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Curti M, Maffeis V, Teixeira Alves Duarte LG, Shareef S, Hallado LX, Curutchet C, Romero E. Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling. Protein Sci 2023; 32:e4579. [PMID: 36715022 PMCID: PMC9951196 DOI: 10.1002/pro.4579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
In photosynthesis, pigment-protein complexes achieve outstanding photoinduced charge separation efficiencies through a set of strategies in which excited states delocalization over multiple pigments ("excitons") and charge-transfer states play key roles. These concepts, and their implementation in bioinspired artificial systems, are attracting increasing attention due to the vast potential that could be tapped by realizing efficient photochemical reactions. In particular, de novo designed proteins provide a diverse structural toolbox that can be used to manipulate the geometric and electronic properties of bound chromophore molecules. However, achieving excitonic and charge-transfer states requires closely spaced chromophores, a non-trivial aspect since a strong binding with the protein matrix needs to be maintained. Here, we show how a general-purpose artificial protein can be optimized via molecular dynamics simulations to improve its binding capacity of a chlorophyll derivative, achieving complexes in which chromophores form two closely spaced and strongly interacting dimers. Based on spectroscopy results and computational modeling, we demonstrate each dimer is excitonically coupled, and propose they display signatures of charge-transfer state mixing. This work could open new avenues for the rational design of chromophore-protein complexes with advanced functionalities.
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Affiliation(s)
- Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Laboratoire de Chimie, UMR 5182, ENS Lyon, CNRSUniversité Lyon 1LyonFrance
| | | | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Luisa Xiomara Hallado
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, Facultat de Farmàcia i Ciències de l'AlimentacióUniversitat de Barcelona (UB)BarcelonaSpain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB)BarcelonaSpain
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
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2
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Widmann C, Ismail M, Sewald N, Niemann HH. Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties. Acta Crystallogr D Struct Biol 2020; 76:687-697. [PMID: 32627741 PMCID: PMC7336383 DOI: 10.1107/s2059798320007731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/05/2020] [Indexed: 01/18/2023] Open
Abstract
Flavin-dependent halogenases regioselectively introduce halide substituents into electron-rich substrates under mild reaction conditions. For the enzyme Xcc4156 from Xanthomonas campestris, the structure of a complex with the cofactor flavin adenine dinucleotide (FAD) and a bromide ion would be of particular interest as this enzyme exclusively brominates model substrates in vitro. Apo Xcc4156 crystals diffracted to 1.6 Å resolution. The structure revealed an open substrate-binding site lacking the loop regions that close off the active site and contribute to substrate binding in tryptophan halogenases. Therefore, Xcc4156 might accept larger substrates, possibly even peptides. Soaking of apo Xcc4156 crystals with FAD led to crumbling of the intergrown crystals. Around half of the crystals soaked with FAD did not diffract, while in the others there was no electron density for FAD. The FAD-binding loop, which changes its conformation between the apo and the FAD-bound form in related enzymes, is involved in a crystal contact in the apo Xcc4156 crystals. The conformational change that is predicted to occur upon FAD binding would disrupt this crystal contact, providing a likely explanation for the destruction of the apo crystals in the presence of FAD. Soaking with only bromide did not result in bromide bound to the catalytic halide-binding site. Simultaneous soaking with FAD and bromide damaged the crystals more severely than soaking with only FAD. Together, these latter two observations suggest that FAD and bromide bind to Xcc4156 with positive cooperativity. Thus, apo Xcc4156 crystals provide functional insight into FAD and bromide binding, even though neither the cofactor nor the halide is visible in the structure.
