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Jiao W, Fan Y, Blackmore NJ, Parker EJ. A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis. J Biol Chem 2020; 295:6252-6262. [PMID: 32217694 DOI: 10.1074/jbc.ra120.012605] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/20/2020] [Indexed: 01/08/2023] Open
Abstract
Allostery exploits the conformational dynamics of enzymes by triggering a shift in population ensembles toward functionally distinct conformational or dynamic states. Allostery extensively regulates the activities of key enzymes within biosynthetic pathways to meet metabolic demand for their end products. Here, we have examined a critical enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), at the gateway to aromatic amino acid biosynthesis in Mycobacterium tuberculosis, which shows extremely complex dynamic allostery: three distinct aromatic amino acids jointly communicate occupancy to the active site via subtle changes in dynamics, enabling exquisite fine-tuning of delivery of these essential metabolites. Furthermore, this allosteric mechanism is co-opted by pathway branchpoint enzyme chorismate mutase upon complex formation. In this study, using statistical coupling analysis, site-directed mutagenesis, isothermal calorimetry, small-angle X-ray scattering, and X-ray crystallography analyses, we have pinpointed a critical node within the complex dynamic communication network responsible for this sophisticated allosteric machinery. Through a facile Gly to Pro substitution, we have altered backbone dynamics, completely severing the allosteric signal yet remarkably, generating a nonallosteric enzyme that retains full catalytic activity. We also identified a second residue of prime importance to the inter-enzyme communication with chorismate mutase. Our results reveal that highly complex dynamic allostery is surprisingly vulnerable and provide further insights into the intimate link between catalysis and allostery.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Yifei Fan
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Nicola J Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand .,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
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Reichau S, Blackmore NJ, Jiao W, Parker EJ. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids. PLoS One 2016; 11:e0152723. [PMID: 27128682 PMCID: PMC4851294 DOI: 10.1371/journal.pone.0152723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/17/2016] [Indexed: 02/02/2023] Open
Abstract
Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal.
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Affiliation(s)
- Sebastian Reichau
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Nicola J. Blackmore
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Wanting Jiao
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Emily J. Parker
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- * E-mail:
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Blackmore NJ, Nazmi AR, Hutton RD, Webby MN, Baker EN, Jameson GB, Parker EJ. Complex Formation between Two Biosynthetic Enzymes Modifies the Allosteric Regulatory Properties of Both: AN EXAMPLE OF MOLECULAR SYMBIOSIS. J Biol Chem 2015; 290:18187-18198. [PMID: 26032422 DOI: 10.1074/jbc.m115.638700] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 11/06/2022] Open
Abstract
Allostery, where remote ligand binding alters protein function, is essential for the control of metabolism. Here, we have identified a highly sophisticated allosteric response that allows complex control of the pathway for aromatic amino acid biosynthesis in the pathogen Mycobacterium tuberculosis. This response is mediated by an enzyme complex formed by two pathway enzymes: chorismate mutase (CM) and 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Whereas both enzymes are active in isolation, the catalytic activity of both enzymes is enhanced, and in particular that of the much smaller CM is greatly enhanced (by 120-fold), by formation of a hetero-octameric complex between CM and DAH7PS. Moreover, on complex formation M. tuberculosis CM, which has no allosteric response on its own, acquires allosteric behavior to facilitate its own regulatory needs by directly appropriating and partly reconfiguring the allosteric machinery that provides a synergistic allosteric response in DAH7PS. Kinetic and analytical ultracentrifugation experiments demonstrate that allosteric binding of phenylalanine specifically promotes hetero-octameric complex dissociation, with concomitant reduction of CM activity. Together, DAH7PS and CM from M. tuberculosis provide exquisite control of aromatic amino acid biosynthesis, not only controlling flux into the start of the pathway, but also directing the pathway intermediate chorismate into either Phe/Tyr or Trp biosynthesis.
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Affiliation(s)
- Nicola J Blackmore
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Ali Reza Nazmi
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Richard D Hutton
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Melissa N Webby
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
| | - Emily J Parker
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand.
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Abstract
Background Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. Results Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. Conclusions The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0379-x) contains supplementary material, which is available to authorized users.
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Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis. J Mol Biol 2013; 425:1582-92. [DOI: 10.1016/j.jmb.2012.12.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/19/2022]
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Kapnick SM, Zhang Y. New tuberculosis drug development: targeting the shikimate pathway. Expert Opin Drug Discov 2013; 3:565-77. [PMID: 23484927 DOI: 10.1517/17460441.3.5.565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, yet no new drugs have been developed in the last 40 years. OBJECTIVE The exceedingly lengthy TB chemotherapy and the increasing emergence of drug resistance complicated by HIV co-infection call for the development of new TB drugs. These problems are further compounded by a poor understanding of the biology of persister bacteria. METHODS New molecular tools have offered insights into potential new drug targets, particularly the enzymes of the shikimate pathway, which is the focus of this review. RESULTS/CONCLUSION Shikimate pathway enzymes, especially shikimate kinase, may offer attractive targets for new TB drug and vaccine development.
