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Akagashi M, Watanabe S, Kwiatkowski S, Drozak J, Terawaki SI, Watanabe Y. Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates. Sci Rep 2024; 14:14602. [PMID: 38918500 PMCID: PMC11199699 DOI: 10.1038/s41598-024-65627-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
L-2-Keto-3-deoxyfuconate 4-dehydrogenase (L-KDFDH) catalyzes the NAD+-dependent oxidization of L-2-keto-3-deoxyfuconate (L-KDF) to L-2,4-diketo-3-deoxyfuconate (L-2,4-DKDF) in the non-phosphorylating L-fucose pathway from bacteria, and its substrate was previously considered to be the acyclic α-keto form of L-KDF. On the other hand, BDH2, a mammalian homolog with L-KDFDH, functions as a dehydrogenase for cis-4-hydroxy-L-proline (C4LHyp) with the cyclic structure. We found that L-KDFDH and BDH2 utilize C4LHyp and L-KDF, respectively. Therefore, to elucidate unique substrate specificity at the atomic level, we herein investigated for the first time the crystal structures of L-KDFDH from Herbaspirillum huttiense in the ligand-free, L-KDF and L-2,4-DKDF, D-KDP (D-2-keto-3-deoxypentonate; additional substrate), or L-2,4-DKDF and NADH bound forms. In complexed structures, L-KDF, L-2,4-DKDF, and D-KDP commonly bound as a α-furanosyl hemiketal. Furthermore, L-KDFDH showed no activity for L-KDF and D-KDP analogs without the C5 hydroxyl group, which form only the acyclic α-keto form. The C1 carboxyl and α-anomeric C2 hydroxyl groups and O5 oxygen atom of the substrate (and product) were specifically recognized by Arg148, Arg192, and Arg214. The side chain of Trp252 was important for hydrophobically recognizing the C6 methyl group of L-KDF. This is the first example showing the physiological role of the hemiketal of 2-keto-3-deoxysugar acid.
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Affiliation(s)
- Miyu Akagashi
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan.
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan.
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan.
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Shin-Ichi Terawaki
- Division of Structure Analysis of Protein Complex, Proteo-Science Center (PROS), Ehime University, Matsuyama, Ehime, Japan
| | - Yasunori Watanabe
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
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Gao Y, Cheng H, Song Q, Huang J, Liu J, Pan D, Wu X. Characteristics and catalytic mechanism of a novel multifunctional oxidase, CpmO, for chloramphenicols degradation from Sphingobium sp. WTD-1. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133348. [PMID: 38154177 DOI: 10.1016/j.jhazmat.2023.133348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Chloramphenicols (CAPs) are ubiquitous emerging pollutants that threaten ecological environments and human health. Microbial and enzyme-based biodegradation strategies offer a cost-effective environmentally friendly approach for CAPs removal from contaminated sites. Here, CpmO, a novel multifunctional oxidase for CAP degradation was identified from the CAP-degrading strain Sphingobium sp. WTD-1. This enzyme was found to be responsible for both the oxidation of the C3-hydroxyl and oxidative cleavage of the C1-C2 bond of CAP, and the oxidative cleavage pathway of CAP was dominant. The catalytic efficiency of CpmO for CAP was 41.6 times that for thiamphenicol (TAP) under the optimal conditions (40 °C, pH 6.0). CpmO was identified as a member of the glucose-methanol-choline oxidoreductase family. Molecular docking and site-directed mutagenesis analysis indicated that CAP was connected to the key amino acid residues E231/E395, K277, and I273/A276 in CpmO through hydrogen bonding, nonclassical hydrogen bonding, and π-π stacking forces, respectively. The catalytic activities of the A276W, K277P, and E231S mutants were found to be 1.1 times, 6.4 times, and 13.2 times higher than that of the wild type, respectively. These findings provide genetic resources and theoretical guidance for future application in biotechnological and metabolic engineering efforts for the remediation of CAPs-contaminated environments.