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Affiliation(s)
- Christiane Widmann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Mohamed Ismail
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Hartmut H. Niemann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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3
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Moritzer AC, Niemann HH. Binding of FAD and tryptophan to the tryptophan 6-halogenase Thal is negatively coupled. Protein Sci 2019; 28:2112-2118. [PMID: 31589794 PMCID: PMC6863734 DOI: 10.1002/pro.3739] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 11/08/2022]
Abstract
Flavin-dependent halogenases require reduced flavin adenine dinucleotide (FADH2 ), O2 , and halide salts to halogenate their substrates. We describe the crystal structures of the tryptophan 6-halogenase Thal in complex with FAD or with both tryptophan and FAD. If tryptophan and FAD were soaked simultaneously, both ligands showed impaired binding and in some cases only the adenosine monophosphate or the adenosine moiety of FAD was resolved, suggesting that tryptophan binding increases the mobility mainly of the flavin mononucleotide moiety. This confirms a negative cooperativity between the binding of substrate and cofactor that was previously described for other tryptophan halogenases. Binding of substrate to tryptophan halogenases reduces the affinity for the oxidized cofactor FAD presumably to facilitate the regeneration of FADH2 by flavin reductases.
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Alonso-Cotchico L, Rodríguez-Guerra Pedregal J, Lledós A, Maréchal JD. The Effect of Cofactor Binding on the Conformational Plasticity of the Biological Receptors in Artificial Metalloenzymes: The Case Study of LmrR. Front Chem 2019; 7:211. [PMID: 31024897 PMCID: PMC6467942 DOI: 10.3389/fchem.2019.00211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/18/2019] [Indexed: 12/21/2022] Open
Abstract
The design of Artificial Metalloenzymes (ArMs), which result from the incorporation of organometallic cofactors into biological structures, has grown steadily in the last two decades and important new-to-Nature reactions have been reached. These type of exercises could greatly benefit from an understanding of the structural impact that the inclusion of organometallic moieties may have on the biological host. To date though, our understanding of this phenomenon is highly partial. This lack of knowledge is one of the elements that condition that first-generation ArMs generally display relatively poor catalytic profiles. In this work, we approach this matter by assessing the dynamics and stability of a series of ArMs resulting from the inclusion, via different anchoring strategies, of a variety of organometallic cofactors into the Lactococcal multidrug resistance regulator (LmrR) protein. To this aim, we coupled standard force field-based techniques such as Protein-Ligand Docking and Molecular Dynamics simulations with a variety of trajectory convergence analyses, capable of assessing both the stability and flexibility of the different systems under study upon the binding of cofactors. Together with the experimental evidence obtained in other studies, we provide an overview on how these changes can affect the catalytic outcomes obtained from the different ArMs. Fundamentally, our results show that the convergence analysis used in this work can assess how the inclusion of synthetic metallic cofactors in proteins can condition different structural modulations of their host. Those conformational modifications are key to the success of the desired catalytic activity and their proper identification can be wisely used to improve the quality and the rate of success of the ArMs.
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Affiliation(s)
- Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | | | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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5
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Quehenberger J, Reichenbach T, Baumann N, Rettenbacher L, Divne C, Spadiut O. Kinetics and Predicted Structure of a Novel Xylose Reductase from Chaetomium thermophilum. Int J Mol Sci 2019; 20:ijms20010185. [PMID: 30621365 PMCID: PMC6337131 DOI: 10.3390/ijms20010185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/29/2018] [Accepted: 01/01/2019] [Indexed: 11/16/2022] Open
Abstract
While in search of an enzyme for the conversion of xylose to xylitol at elevated temperatures, a xylose reductase (XR) gene was identified in the genome of the thermophilic fungus Chaetomium thermophilum. The gene was heterologously expressed in Escherichia coli as a His6-tagged fusion protein and characterized for function and structure. The enzyme exhibits dual cofactor specificity for NADPH and NADH and prefers D-xylose over other pentoses and investigated hexoses. A homology model based on a XR from Candida tenuis was generated and the architecture of the cofactor binding site was investigated in detail. Despite the outstanding thermophilicity of its host the enzyme is, however, not thermostable.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Tom Reichenbach
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, SE-100 44 Stockholm, Sweden.
| | - Niklas Baumann
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Lukas Rettenbacher
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, SE-100 44 Stockholm, Sweden.