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Affiliation(s)
- Senta M Kapnick
- Johns Hopkins University, Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA +1 410 614 2975 ; +1 410 955 0105 ;
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Reichau S, Parker EJ. Active site plasticity of a critical enzyme from Mycobacterium tuberculosis. RSC Adv 2013. [DOI: 10.1039/c3ra00037k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Reichau S, Jiao W, Walker SR, Hutton RD, Baker EN, Parker EJ. Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis: combining mechanism- and modeling-based design. J Biol Chem 2011; 286:16197-207. [PMID: 21454647 PMCID: PMC3093739 DOI: 10.1074/jbc.m110.211649] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/07/2011] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis remains a serious global health threat, with the emergence of multidrug-resistant strains highlighting the urgent need for novel antituberculosis drugs. The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the first step of the shikimate pathway for the biosynthesis of aromatic compounds. This pathway has been shown to be essential in Mycobacterium tuberculosis, the pathogen responsible for tuberculosis. DAH7PS catalyzes a condensation reaction between P-enolpyruvate and erythrose 4-phosphate to give 3-deoxy-D-arabino-heptulosonate 7-phosphate. The enzyme reaction mechanism is proposed to include a tetrahedral intermediate, which is formed by attack of an active site water on the central carbon of P-enolpyruvate during the course of the reaction. Molecular modeling of this intermediate into the active site reported in this study shows a configurational preference consistent with water attack from the re face of P-enolpyruvate. Based on this model, we designed and synthesized an inhibitor of DAH7PS that mimics this reaction intermediate. Both enantiomers of this intermediate mimic were potent inhibitors of M. tuberculosis DAH7PS, with inhibitory constants in the nanomolar range. The crystal structure of the DAH7PS-inhibitor complex was solved to 2.35 Å. Both the position of the inhibitor and the conformational changes of active site residues observed in this structure correspond closely to the predictions from the intermediate modeling. This structure also identifies a water molecule that is located in the appropriate position to attack the re face of P-enolpyruvate during the course of the reaction, allowing the catalytic mechanism for this enzyme to be clearly defined.
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Affiliation(s)
- Sebastian Reichau
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Wanting Jiao
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Scott R. Walker
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Richard D. Hutton
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Edward N. Baker
- the Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Emily J. Parker
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
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Webby CJ, Jiao W, Hutton RD, Blackmore NJ, Baker HM, Baker EN, Jameson GB, Parker EJ. Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. J Biol Chem 2010; 285:30567-76. [PMID: 20667835 DOI: 10.1074/jbc.m110.111856] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. The first reaction is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Feedback regulation of DAH7PS activity by aromatic amino acids controls shikimate pathway flux. Whereas Mycobacterium tuberculosis DAH7PS (MtuDAH7PS) is not inhibited by the addition of Phe, Tyr, or Trp alone, combinations cause significant loss of enzyme activity. In the presence of 200 μm Phe, only 2.4 μm Trp is required to reduce enzymic activity to 50%. Reaction kinetics were analyzed in the presence of inhibitory concentrations of Trp/Phe or Trp/Tyr. In the absence of inhibitors, the enzyme follows Michaelis-Menten kinetics with respect to substrate erythrose 4-phosphate (E4P), whereas the addition of inhibitor combinations caused significant homotropic cooperativity with respect to E4P, with Hill coefficients of 3.3 (Trp/Phe) and 2.8 (Trp/Tyr). Structures of MtuDAH7PS/Trp/Phe, MtuDAH7PS/Trp, and MtuDAH7PS/Phe complexes were determined. The MtuDAH7PS/Trp/Phe homotetramer binds four Trp and six Phe molecules. Binding sites for both aromatic amino acids are formed by accessory elements to the core DAH7PS (β/α)(8) barrel that are unique to the type II DAH7PS family and contribute to the tight dimer and tetramer interfaces. A comparison of the liganded and unliganded MtuDAH7PS structures reveals changes in the interface areas associated with inhibitor binding and a small displacement of the E4P binding loop. These studies uncover a previously unrecognized mode of control for the branched pathways of aromatic amino acid biosynthesis involving synergistic inhibition by specific pairs of pathway end products.
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Affiliation(s)
- Celia J Webby
- From the Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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Tomioka H. Development of new antituberculous agents based on new drug targets and structure–activity relationship. Expert Opin Drug Discov 2007; 3:21-49. [DOI: 10.1517/17460441.3.1.21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Webby CJ, Baker HM, Lott JS, Baker EN, Parker EJ. The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes. J Mol Biol 2005; 354:927-39. [PMID: 16288916 DOI: 10.1016/j.jmb.2005.09.093] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/28/2022]
Abstract
The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties.
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Affiliation(s)
- Celia J Webby
- Centre of Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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