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Wang Q, Zhu B, Chen C, Yuan Z, Guo J, Yang X, Wang S, Lv Y, Liu Q, Yang B, Sun C, Wang P, Deng X. A Single Nucleotide Substitution of GSAM Gene Causes Massive Accumulation of Glutamate 1-Semialdehyde and Yellow Leaf Phenotype in Rice. RICE (NEW YORK, N.Y.) 2021; 14:50. [PMID: 34089406 PMCID: PMC8179877 DOI: 10.1186/s12284-021-00492-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/12/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Tetrapyrroles play indispensable roles in various biological processes. In higher plants, glutamate 1-semialdehyde 2,1-aminomutase (GSAM) converts glutamate 1-semialdehyde (GSA) to 5-aminolevulinic acid (ALA), which is the rate-limiting step of tetrapyrrole biosynthesis. Up to now, GSAM genes have been successively identified from many species. Besides, it was found that GSAM could form a dimeric protein with itself by x-ray crystallography. However, no mutant of GSAM has been identified in monocotyledonous plants, and no experiment on interaction of GSAM protein with itself has been reported so far. RESULT We isolated a yellow leaf mutant, ys53, in rice (Oryza sativa). The mutant showed decreased photosynthetic pigment contents, suppressed chloroplast development, and reduced photosynthetic capacity. In consequence, its major agronomic traits were significantly affected. Map-based cloning revealed that the candidate gene was LOC_Os08g41990 encoding GSAM protein. In ys53 mutant, a single nucleotide substitution in this gene caused an amino acid change in the encoded protein, so its ALA-synthesis ability was significantly reduced and GSA was massively accumulated. Complementation assays suggested the mutant phenotype of ys53 could be rescued by introducing wild-type OsGSAM gene, confirming that the point mutation in OsGSAM is the cause of the mutant phenotype. OsGSAM is mainly expressed in green tissues, and its encoded protein is localized to chloroplast. qRT-PCR analysis indicated that the mutation of OsGSAM not only affected the expressions of tetrapyrrole biosynthetic genes, but also influenced those of photosynthetic genes in rice. In addition, the yeast two-hybrid experiment showed that OsGSAM protein could interact with itself, which could largely depend on the two specific regions containing the 81th-160th and the 321th-400th amino acid residues at its N- and C-terminals, respectively. CONCLUSIONS We successfully characterized rice GSAM gene by a yellow leaf mutant and map-based cloning approach. Meanwhile, we verified that OsGSAM protein could interact with itself mainly by means of the two specific regions of amino acid residues at its N- and C-terminals, respectively.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Baiyang Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congping Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhaodi Yuan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jia Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorong Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - San Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Lv
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingsong Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Vila-Santa A, Islam MA, Ferreira FC, Prather KLJ, Mira NP. Prospecting Biochemical Pathways to Implement Microbe-Based Production of the New-to-Nature Platform Chemical Levulinic Acid. ACS Synth Biol 2021; 10:724-736. [PMID: 33764057 DOI: 10.1021/acssynbio.0c00518] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Levulinic acid is a versatile platform molecule with potential to be used as an intermediate in the synthesis of many value-added products used across different industries, from cosmetics to fuels. Thus far, microbial biosynthetic pathways having levulinic acid as a product or an intermediate are not known, which restrains the development and optimization of a microbe-based process envisaging the sustainable bioproduction of this chemical. One of the doors opened by synthetic biology in the design of microbial systems is the implementation of new-to-nature pathways, that is, the assembly of combinations of enzymes not observed in vivo, where the enzymes can use not only their native substrates but also non-native ones, creating synthetic steps that enable the production of novel compounds. Resorting to a combined approach involving complementary computational tools and extensive manual curation, in this work, we provide a thorough prospect of candidate biosynthetic pathways that can be assembled for the production of levulinic acid in Escherichia coli or Saccharomyces cerevisiae. Out of the hundreds of combinations screened, five pathways were selected as best candidates on the basis of the availability of substrates and of candidate enzymes to catalyze the synthetic steps (that is, those steps that involve conversions not previously described). Genome-scale metabolic modeling was used to assess the performance of these pathways in the two selected hosts and to anticipate possible bottlenecks. Not only does the herein described approach offer a platform for the future implementation of the microbial production of levulinic acid but also it provides an organized research strategy that can be used as a framework for the implementation of other new-to-nature biosynthetic pathways for the production of value-added chemicals, thus fostering the emerging field of synthetic industrial microbiotechnology.
