1
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Prout L, Hailes HC, Ward JM. Natural transaminase fusions for biocatalysis. RSC Adv 2024; 14:4264-4273. [PMID: 38298934 PMCID: PMC10829540 DOI: 10.1039/d3ra07081f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Biocatalytic approaches are used widely for the synthesis of amines from abundant or low cost starting materials. This is a fast-developing field where novel enzymes and enzyme combinations emerge quickly to enable the production of new and complex compounds. Natural multifunctional enzymes represent a part of multi-step biosynthetic pathways that ensure a one-way flux of reactants. In vivo, they confer a selective advantage via increased reaction rates and chemical stability or prevention of toxicity from reactive intermediates. Here we report the identification and analysis of a natural transaminase fusion, PP_2782, from Pseudomonas putida KT2440, as well as three of its thermophilic homologs from Thermaerobacter marianensis, Thermaerobacter subterraneus, and Thermincola ferriacetica. Both the fusions and their truncated transaminase-only derivatives showed good activity with unsubstituted aliphatic and aromatic aldehydes and amines, as well as with a range of α-keto acids, and l-alanine, l-glutamate, and l-glutamine. Through structural similarity, the fused domain was recognised as the acyl-[acyl-carrier-protein] reductase that affects reductive chain release. These natural transaminase fusions could have a great potential for industrial applications.
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Affiliation(s)
- Luba Prout
- Department of Biochemical Engineering, University College London London WC1E 6BT UK
| | - Helen C Hailes
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - John M Ward
- Department of Biochemical Engineering, University College London London WC1E 6BT UK
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2
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BarA/UvrY differentially regulates prodigiosin biosynthesis and swarming motility in Serratia marcescens FS14. Res Microbiol 2023; 174:104010. [PMID: 36410584 DOI: 10.1016/j.resmic.2022.104010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
BarA/UvrY, a two-component system and global regulator that controls expression of more than a hundred of genes involved in virulence, motility, biofilm formation, and central carbon metabolism under various stress conditions. In this study, we investigated the function of BarA/UvrY system in Serratia marcescens FS14. The disruption of barA or/and uvrY results in the yield increase of secondary metabolite prodigiosin. We further demonstrated that BarA/UvrY system represses prodigiosin production by inhibiting the transcription level of pig gene cluster with direct binding to the pigA promoter. In addition, deletion of barA or/and uvrY abolished the swarming motility of FS14, but not the swimming motility. We revealed that BarA/UvrY activates swarming through directly upregulating the expression of the biosurfactant synthesis gene swrW rather than flagella system. We also observed that BarA/UvrY positively regulates the resistance to H2O2 same as in Escherichia coli highlighting the importance of BarA/UvrY on hydrogen peroxide resistance. Our results demonstrated that the BarA/UvrY system differentially regulates the biosynthesis of the secondary metabolite prodigiosin and swarming motility in S. marcescens FS14. Comparison of our results with those observed for Serratia sp. 39006 suggests that BarA/UvrY's role in regulation of secondary metabolite production is different among Serratia species.
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3
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Richardson SM, Marchetti PM, Herrera MA, Campopiano DJ. Coupled Natural Fusion Enzymes in a Novel Biocatalytic Cascade Convert Fatty Acids to Amines. ACS Catal 2022; 12:12701-12710. [PMID: 36313522 PMCID: PMC9594044 DOI: 10.1021/acscatal.2c02954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/29/2022] [Indexed: 11/28/2022]
Abstract
![]()
Tambjamine YP1 is a pyrrole-containing natural product.
Analysis
of the enzymes encoded in the Pseudoalteromonas tunicata “tam” biosynthetic gene cluster (BGC)
identified a unique di-domain biocatalyst (PtTamH).
Sequence and bioinformatic analysis predicts that PtTamH comprises an N-terminal, pyridoxal 5′-phosphate (PLP)-dependent
transaminase (TA) domain fused to a NADH-dependent C-terminal thioester
reductase (TR) domain. Spectroscopic and chemical analysis revealed
that the TA domain binds PLP, utilizes l-Glu as an amine
donor, accepts a range of fatty aldehydes (C7–C14 with a preference for C12), and produces the
corresponding amines. The previously characterized PtTamA from the “tam” BGC is an ATP-dependent, di-domain
enzyme comprising a class I adenylation domain fused to an acyl carrier
protein (ACP). Since recombinant PtTamA catalyzes
the activation and thioesterification of C12 acid to the holo-ACP domain, we hypothesized that C12 ACP
is the natural substrate for PtTamH. PtTamA and PtTamH were successfully coupled together
in a biocatalytic cascade that converts fatty acids (FAs) to amines
in one pot. Moreover, a structural model of PtTamH
provides insights into how the TA and TR domains are organized. This
work not only characterizes the formation of the tambjamine YP1 tail
but also suggests that PtTamA and PtTamH could be useful biocatalysts for FA to amine functional group
conversion.