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Affiliation(s)
- Yongsheng Gao
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Huan Cheng
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Qinghui Song
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Junwei Huang
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Junwei Liu
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Pan
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Xiangwei Wu
- Key Laboratory of Agri-food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
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Dvořák P, Galvão TC, Pflüger‐Grau K, Banks AM, de Lorenzo V, Jiménez JI. Water potential governs the effector specificity of the transcriptional regulator XylR of Pseudomonas putida. Environ Microbiol 2023; 25:1041-1054. [PMID: 36683138 PMCID: PMC10946618 DOI: 10.1111/1462-2920.16342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 01/24/2023]
Abstract
The biodegradative capacity of bacteria in their natural habitats is affected by water availability. In this work, we have examined the activity and effector specificity of the transcriptional regulator XylR of the TOL plasmid pWW0 of Pseudomonas putida mt-2 for biodegradation of m-xylene when external water potential was manipulated with polyethylene glycol PEG8000. By using non-disruptive luxCDEAB reporter technology, we noticed that the promoter activated by XylR (Pu) restricted its activity and the regulator became more effector-specific towards head TOL substrates when cells were grown under water subsaturation. Such a tight specificity brought about by water limitation was relaxed when intracellular osmotic stress was counteracted by the external addition of the compatible solute glycine betaine. With these facts in hand, XylR variants isolated earlier as effector-specificity responders to the non-substrate 1,2,4-trichlorobenzene under high matric stress were re-examined and found to be unaffected by water potential in vivo. All these phenomena could be ultimately explained as the result of water potential-dependent conformational changes in the A domain of XylR and its effector-binding pocket, as suggested by AlphaFold prediction of protein structures. The consequences of this scenario for the evolution of specificities in regulators and the emergence of catabolic pathways are discussed.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | | | - Katharina Pflüger‐Grau
- Specialty Division for Systems BiotechnologyTechnische Universität MünchenGarchingGermany
| | - Alice M. Banks
- Department of Life SciencesImperial College LondonLondonUK
| | - Víctor de Lorenzo
- Systems Biology DepartmentCentro Nacional de Biotecnología‐CSICMadridSpain
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Lyons NS, Bogner AN, Tanner JJ, Sobrado P. Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N-Hydroxylase from Acinetobacter baumannii. Biochemistry 2022; 61:2607-2620. [DOI: 10.1021/acs.biochem.2c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noah S. Lyons
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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Maczuga N, Tran ENH, Morona R. Subcellular localization of the enterobacterial common antigen GT-E-like glycosyltransferase, WecG. Mol Microbiol 2022; 118:403-416. [PMID: 36006410 PMCID: PMC9804384 DOI: 10.1111/mmi.14973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 01/05/2023]
Abstract
Enterobacterales have developed a specialized outer membrane polysaccharide (enterobacterial common antigen [ECA]). ECA biosynthesis begins on the cytoplasmic side of the inner membrane (IM) where glycosyltransferases sequentially add sugar moieties to form a complete repeat unit which is then translocated across the IM by WzxE before being polymerized into short linear chains by WzyE/WzzE. Research into WecG, the enzyme responsible for generating ECA lipid-II, has not progressed beyond Barr et al. (1988) who described WecG as a membrane protein. Here we revise our understanding of WecG and re-characterize it as a peripherally associated membrane protein. Through the use of Western immunoblotting we show that WecG in Shigella flexneri is maintained to the IM via its three C-terminal helices and further identify key residues in helix II which are critical for this interaction which has allowed us to identify WecG as a GT-E glycosyltransferase. We investigate the possibility of protein complexes and ultimately show that ECA lipid-I maintains WecG to the membrane which is crucial for its function. This research is the first since Barr et al. (1988) to investigate the biochemistry of WecG and reveals possible novel drug targets to inhibit WecG and thus ECA function and cell viability.
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Affiliation(s)
- Nicholas Maczuga
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Elizabeth N. H. Tran
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Renato Morona
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
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Ruan H, Shi X, Gao L, Rashid A, Li Y, Lei T, Dai X, Xia T, Wang Y. Functional analysis of the dihydroflavonol 4-reductase family of Camellia sinensis: exploiting key amino acids to reconstruct reduction activity. HORTICULTURE RESEARCH 2022; 9:uhac098. [PMID: 35795397 PMCID: PMC9250652 DOI: 10.1093/hr/uhac098] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 05/28/2023]
Abstract
Anthocyanins and proanthocyanidins (PAs) are important types of flavonoids, plant secondary metabolites with a wide range of industrial and pharmaceutical applications. DFR (dihydroflavonol 4-reductase) is a pivotal enzyme that plays an important role in the flavonoid pathway. Here, four CsDFR genes were isolated from Camellia sinensis, and their overexpression was analyzed in vitro and in vivo. Based on transcription and metabolic analyses, CsDFR expression was closely consistent with catechins and PAs accumulation. Moreover, enzyme activity analyses revealed that the two recombinant proteins CsDFRa and CsDFRc exhibited DFR activity, converting dihydroflavonols into leucoanthocyanins in vitro, but CsDFRb1 and CsDFRb3 did not. CsDFRa and CsDFRc overexpression in AtDFR mutants (tt3) revealed that CsDFRs are involved in the biosynthesis of anthocyanins and PAs, as CsDFRa and CsDFRc restored not only the purple petiole phenotype but also the seed coat color. Site-directed mutagenesis revealed that the two amino acid residues S117 and T123 of CsDFRa play a prominent role in controlling DFR reductase activity. Enzymatic assays indicated that CsDFRa and CsDFRc exhibited a higher affinity for DHQ and DHK, respectively, whereas CsDFRb1N120S and CsDFRb1C126T exhibited a higher affinity for DHM. Our findings comprehensively characterize the DFRs from C. sinensis and shed light on their critical role in metabolic engineering.