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Affiliation(s)
- Ana Vila-Santa
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - M. Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Leicestershire, LE11 3TU Loughborough, United Kingdom
| | - Frederico C. Ferreira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Kristala L. J. Prather
- Department of Chemical Engineering and Center for Integrative Synthetic Biology (CISB), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nuno P. Mira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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Nardella C, Boi D, di Salvo ML, Barile A, Stetefeld J, Tramonti A, Contestabile R. Isolation of a Complex Formed Between Acinetobacter baumannii HemA and HemL, Key Enzymes of Tetrapyrroles Biosynthesis. Front Mol Biosci 2019; 6:6. [PMID: 30863751 PMCID: PMC6399207 DOI: 10.3389/fmolb.2019.00006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/06/2019] [Indexed: 01/19/2023] Open
Abstract
Plants, algae and most bacteria synthesize 5-aminolevulinic acid (ALA), the universal precursor of tetrapyrroles such as heme, chlorophyll and coenzyme B12, by a two-step transformation involving the NADPH-dependent glutamyl-tRNA reductase (HemA), which reduces tRNA-bound glutamate to glutamate-1-semialdehyde (GSA), and the pyridoxamine 5′-phosphate-dependent glutamate-1-semialdehyde-2,1-aminomutase (HemL), responsible for the isomerization of GSA into ALA. Since GSA is a very unstable compound at pH values around neutrality, the formation of a HemA-HemL complex has been proposed to occur, allowing for direct channeling of this intermediate from HemA to HemL. Experimental evidence of the formation of this complex has been obtained with the enzymes from Escherichia coli and Chlamydomonas reinhardtii. However, its isolation has never been attained, probably because HemA is degraded when intracellular heme accumulates. In this work, we devised a co-expression and co-purification strategy of HemA and HemL from Acinetobacter baumannii, which allowed the isolation of the HemA-HemL complex. Our results indicate that HemA is stabilized when co-expressed with HemL. The addition of citrate throughout the expression and purification procedure further promotes the formation of the HemA-HemL complex, which can be isolated in fair amount for functional and structural studies. This work lays the bases for a rational design of HemA-HemA inhibitors to be developed as antibacterial agents against A. baumannii, a multidrug resistant opportunistic pathogen responsible for a broad range of severe nosocomial infections.
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Affiliation(s)
- Caterina Nardella
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Dalila Boi
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Martino L di Salvo
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Anna Barile
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Angela Tramonti
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberto Contestabile
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
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Schiroli D, Peracchi A. A subfamily of PLP-dependent enzymes specialized in handling terminal amines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1200-11. [PMID: 25770684 DOI: 10.1016/j.bbapap.2015.02.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 01/04/2023]
Abstract
The present review focuses on a subfamily of pyridoxal phosphate (PLP)-dependent enzymes, belonging to the broader fold-type I structural group and whose archetypes can be considered ornithine δ-transaminase and γ-aminobutyrate transaminase. These proteins were originally christened "subgroup-II aminotransferases" (AT-II) but are very often referred to as "class-III aminotransferases". As names suggest, the subgroup includes mainly transaminases, with just a few interesting exceptions. However, at variance with most other PLP-dependent enzymes, catalysts in this subfamily seem specialized at utilizing substrates whose amino function is not adjacent to a carboxylate group. AT-II enzymes are widespread in biology and play mostly catabolic roles. Furthermore, today several transaminases in this group are being used as bioorganic tools for the asymmetric synthesis of chiral amines. We present an overview of the biochemical and structural features of these enzymes, illustrating how they are distinctive and how they compare with those of the other fold-type I enzymes. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Davide Schiroli
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy
| | - Alessio Peracchi
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy.