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Affiliation(s)
- Shona M. Richardson
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Piera M. Marchetti
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Michael A. Herrera
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Dominic J. Campopiano
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
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4
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Araújo RG, Zavala NR, Castillo-Zacarías C, Barocio ME, Hidalgo-Vázquez E, Parra-Arroyo L, Rodríguez-Hernández JA, Martínez-Prado MA, Sosa-Hernández JE, Martínez-Ruiz M, Chen WN, Barceló D, Iqbal HM, Parra-Saldívar R. Recent Advances in Prodigiosin as a Bioactive Compound in Nanocomposite Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154982. [PMID: 35956931 PMCID: PMC9370345 DOI: 10.3390/molecules27154982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022]
Abstract
Bionanocomposites based on natural bioactive entities have gained importance due to their abundance; renewable and environmentally benign nature; and outstanding properties with applied perspective. Additionally, their formulation with biological molecules with antimicrobial, antioxidant, and anticancer activities has been produced nowadays. The present review details the state of the art and the importance of this pyrrolic compound produced by microorganisms, with interest towards Serratia marcescens, including production strategies at a laboratory level and scale-up to bioreactors. Promising results of its biological activity have been reported to date, and the advances and applications in bionanocomposites are the most recent strategy to potentiate and to obtain new carriers for the transport and controlled release of prodigiosin. Prodigiosin, a bioactive secondary metabolite, produced by Serratia marcescens, is an effective proapoptotic agent against bacterial and fungal strains as well as cancer cell lines. Furthermore, this molecule presents antioxidant activity, which makes it ideal for treating wounds and promoting the general improvement of the immune system. Likewise, some of the characteristics of prodigiosin, such as hydrophobicity, limit its use for medical and biotechnological applications; however, this can be overcome by using it as a component of a bionanocomposite. This review focuses on the chemistry and the structure of the bionanocomposites currently developed using biorenewable resources. Moreover, the work illuminates recent developments in pyrrole-based bionanocomposites, with special insight to its application in the medical area.
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Affiliation(s)
- Rafael G. Araújo
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Natalia Rodríguez Zavala
- Chemical & Biochemical Engineering Department, Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Blvd. Felipe Pescador 1830 Ote. Durango, Durango 34080, Mexico
| | - Carlos Castillo-Zacarías
- Universidad Autónoma de Nuevo León, Facultad de Ingeniería Civil, Departamento de Ingeniería Ambiental, Ciudad Universitaria S/N, San Nicolás de los Garza 66455, Mexico
| | - Mario E. Barocio
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | - Lizeth Parra-Arroyo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | - María Adriana Martínez-Prado
- Chemical & Biochemical Engineering Department, Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Blvd. Felipe Pescador 1830 Ote. Durango, Durango 34080, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637457, Singapore
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, 08034 Barcelona, Spain
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Edifici H2O, 17003 Girona, Spain
- Sustainability Cluster, School of Engineering, UPES, Dehradun 248007, India
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Correspondence: (H.M.N.I.); (R.P.-S.)
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing Monterrey, Monterrey 64849, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Correspondence: (H.M.N.I.); (R.P.-S.)
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5
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Couturier M, Bhalara HD, Monson RE, Salmond GPC, Leeper FJ. Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate. RSC Chem Biol 2021; 2:551-555. [PMID: 34458798 PMCID: PMC8341465 DOI: 10.1039/d0cb00173b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/05/2021] [Indexed: 01/14/2023] Open
Abstract
A biosynthetic pathway for the red-antibiotic, prodigiosin, was proposed over a decade ago but not all the suggested intermediates could be detected experimentally. Here we show that a thioester that was not originally included in the pathway is an intermediate. In addition, the enzyme PigE was originally described as a transaminase but we present evidence that it also catalyses the reduction of the thioester intermediate to its aldehyde substrate. A revision is proposed to the biosynthetic pathway to the well-known red pigment prodigiosin via a new thioester intermediate.![]()
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Affiliation(s)
- Maxime Couturier
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Hiral D Bhalara
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Rita E Monson
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - George P C Salmond
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - Finian J Leeper
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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6
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Wang SL, Nguyen VB, Doan CT, Tran TN, Nguyen MT, Nguyen AD. Production and Potential Applications of Bioconversion of Chitin and Protein-Containing Fishery Byproducts into Prodigiosin: A Review. Molecules 2020; 25:E2744. [PMID: 32545769 PMCID: PMC7356639 DOI: 10.3390/molecules25122744] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
The technology of microbial conversion provides a potential way to exploit compounds of biotechnological potential. The red pigment prodigiosin (PG) and other PG-like pigments from bacteria, majorly from Serratia marcescens, have been reported as bioactive secondary metabolites that can be used in the broad fields of agriculture, fine chemicals, and pharmacy. Increasing PG productivity by investigating the culture conditions especially the inexpensive carbon and nitrogen (C/N) sources has become an important factor for large-scale production. Investigations into the bioactivities and applications of PG and its related compounds have also been given increased attention. To save production cost, chitin and protein-containing fishery byproducts have recently been investigated as the sole C/N source for the production of PG and chitinolytic/proteolytic enzymes. This strategy provides an environmentally-friendly selection using inexpensive C/N sources to produce a high yield of PG together with chitinolytic and proteolytic enzymes by S. marcescens. The review article will provide effective references for production, bioactivity, and application of S. marcescens PG in various fields such as biocontrol agents and potential pharmaceutical drugs.