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Faculty of Technical Chemistry, TU Wien, 1060 Vienna, Austria.
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6
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Rao MV, Williams DR, Cocklin S, Loll PJ. Interaction between the AAA + ATPase p97 and its cofactor ataxin3 in health and disease: Nucleotide-induced conformational changes regulate cofactor binding. J Biol Chem 2017; 292:18392-18407. [PMID: 28939772 DOI: 10.1074/jbc.m117.806281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/16/2017] [Indexed: 12/29/2022] Open
Abstract
p97 is an essential ATPase associated with various cellular activities (AAA+) that functions as a segregase in diverse cellular processes, including the maintenance of proteostasis. p97 interacts with different cofactors that target it to distinct pathways; an important example is the deubiquitinase ataxin3, which collaborates with p97 in endoplasmic reticulum-associated degradation. However, the molecular details of this interaction have been unclear. Here, we characterized the binding of ataxin3 to p97, showing that ataxin3 binds with low-micromolar affinity to both wild-type p97 and mutants linked to degenerative disorders known as multisystem proteinopathy 1 (MSP1); we further showed that the stoichiometry of binding is one ataxin3 molecule per p97 hexamer. We mapped the binding determinants on each protein, demonstrating that ataxin3's p97/VCP-binding motif interacts with the inter-lobe cleft in the N-domain of p97. We also probed the nucleotide dependence of this interaction, confirming that ataxin3 and p97 associate in the presence of ATP and in the absence of nucleotide, but not in the presence of ADP. Our experiments suggest that an ADP-driven downward movement of the p97 N-terminal domain dislodges ataxin3 by inducing a steric clash between the D1-domain and ataxin3's C terminus. In contrast, MSP1 mutants of p97 bind ataxin3 irrespective of their nucleotide state, indicating a failure by these mutants to translate ADP binding into a movement of the N-terminal domain. Our model provides a mechanistic explanation for how nucleotides regulate the p97-ataxin3 interaction and why atypical cofactor binding is observed with MSP1 mutants.
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Affiliation(s)
- Maya V Rao
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Dewight R Williams
- the LeRoy Eyring Center for Solid State Science, Arizona State University, Tempe, Arizona 85287
| | - Simon Cocklin
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Patrick J Loll
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
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7
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Dutta SK, Serrano P, Geralt M, Axelrod HL, Xu Q, Lesley SA, Godzik A, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K. Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus. Protein Sci 2015; 24:1600-8. [PMID: 26177955 DOI: 10.1002/pro.2743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/06/2022]
Abstract
Flavodoxins in combination with the flavin mononucleotide (FMN) cofactor play important roles for electron transport in prokaryotes. Here, novel insights into the FMN-binding mechanism to flavodoxins-4 were obtained from the NMR structures of the apo-protein from Lactobacillus acidophilus (YP_193882.1) and comparison of its complex with FMN. Extensive reversible conformational changes were observed upon FMN binding and release. The NMR structure of the FMN complex is in agreement with the crystal structure (PDB ID: 3EDO) and exhibits the characteristic flavodoxin fold, with a central five-stranded parallel β-sheet and five α-helices forming an α/β-sandwich architecture. The structure differs from other flavoproteins in that helix α2 is oriented perpendicular to the β-sheet and covers the FMN-binding site. This helix reversibly unfolds upon removal of the FMN ligand, which represents a unique structural rearrangement among flavodoxins.