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Steffen-Munsberg F, Vickers C, Kohls H, Land H, Mallin H, Nobili A, Skalden L, van den Bergh T, Joosten HJ, Berglund P, Höhne M, Bornscheuer UT. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv 2015; 33:566-604. [PMID: 25575689 DOI: 10.1016/j.biotechadv.2014.12.012] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/25/2023]
Abstract
In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
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Affiliation(s)
- Fabian Steffen-Munsberg
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Clare Vickers
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hannes Kohls
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrik Land
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Hendrik Mallin
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Alberto Nobili
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Lilly Skalden
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Per Berglund
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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6
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Asymmetry of the active site loop conformation between subunits of glutamate-1-semialdehyde aminomutase in solution. BIOMED RESEARCH INTERNATIONAL 2013; 2013:353270. [PMID: 23984351 PMCID: PMC3747428 DOI: 10.1155/2013/353270] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 06/27/2013] [Indexed: 02/02/2023]
Abstract
Glutamate-1-semialdehyde aminomutase (GSAM) is a dimeric, pyridoxal 5′-phosphate (PLP)- dependent enzyme catalysing in plants and some bacteria the isomerization of L-glutamate-1-semialdehyde to 5-aminolevulinate, a common precursor of chlorophyll, haem, coenzyme B12, and other tetrapyrrolic compounds. During the catalytic cycle, the coenzyme undergoes conversion from pyridoxamine 5′-phosphate (PMP) to PLP. The entrance of the catalytic site is protected by a loop that is believed to switch from an open to a closed conformation during catalysis. Crystallographic studies indicated that the structure of the mobile loop is related to the form of the cofactor bound to the active site, allowing for asymmetry within the dimer. Since no information on structural and functional asymmetry of the enzyme in solution is available in the literature, we investigated the active site accessibility by determining the cofactor fluorescence quenching of PMP- and PLP-GSAM forms. PLP-GSAM is partially quenched by potassium iodide, suggesting that at least one catalytic site is accessible to the anionic quencher and therefore confirming the asymmetry observed in the crystal structure. Iodide induces release of the cofactor from PMP-GSAM, apparently from only one catalytic site, therefore suggesting an asymmetry also in this form of the enzyme in solution, in contrast with the crystallographic data.
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7
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Ge H, Lv X, Fan J, Gao Y, Teng M, Niu L. Crystal structure of glutamate-1-semialdehyde aminotransferase from Bacillus subtilis with bound pyridoxamine-5'-phosphate. Biochem Biophys Res Commun 2010; 402:356-60. [PMID: 20946885 DOI: 10.1016/j.bbrc.2010.10.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 10/07/2010] [Indexed: 11/18/2022]
Abstract
Glutamate-1-semialdehyde aminotransferase (GSA-AT), also named glutamate-1-semialdehyde aminomutase (GSAM), a pyridoxamine-5'-phosphate (PMP)/pyridoxal-5'-phosphate (PLP) dependent enzyme, catalyses the transamination of the substrate glutamate-1-semialdehyde (GSA) to the product 5-Aminolevulinic acid (ALA) by an unusual intramolecular exchange of amino and oxo groups within the catalytic intermediate 4,5-diaminovalerate (DAVA). This paper presents the crystal structure of GSA-AT from Bacillus subtilis (GSA-ATBsu) in its PMP-bound form at 2.3Å resolution. The structure was determined by molecular replacement using the Synechococcus GSAM (GSAMSyn) structure as a search model. Unlike the previous reported GSAM/GSA-AT structures, GSA-ATBsu is a symmetric homodimer in the PMP-bound form, which shows the structural symmetry at the gating loop region with open state, as well as identical cofactor (PMP) binding in each monomer. This observation of PMP in combination with an "open" lid supports one characteristic feature for this enzyme, as the catalyzed reaction is believed to be initiated by PMP. Furthermore, the symmetry of GSA-ATBsu structure challenges the previously proposed negative cooperativity between monomers of this enzyme.
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Affiliation(s)
- Honghua Ge
- Modern Experiment Technology Center, Anhui University, Hefei, Anhui 230039, China.