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Affiliation(s)
- San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
| | - Van Bon Nguyen
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam
| | - Chien Thang Doan
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Thi Ngoc Tran
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Minh Trung Nguyen
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
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7
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Marchetti PM, Kelly V, Simpson JP, Ward M, Campopiano DJ. The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis. Org Biomol Chem 2019; 16:2735-2740. [PMID: 29594310 PMCID: PMC5939613 DOI: 10.1039/c8ob00441b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
TamA is the adenylating enzyme that selects and activates fatty acids for tambjamine biosynthesis.
The marine bacterium Pseudoalteromonas tunicata produces the bipyrrole antibiotic tambjamine YP1. This natural product is built from common amino acid and fatty acid building blocks in a biosynthetic pathway that is encoded in the tam operon which contains 19 genes. The exact role that each of these Tam proteins plays in tambjamine biosynthesis is not known. Here, we provide evidence that TamA initiates the synthesis and controls the chain length of the essential tambjamine fatty amine tail. Sequence analysis suggests the unusual TamA is comprised of an N-terminal adenylation (ANL) domain fused to a C-terminal acyl carrier protein (ACP). Mass spectrometry analysis of recombinant TamA revealed the surprising presence of bound C11 and C12 acyl-adenylate intermediates. Acylation of the ACP domain was observed upon attachment of the phosphopantetheine (4′-PP) arm to the ACP. We also show that TamA can transfer fatty acids ranging in chain length from C6–C13 to an isolated ACP domain. Thus TamA bridges the gap between primary and secondary metabolism by linking fatty acid and pyrrole biosynthetic pathways.
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Affiliation(s)
- Piera M Marchetti
- EaStCHEM School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
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8
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Lee CC, Ko TP, Chen CT, Chan YT, Lo SY, Chang JY, Chen YW, Chung TF, Hsieh HJ, Hsiao CD, Wang AHJ. Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis. Chembiochem 2018; 20:193-202. [DOI: 10.1002/cbic.201800409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Cheng-Chung Lee
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Chun-Ting Chen
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Yueh-Te Chan
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Shin-Yi Lo
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Jen-Yu Chang
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Ya-Wen Chen
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Ting-Fang Chung
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Hsin-Ju Hsieh
- Industrial Technology Research Institute; 195 Chung Hsing Road Section 4, Chutung Hsinchu 31057 Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
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9
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Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14. Int J Biol Macromol 2017; 99:394-400. [PMID: 28258005 DOI: 10.1016/j.ijbiomac.2017.02.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 11/23/2022]
Abstract
Prodigiosin, a tripyrrole red pigment is synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway; MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. PigI, PigG and PigA have been shown to be involved in the first steps of MBC biosynthesis (proline incorporation). The crystal structure of PigG was resolved to elucidate its function and mechanism. PigG, an acyl carrier protein (ACP), features the ACP architecture:, a helical bundle fold containing three major helices and a minor distorted helix together with a conserved "S" motif. An in-frame deletion mutation of the pigG gene abolished the synthesis of prodigiosin in Serratia marcescens FS14. The production of prodigiosin was fully restored by complementation of intact pigG; however the S36A mutant was not able to restore function in the in-frame deletion pigG mutant, indicating that PigG and the conserved serine residue (S36) of PigG are essential for the synthesis of prodigiosin.
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10
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Zhu Y, Xu J, Mei X, Feng Z, Zhang L, Zhang Q, Zhang G, Zhu W, Liu J, Zhang C. Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis. ACS Chem Biol 2016; 11:943-52. [PMID: 26714051 DOI: 10.1021/acschembio.5b00984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Caerulomycin A (CRM A 1) belongs to a family of natural products containing a 2,2'-bipyridyl ring core structure and is currently under development as a potent novel immunosuppressive agent. Herein, we report the functional characterization, kinetic analysis, substrate specificity, and structure insights of an aminotransferase CrmG in 1 biosynthesis. The aminotransferase CrmG was confirmed to catalyze a key transamination reaction to convert an aldehyde group to an amino group in the 1 biosynthetic pathway, preferring l-glutamate and l-glutamine as the amino donor substrates. The crystal structures of CrmG in complex with the cofactor 5'-pyridoxal phosphate (PLP) or 5'-pyridoxamine phosphate (PMP) or the acceptor substrate were determined to adopt a canonical fold-type I of PLP-dependent enzymes with a unique small additional domain. The structure guided site-directed mutagenesis identified key amino acid residues for substrate binding and catalytic activities, thus providing insights into the transamination mechanism of CrmG.
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Affiliation(s)
- Yiguang Zhu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jinxin Xu
- Key
Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiangui Mei
- Key
Laboratory of Marine Drugs, Ministry of Education of China, School
of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zhan Feng
- Key
Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Liping Zhang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Qingbo Zhang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Guangtao Zhang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Weiming Zhu
- Key
Laboratory of Marine Drugs, Ministry of Education of China, School
of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jinsong Liu
- Key
Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changsheng Zhang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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11
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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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12
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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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