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Ito S, Yagi K, Sugita Y. Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. J Chem Phys 2023; 158:115101. [PMID: 36948822 DOI: 10.1063/5.0134117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3-10-fold upon the binding of 3-indole-D-glycerol-3'-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Ito S, Yagi K, Sugita Y. Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure. J Phys Chem B 2022; 126:3300-3308. [PMID: 35446577 PMCID: PMC9083551 DOI: 10.1021/acs.jpcb.2c01556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α and β-subunits and catalyzes the last two steps of l-tryptophan (L-Trp) biosynthesis, namely, cleavage of 3-indole-d-glycerol-3'-phosphate (IGP) into indole and glyceraldehyde-3-phosphate (G3P) in the α-subunit, and a pyridoxal phosphate (PLP)-dependent reaction of indole and l-serine (L-Ser) to produce L-Trp in the β-subunit. Importantly, the IGP binding at the α-subunit affects the β-subunit conformation and its ligand-binding affinity, which, in turn, enhances the enzymatic reaction at the α-subunit. The intersubunit communications in TRPS have been investigated extensively for decades because of the fundamental and pharmaceutical importance, while it is still difficult to answer how TRPS allostery is regulated at the atomic detail. Here, we investigate the allosteric regulation of TRPS by all-atom classical molecular dynamics (MD) simulations and analyze the potential of mean-force (PMF) along conformational changes of the α- and β-subunits. The present simulation has revealed a widely opened conformation of the β-subunit, which provides a pathway for L-Ser to enter into the β-active site. The IGP binding closes the α-subunit and induces a wide opening of the β-subunit, thereby enhancing the binding affinity of L-Ser to the β-subunit. Structural analyses have identified critical hydrogen bonds (HBs) at the interface of the two subunits (αG181-βS178, αP57-βR175, etc.) and HBs between the β-subunit (βT110 - βH115) and a complex of PLP and L-Ser (an α-aminoacrylate intermediate). The former HBs regulate the allosteric, β-subunit opening, whereas the latter HBs are essential for closing the β-subunit in a later step. The proposed mechanism for how the interdomain communication in TRPS is realized with ligand bindings is consistent with the previous experimental data, giving a general idea to interpret the allosteric regulations in multidomain proteins.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Mohan S, Jade D, Gupta S, Ayyamperumal S, Chandrasekar MJN, Nanjan MJ. Virtual high-throughput screening: potential inhibitors for the mycobacterial α-subunit of tryptophan synthase. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2021.2015069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Surender Mohan
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Dhananjay Jade
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Sonal Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Selvaraj Ayyamperumal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, India
- School of Life Sciences, JSS Academy of Higher Education & Research, Long Wood Campus, Ooty, India
| | - M. J. N Chandrasekar
- School of Life Sciences, JSS Academy of Higher Education & Research, Long Wood Campus, Ooty, India
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Teixeira CSS, Ramos MJ, Sousa SF, Cerqueira NMFSA. Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla S. Silva Teixeira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTEDepartamento de Química e BioquímicaFaculdade de CiênciasUniversidade do Porto Porto 4169-007 Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
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Busch F, Rajendran C, Heyn K, Schlee S, Merkl R, Sterner R. Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes. Cell Chem Biol 2016; 23:709-15. [DOI: 10.1016/j.chembiol.2016.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/26/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022]
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Wang W, Baker P, Seah SYK. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 2010; 49:3774-82. [PMID: 20364820 DOI: 10.1021/bi100251u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order mechanism while BphI exhibits a compulsory order mechanism, with pyruvate binding first. Both aldolases are able to utilize aldehyde acceptors two to five carbons in length; however, HpaI showed broader specificity and had a preference for aldehydes containing longer linear alkyl chains or C2-OH substitutions. Both enzymes were able to bind 2-keto acids larger than pyruvate, but only HpaI was able to utilize both pyruvate and 2-ketobutanoate as carbonyl donors in the aldol addition reaction. HpaI lacks stereospecific control producing racemic mixtures of 4-hydroxy-2-oxopentanoate (HOPA) from pyruvate and acetaldehyde while BphI synthesizes only (4S)-HOPA. BphI is also able to utilize acetaldehyde produced by the reduction of acetyl-CoA catalyzed by the associated aldehyde dehydrogenase, BphJ. This aldehyde was directly channeled from the dehydrogenase to the aldolase active sites, with an efficiency of 84%. Furthermore, the BphJ reductive deacylation reaction increased 4-fold when BphI was catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.