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8
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Orriss GL, Patel TR, Sorensen J, Stetefeld J. Absence of a catalytic water confers resistance to the neurotoxin gabaculine. FASEB J 2009; 24:404-14. [DOI: 10.1096/fj.09-138297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- George L. Orriss
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Trushar R. Patel
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - John Sorensen
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Jörg Stetefeld
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
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9
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Heinemann IU, Jahn M, Jahn D. The biochemistry of heme biosynthesis. Arch Biochem Biophys 2008; 474:238-51. [PMID: 18314007 DOI: 10.1016/j.abb.2008.02.015] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 02/14/2008] [Accepted: 02/14/2008] [Indexed: 02/03/2023]
Abstract
Heme is an integral part of proteins involved in multiple electron transport chains for energy recovery found in almost all forms of life. Moreover, heme is a cofactor of enzymes including catalases, peroxidases, cytochromes of the P(450) class and part of sensor molecules. Here the step-by-step biosynthesis of heme including involved enzymes, their mechanisms and detrimental health consequences caused by their failure are described. Unusual and challenging biochemistry including tRNA-dependent reactions, radical SAM enzymes and substrate derived cofactors are reported.
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Affiliation(s)
- Ilka U Heinemann
- Institute of Microbiology, Technical University of Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
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10
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Stetefeld J, Jenny M, Burkhard P. Intersubunit signaling in glutamate-1-semialdehyde-aminomutase. Proc Natl Acad Sci U S A 2006; 103:13688-93. [PMID: 16954186 PMCID: PMC1564225 DOI: 10.1073/pnas.0600306103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Indexed: 11/18/2022] Open
Abstract
Enzymes are highly dynamic and tightly controlled systems. However, allosteric communication linked to catalytic turnover is poorly understood. We have performed an integrated approach to trap several catalytic intermediates in the alpha2-dimeric key enzyme of chlorophyll biosynthesis, glutamate-1-semialdehyde aminomutase. Our data reveal an active-site "gating loop," which undergoes a dramatic conformational change during catalysis, that is simultaneously open in one subunit and closed in the other. This loop movement requires a beta-sheet-to-alpha-helix transition to assume the closed conformation, thus facilitating transport of substrate toward, and concomitantly forming, an integral part of the active site. The accompanying intersubunit cross-talk, which controls negative cooperativity between the allosteric pair, was explored at the atomic level. The central elements of the communication triad are the cofactor bound to different catalytic intermediates, the interface helix, and the gating loop. Together, they form a molecular switch in which the cofactor acts as a central signal transmitter linking the subunit interface with the gating loop.
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Affiliation(s)
- J Stetefeld
- Department of Structural Biology and M. E. Müller Institute for Structural Biology, Biozentrum Universität Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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11
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Schulze JO, Schubert WD, Moser J, Jahn D, Heinz DW. Evolutionary relationship between initial enzymes of tetrapyrrole biosynthesis. J Mol Biol 2006; 358:1212-20. [PMID: 16564539 DOI: 10.1016/j.jmb.2006.02.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 02/21/2006] [Accepted: 02/23/2006] [Indexed: 11/23/2022]
Abstract
Glutamate-1-semialdehyde 2,1-aminomutase (GSAM) is the second enzyme in the C(5) pathway of tetrapyrrole biosynthesis found in most bacteria, in archaea and in plants. It catalyzes the transamination of glutamate-1-semialdehyde to 5-aminolevulinic acid (ALA) in a pyridoxal 5'-phosphate (PLP)-dependent manner. We present the crystal structure of GSAM from the thermophilic cyanobacterium Thermosynechococcus elongatus (GSAM(Tel)) in its PLP-bound form at 2.85A resolution. GSAM(Tel) is a symmetric homodimer, whereas GSAM from Synechococcus (GSAM(Syn)) has been described as asymmetric. The symmetry of GSAM(Tel) thus challenges the previously proposed negative cooperativity between monomers of this enzyme. Furthermore, GSAM(Tel) reveals an extensive flexible region at the interface of the proposed complex of GSAM with glutamyl-tRNA reductase (GluTR), the preceding enzyme in tetrapyrrole biosynthesis. Compared to GSAM(Syn), the monomers of GSAM(Tel) are rotated away from each other along the dimerization interface by 10 degrees . The associated flexibility of GSAM may be essential for complex formation with GluTR to occur. Unexpectedly, we find that GSAM is structurally related to 5-aminolevulinate synthase (ALAS), the ALA-producing enzyme in the Shemin pathway of alpha-proteobacteria and non-plant eukaryotes. This structural relationship applies also to the corresponding subfamilies of PLP-dependent enzymes. We thus propose that the CoA-subfamily (including ALAS) and the aminotransferase subfamily II (including GSAM) are evolutionarily closely related and that ALAS may thus have evolved from GSAM.