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Affiliation(s)
- Samit Kumar Dutta
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Pedro Serrano
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Michael Geralt
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Herbert L Axelrod
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Scott A Lesley
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121
| | - Adam Godzik
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, 92037.,Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, 92093
| | - Ashley M Deacon
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Ian A Wilson
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Kurt Wüthrich
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
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8
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Cahn JK, Brinkmann-Chen S, Spatzal T, Wiig JA, Buller AR, Einsle O, Hu Y, Ribbe MW, Arnold FH. Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. Biochem J 2015; 468:475-84. [PMID: 25849365 DOI: 10.1042/BJ20150183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/07/2015] [Indexed: 11/17/2022]
Abstract
Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are class I enzymes, structural studies to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs. These include the first structure of a KARI with a six-residue β2αB (cofactor specificity determining) loop and an NADPH phosphate-binding geometry distinct from that of the seven- and 12-residue loops. We also present the first structures of naturally occurring KARIs that utilize NADH as cofactor. These results show insertions in the specificity loops that confounded previous attempts to classify them according to loop length. Lastly, we explore the conformational changes that occur in class I KARIs upon binding of cofactor and metal ions. The class I KARI structures indicate that the active sites close upon binding NAD(P)H, similar to what is observed in the class II KARIs of rice and spinach and different from the opening of the active site observed in the class II KARI of Escherichia coli. This conformational change involves a decrease in the bending of the helix that runs between the domains and a rearrangement of the nicotinamide-binding site.
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9
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Kim J, Beak DG, Kim YT, Choi JD, Yoon MY. Effects of deletions at the C-terminus of tobacco acetohydroxyacid synthase on the enzyme activity and cofactor binding. Biochem J 2004; 384:59-68. [PMID: 15521822 PMCID: PMC1134088 DOI: 10.1042/bj20040427] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Revised: 06/17/2004] [Accepted: 07/22/2004] [Indexed: 11/17/2022]
Abstract
AHAS (acetohydroxyacid synthase) catalyses the first committed step in the biosynthesis of branched-chain amino acids, such as valine, leucine and isoleucine. Owing to the unique presence of these biosynthetic pathways in plants and micro-organisms, AHAS has been widely investigated as an attractive target of several classes of herbicides. Recently, the crystal structure of the catalytic subunit of yeast AHAS has been resolved at 2.8 A (1 A=0.1 nm), showing that the active site is located at the dimer interface and is near the herbicide-binding site. In this structure, the existence of two disordered regions, a 'mobile loop' and a C-terminal 'lid', is worth notice. Although these regions contain the residues that are known to be important in substrate specificity and in herbicide resistance, they are poorly folded into any distinct secondary structure and are not within contact distance of the cofactors. In the present study, we have tried to demonstrate the role of these regions of tobacco AHAS by constructing variants with serial deletions, based on the structure of yeast AHAS. In contrast with the wild-type AHAS, the truncated mutant which removes the C-terminal lid, Delta630, and the internal deletion mutant without the mobile loop, Delta567-582, impaired the binding affinity for ThDP (thiamine diphosphate), and showed different elution profiles representing a monomeric form in gel-filtration chromatography. Our results suggest that these regions are involved in the binding/stabilization of the active dimer and ThDP binding.
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Affiliation(s)
- Joungmok Kim
- *Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, South Korea
| | - Dong-Gil Beak
- *Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, South Korea
| | - Young-Tae Kim
- †Department of Microbiology, Pukyung National University, Busan 608-737, South Korea
| | - Jung-Do Choi
- ‡School of Life Science and Research Institute for Genetic Engineering, Chungbuk National University, Cheongju 361-763, South Korea
| | - Moon-Young Yoon
- *Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, South Korea
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Abstract
A mutant of Salmonella typhimurium LT-2 that requires either vitamin B(6) or histidine for growth was found to synthesize vitamin B(5) in amounts comparable to the parent strain, but to be deficient in imidazoleacetol phosphate transaminase (L-histidinolphosphate: 2-oxoglutarate aminotransferase, EC 2.6.1.9), an enzyme required for histidine biosynthesis. The mutant apotransaminase required a 50-fold higher concentration of pyridoxal 5'-phosphate for half-maximum activation than the corresponding wild-type enzyme; the fully activated mutant enzyme also displays a much lower maximum rate of catalysis than the enzyme from the parent strain. Such mutational changes in bacteria resemble those in certain vitamin B(6)-responsive genetic diseases in man and provide useful experimental material for the study of factors involved in coenzyme binding and enzymatic catalysis.
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