, obtained from the molecular dynamics simulation, and the hydrogen bond strength, evaluated by HINT, an empirical force field that takes into account both enthalpic and entropic contributions. Comparison of the open and closed conformations of alphaloop6 suggests a pathway for substrate entrance into the alpha-active site and provides an explanation for the limited catalytic efficiency of the open state.
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Affiliation(s)
- Francesca Spyrakis
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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26
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Sosa-Peinado A, González-Andrade M. Site-Directed Fluorescence Labeling Reveals Differences on the R-Conformer of Glucosamine 6-Phosphate Deaminase of Escherichia coli Induced by Active or Allosteric Site Ligands at Steady State. Biochemistry 2005; 44:15083-92. [PMID: 16285712 DOI: 10.1021/bi050306o] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Engineered glucosamine 6-phosphate deaminase of Escherichia coli with unique reactive cysteines at positions 164 or 206 was created by site-directed mutagenesis to monitor the allosteric transition in solution by the fluorescence emission of the bimane or dansyl-amidoethyl groups attached to the indicated residues. The selection of both positions was due to the differential interaction of these residues between T- and R-conformers at the interface of two trimers that form the hexameric structure; in the T-conformer, residue 164 or 206 presents only intrasubunit contacts, but in the R-conformer, new intersubunit contacts are established. As in the wild-type enzyme, fluorescent-labeled mutants show no modification on the allosteric activation of the K-system, only the kcat was reduced to a value of 72 s(-1) (approximately 50% of wild-type). With these preparations, conformational changes were detected by the fluorescence emission spectra at steady state when the active site or the allosteric site ligands were titrated. Despite the similar changes in the fluorescence spectra that were correlated with the induction of the R-state, differences were observed at the maximal change in the fluorescence spectra and in the relative solvent polarities at the positions labeled. These data suggested structural differences in the conformation of the R-state when it is induced from the active site or from the allosteric site, which is not consistent with the two-state structural model proposed by previous crystallographic studies of this enzyme.
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Affiliation(s)
- Alejandro Sosa-Peinado
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, P.O. Box 70-159, México, DF 04510, México.
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27
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Stieglitz KA, Dusinberre KJ, Cardia JP, Tsuruta H, Kantrowitz ER. Structure of the E.coli Aspartate Transcarbamoylase Trapped in the Middle of the Catalytic Cycle. J Mol Biol 2005; 352:478-86. [PMID: 16120448 DOI: 10.1016/j.jmb.2005.07.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 07/13/2005] [Accepted: 07/13/2005] [Indexed: 11/30/2022]
Abstract
Snapshots of the catalytic cycle of the allosteric enzyme aspartate transcarbamoylase have been obtained via X-ray crystallography. The enzyme in the high-activity high-affinity R state contains two catalytic chains in the asymmetric unit that are different. The active site in one chain is empty, while the active site in the other chain contains an analog of the first substrate to bind in the ordered mechanism of the reaction. Small angle X-ray scattering shows that once the enzyme is converted to the R state, by substrate binding, the enzyme remains in the R state until substrates are exhausted. Thus, this structure represents the active form of the enzyme trapped at two different stages in the catalytic cycle, before the substrates bind (or after the products are released), and after the first substrate binds. Opening and closing of the catalytic chain domains explains how the catalytic cycle occurs while the enzyme remains globally in the R-quaternary structure.
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Affiliation(s)
- Kimberly A Stieglitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
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28
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Wang J, Stieglitz KA, Cardia JP, Kantrowitz ER. Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase. Proc Natl Acad Sci U S A 2005; 102:8881-6. [PMID: 15951418 PMCID: PMC1157055 DOI: 10.1073/pnas.0503742102] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-ray structures of aspartate transcarbamoylase in the absence and presence of the first substrate carbamoyl phosphate are reported. These two structures in conjunction with in silico docking experiments provide snapshots of critical events in the function of the enzyme. The ordered substrate binding, observed experimentally, can now be structurally explained by a conformational change induced upon the binding of carbamoyl phosphate. This induced fit dramatically alters the electrostatics of the active site, creating a binding pocket for aspartate. Upon aspartate binding, a further change in electrostatics causes a second induced fit, the domain closure. This domain closure acts as a clamp that both facilitates catalysis by approximation and also initiates the global conformational change that manifests homotropic cooperativity.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467, USA
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29
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Abstract
Forty years ago, a simple model of allosteric mechanisms (indirect interactions between distinct sites), used initially to explain feedback-inhibited enzymes, was presented by Monod, Wyman, and Changeux. We review the MWC theory and its applications for the understanding of signal transduction in biology, and also identify remaining issues that deserve theoretical and experimental substantiation.
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30
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Stieglitz KA, Pastra-Landis SC, Xia J, Tsuruta H, Kantrowitz ER. A single amino acid substitution in the active site of Escherichia coli aspartate transcarbamoylase prevents the allosteric transition. J Mol Biol 2005; 349:413-23. [PMID: 15890205 PMCID: PMC1479453 DOI: 10.1016/j.jmb.2005.03.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 03/13/2005] [Accepted: 03/17/2005] [Indexed: 11/26/2022]
Abstract
Modeling of the tetrahedral intermediate within the active site of Escherichia coli aspartate transcarbamoylase revealed a specific interaction with the side-chain of Gln137, an interaction not previously observed in the structure of the X-ray enzyme in the presence of N-phosphonacetyl-L-aspartate (PALA). Previous site-specific mutagenesis experiments showed that when Gln137 was replaced by alanine, the resulting mutant enzyme (Q137A) exhibited approximately 50-fold less activity than the wild-type enzyme, exhibited no homotropic cooperativity, and the binding of both carbamoyl phosphate and aspartate were extremely compromised. To elucidate the structural alterations in the mutant enzyme that might lead to such pronounced changes in kinetic and binding properties, the Q137A enzyme was studied by time-resolved, small-angle X-ray scattering and its structure was determined in the presence of PALA to 2.7 angstroms resolution. Time-resolved, small-angle X-ray scattering established that the natural substrates, carbamoyl phosphate and L-aspartate, do not induce in the Q137A enzyme the same conformational changes as observed for the wild-type enzyme, although the scattering pattern of the Q137A and wild-type enzymes in the presence of PALA were identical. The overall structure of the Q137A enzyme is similar to that of the R-state structure of wild-type enzyme with PALA bound. However, there are differences in the manner by which the Q137A enzyme coordinates PALA, especially in the side-chain positions of Arg105 and His134. The replacement of Gln137 by Ala also has a dramatic effect on the electrostatics of the active site. These data taken together suggest that the side-chain of Gln137 in the wild-type enzyme is required for the binding of carbamoyl phosphate in the proper orientation so as to induce conformational changes required for the creation of the high-affinity aspartate-binding site. The inability of carbamoyl phosphate to create the high-affinity binding site in the Q137A enzyme results in an enzyme locked in the low-activity low-affinity T state. These results emphasize the absolute requirement of the binding of carbamoyl phosphate for the creation of the high-affinity aspartate-binding site and for inducing the homotropic cooperativity in aspartate transcarbamoylase.
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Affiliation(s)
- Kimberly A. Stieglitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Jiarong Xia
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
| | - Hiro Tsuruta
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, MS69, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Evan R. Kantrowitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
- * Corresponding author, E-mail address of corresponding author:
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