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Affiliation(s)
- Jörg O Schulze
- Division of Structural Biology, German Research Centre for Biotechnology (GBF), Mascheroder Weg 1, D-38124 Braunschweig, Germany
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12
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D'Aguanno S, Gonzales IN, Simmaco M, Contestabile R, John RA. Stereochemistry of the reactions of glutamate-1-semialdehyde aminomutase with 4,5-diaminovalerate. J Biol Chem 2003; 278:40521-6. [PMID: 12878592 DOI: 10.1074/jbc.m306223200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conversion of glutamate 1-semialdehyde to the tetrapyrrole precursor, 5-aminolevulinate, takes place in an aminomutase-catalyzed reaction involving transformations at both the non-chiral C5 and the chiral C4 of the intermediate 4,5-diaminovalerate. Presented with racemic diaminovalerate and an excess of succinic semialdehyde, the enzyme catalyzes a transamination in which only the l-enantiomer is consumed. Simultaneously, equimolar 4-aminobutyrate and aminolevulinate are formed. The enzyme is also shown to transaminate aminolevulinate and 4-aminohexenoate to l-diaminovalerate as the exclusive amino product. The interaction of the enzyme with pure d- and l-enantiomers of diaminovalerate prepared by these reactions is described. Transamination of l-diaminovalerate yielded aminolevulinate quantitatively showing that reaction at the C5 amine does not occur significantly. A much slower transamination reaction was catalyzed with d-diaminovalerate as substrate. One product of this reaction, 4-aminobutyrate, was formed in the amount equal to that of the diaminovalerate consumed. Glutamate semialdehyde was deduced to be the other primary product and was also measured in significant amounts when a high concentration of the enzyme in its pyridoxal form was reacted with d-diaminovalerate in a single turnover. Single turnover reactions showed that both enantiomers of diaminovalerate converted the enzyme from its 420-nm absorbing pyridoxaldimine form to the 330-nm absorbing pyridoxamine via rapidly formed intermediates with different absorption spectra. The intermediate formed with l-DAVA (lambdamax = 420 nm) was deduced to be the protonated external aldimine with the 4-amino group. The intermediate formed with d-DAVA (lambdamax = 390 nm) was deduced to be the unprotonated external aldimine with the 5-amino group.
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Affiliation(s)
- Simona D'Aguanno
- Dipartimento di Scienze Biochimiche "A Rossi Fanelli," Università degli Studi di Roma "La Sapienza," Rome, Italy
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13
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Bertoldi M, Gonsalvi M, Contestabile R, Voltattorni CB. Mutation of tyrosine 332 to phenylalanine converts dopa decarboxylase into a decarboxylation-dependent oxidative deaminase. J Biol Chem 2002; 277:36357-62. [PMID: 12118007 DOI: 10.1074/jbc.m204867200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A flexible loop (residues 328-339), presumably covering the active site upon substrate binding, has been revealed in 3,4-dihydroxyphenylalanine decarboxylase by means of kinetic and structural studies. The function of tyrosine 332 has been investigated by substituting it with phenylalanine. Y332F displays coenzyme content and spectroscopic features identical to those of the wild type. Unlike wild type, during reactions with l-aromatic amino acids under both aerobic and anaerobic conditions, Y332F does not catalyze the formation of aromatic amines. However, analysis of the products shows that in aerobiosis, l-aromatic amino acids are converted into the corresponding aromatic aldehydes, ammonia, and CO(2) with concomitant O(2) consumption. Therefore, substitution of Tyr-332 with phenylalanine results in the suppression of the original activity and in the generation of a decarboxylation-dependent oxidative deaminase activity. In anaerobiosis, Y332F catalyzes exclusively a decarboxylation-dependent transamination of l-aromatic amino acids. A role of Tyr-332 in the Calpha protonation step that catalyzes the formation of physiological products has been proposed. Furthermore, Y332F catalyzes oxidative deamination of aromatic amines and half-transamination of d-aromatic amino acids with k(cat) values comparable with those of the wild type. However, for all the mutant-catalyzed reactions, an increase in K(m) values is observed, suggesting that Y --> F replacement also affects substrate binding.