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Affiliation(s)
- Weijun Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K. Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding. FEBS J 2010; 277:2157-70. [PMID: 20370823 DOI: 10.1111/j.1742-4658.2010.07631.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To understand the basis for the lower activity of the tryptophan synthase beta(2) subunit in comparison to the alpha(2)beta(2) complex, we determined the crystal structures of apo-beta(2) and holo-beta(2) from Escherichia coli at 3.0 and 2.9 A resolutions, respectively. To our knowledge, this is the first report of both beta(2) subunit structures with and without pyridoxal-5'-phosphate. The apo-type molecule retained a dimeric form in solution, as in the case of the holo-beta(2) subunit. The subunit structures of both the apo-beta(2) and the holo-beta(2) forms consisted of two domains, namely the N domain and the C domain. Although there were significant structural differences between the apo- and holo-structures, they could be easily superimposed with a 22 degrees rigid body rotation of the C domain. The pyridoxal-5'-phosphate-bound holo-form had multiple interactions between the two domains and a long loop (residues 260-310), which were missing in the apo-form. Comparison of the structures of holo-Ecbeta(2) and Stbeta(2) in the alpha(2)beta(2) complex from Salmonella typhimurium (Stalpha(2)beta(2)) identified the cause of the lower enzymatic activity of holo-Ecbeta(2) in comparison with Stalpha(2)beta(2). The substrate (indole) gate residues, Tyr279 and Phe280, block entry of the substrate into the beta(2) subunit, although the indole can directly access the active site as a result of a wider cleft between the N and C domains in the holo-Ecbeta(2) subunit. In addition, the structure around betaAsp305 of the holo-Ecbeta(2) subunit was similar to the open state of Stalpha(2)beta(2) with low activity, resulting in lower activity of holo-Ecbeta(2).
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Affiliation(s)
- Kazuya Nishio
- Institute for Protein Research, Osaka University, Japan
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Raboni S, Bettati S, Mozzarelli A. Tryptophan synthase: a mine for enzymologists. Cell Mol Life Sci 2009; 66:2391-403. [PMID: 19387555 PMCID: PMC11115766 DOI: 10.1007/s00018-009-0028-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/30/2009] [Accepted: 03/31/2009] [Indexed: 01/12/2023]
Abstract
Tryptophan synthase is a pyridoxal 5'-phosphate-dependent alpha(2)beta(2) complex catalyzing the last two steps of tryptophan biosynthesis in bacteria, plants and fungi. Structural, dynamic and functional studies, carried out over more than 40 years, have unveiled that: (1) alpha- and beta-active sites are separated by about 20 A and communicate via the selective stabilization of distinct conformational states, triggered by the chemical nature of individual catalytic intermediates and by allosteric ligands; (2) indole, formed at alpha-active site, is intramolecularly channeled to the beta-active site; and (3) naturally occurring as well as genetically generated mutants have allowed to pinpoint functional and regulatory roles for several individual amino acids. These key features have made tryptophan synthase a text-book case for the understanding of the interplay between chemistry and conformational energy landscapes.
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Affiliation(s)
- Samanta Raboni
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Present Address: CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Stefano Bettati
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Italian National Institute of Biostructures and Biosystems, Parma, Italy
| | - Andrea Mozzarelli
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Italian National Institute of Biostructures and Biosystems, Parma, Italy
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Barends TRM, Dunn MF, Schlichting I. Tryptophan synthase, an allosteric molecular factory. Curr Opin Chem Biol 2008; 12:593-600. [DOI: 10.1016/j.cbpa.2008.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 07/07/2008] [Indexed: 11/25/2022]
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Dunn MF, Niks D, Ngo H, Barends TR, Schlichting I. Tryptophan synthase: the workings of a channeling nanomachine. Trends Biochem Sci 2008; 33:254-64. [DOI: 10.1016/j.tibs.2008.04.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/07/2008] [Accepted: 04/08/2008] [Indexed: 01/25/2023]
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