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Affiliation(s)
- Mariarita Bertoldi
- Dipartimento di Scienze Neurologiche e della Visione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università degli Studi di Verona, Strada Le Grazie, 8, 37134 Verona, Italy
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Moser J, Schubert WD, Beier V, Bringemeier I, Jahn D, Heinz DW. V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. EMBO J 2001; 20:6583-90. [PMID: 11726494 PMCID: PMC125327 DOI: 10.1093/emboj/20.23.6583] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. tRNA-dependent catalysis generally is associated with protein biosynthesis. An exception is the reduction of glutamyl-tRNA to glutamate-1-semialdehyde by the enzyme glutamyl-tRNA reductase. This reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. The crystal structure of glutamyl-tRNA reductase from the archaeon Methanopyrus kandleri in complex with the substrate-like inhibitor glutamycin at 1.9 A resolution reveals an extended yet planar V-shaped dimer. The well defined interactions of the inhibitor with the active site support a thioester-mediated reduction process. Modeling the glutamyl-tRNA onto each monomer reveals an extensive protein-tRNA interface. We furthermore propose a model whereby the large void of glutamyl-tRNA reductase is occupied by glutamate-1-semialdehyde-1,2-mutase, the subsequent enzyme of this pathway, allowing for the efficient synthesis of 5-aminolevulinic acid, the common precursor of all tetrapyrroles.
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Affiliation(s)
| | - Wolf-Dieter Schubert
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | - Viola Beier
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | - Ingo Bringemeier
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | | | - Dirk W. Heinz
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
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Scholz O, Kintrup M, Reich M, Hillen W. Mechanism of Tet repressor induction by tetracyclines: length compensates for sequence in the alpha8-alpha9 loop. J Mol Biol 2001; 310:979-86. [PMID: 11502007 DOI: 10.1006/jmbi.2001.4820] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural Tet repressor (TetR) variants are alpha-helical proteins bearing a large loop between helices 8 and 9, which is variable in sequence and length. We have deleted this loop consisting of 14 amino acid residues in TetR(D) and rebuilt it stepwise with up to 42 alanine residues. All except the mutant with the longest alanine loop show wild-type repression, but none is inducible with tetracycline. This demonstrates the importance of the alpha8-alpha9 loop and its amino acid sequence for induction. The induction efficiencies increase with loop length, when the more tightly binding inducer anhydrotetracycline is used. The largest increase of inducibility was observed for TetR mutants with loop lengths between eight and 17 alanine residues. Since loop residues Asp/Glu157 and Arg158 are conserved in the natural TetR sequence variants, we constructed a mutant in which all other residues of the loop were replaced by alanine. This mutant exhibits increased anhydrotetracycline induction compared to the corresponding alanine variant. Thus, these residues are important for induction. Binding constants for the anhydrotetracycline-TetR interaction are below the detection level of 10(5) M(-1) for the mutant with a loop of two alanine residues and increase sharply until a loop size of ten residues is reached. TetR variants with longer loops have similar anhydrotetracycline-binding constants, ranging between 2.6 x 10(9) M(-1) and 8.0 x 10(9) M(-1), about 500-fold lower than wild-type TetR. The increase of the affinity occurs at shorter loop lengths than that of inducibility. We conclude that the induction defect of the polyalanine variants arises from two increments: (i) the loop must have a minimal length-to allow efficient inducer binding; (ii) the loop must structurally participate in the conformational change associated with induction.
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Affiliation(s)
- O Scholz
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie Biochemie und Genetik, Friedrich-Alexander Universität Erlangen-Nurnberg, Germany
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Metzler DE, Metzler CM, Sauke DJ. Coenzymes. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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