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Affiliation(s)
- Haixiang Ruan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xingxing Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- College of Tea Science, Guizhou University, Guiyang Guizhou 550025, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Arif Rashid
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yan Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ting Lei
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xinlong Dai
- College of Tea Science, Guizhou University, Guiyang Guizhou 550025, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yunsheng Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, China
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7
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M VNUM, Faidh MA, Chadha A. The ornithine cyclodeaminase/µ-crystallin superfamily of proteins: A novel family of oxidoreductases for the biocatalytic synthesis of chiral amines. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Qi F, Zhang W, Xue Y, Geng C, Huang X, Sun J, Lu X. Bienzyme-Catalytic and Dioxygenation-Mediated Anthraquinone Ring Opening. J Am Chem Soc 2021; 143:16326-16331. [PMID: 34586791 DOI: 10.1021/jacs.1c07182] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The C-10-C-4a bond cleavage of anthraquinone is believed to be a crucial step in fungal seco-anthraquinone biosynthesis and has long been proposed as a classic Baeyer-Villiger oxidation. Nonetheless, genetic, enzymatic, and chemical information on ring opening remains elusive. Here, a revised questin ring-opening mechanism was elucidated by in vivo gene disruption, in vitro enzymatic analysis, and 18O chasing experiments. It has been confirmed that the reductase GedF is responsible for the reduction of the keto group at C-10 in questin to a hydroxyl group with the aid of NADPH. The C-10-C-4a bond of the resultant questin hydroquinone is subsequently cleaved by the atypical cofactor-free dioxygenase GedK, giving rise to desmethylsulochrin. This proposed bienzyme-catalytic and dioxygenation-mediated anthraquinone ring-opening reaction shows universality.
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Affiliation(s)
- Feifei Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Xue
- International Centre for Bamboo and Rattan, State Forestry Administration Key Open Laboratory, Beijing 100102, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Sun
- International Centre for Bamboo and Rattan, State Forestry Administration Key Open Laboratory, Beijing 100102, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266101, China
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Dong H, Chang MCY. Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hongjun Dong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720-3200, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
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Kasho K, Stojkovič G, Velázquez-Ruiz C, Martínez-Jiménez MI, Doimo M, Laurent T, Berner A, Pérez-Rivera AE, Jenninger L, Blanco L, Wanrooij S. A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol. Nucleic Acids Res 2021; 49:2179-2191. [PMID: 33533925 PMCID: PMC7913696 DOI: 10.1093/nar/gkab049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 01/19/2021] [Indexed: 01/22/2023] Open
Abstract
Replication forks often stall at damaged DNA. To overcome these obstructions and complete the DNA duplication in a timely fashion, replication can be restarted downstream of the DNA lesion. In mammalian cells, this repriming of replication can be achieved through the activities of primase and polymerase PrimPol. PrimPol is stimulated in DNA synthesis through interaction with PolDIP2, however the exact mechanism of this PolDIP2-dependent stimulation is still unclear. Here, we show that PrimPol uses a flexible loop to interact with the C-terminal ApaG-like domain of PolDIP2, and that this contact is essential for PrimPol's enhanced processivity. PolDIP2 increases primer-template and dNTP binding affinities of PrimPol, which concomitantly enhances its nucleotide incorporation efficiency. This stimulation is dependent on a unique arginine cluster in PolDIP2. Since the polymerase activity of PrimPol alone is very limited, this mechanism, where the affinity for dNTPs gets increased by PolDIP2 binding, might be critical for the in vivo function of PrimPol in tolerating DNA lesions at physiological nucleotide concentrations.
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Affiliation(s)
- Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Gorazd Stojkovič
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Timothée Laurent
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Luis Blanco
- Centro de Biologia Molecular Severo Ochoa, E-28049 Madrid, Spain
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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Tragni V, Cotugno P, De Grassi A, Cavalluzzi MM, Mincuzzi A, Lentini G, Sanzani SM, Ippolito A, Pierri CL. Targeting Penicillium expansum GMC Oxidoreductase with High Affinity Small Molecules for Reducing Patulin Production. BIOLOGY 2020; 10:biology10010021. [PMID: 33396459 PMCID: PMC7824139 DOI: 10.3390/biology10010021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/21/2022]
Abstract
Simple Summary With the urgent necessity of potential treatments for limiting mycotoxin production and postharvest fungal rots, we propose a combined in silico/in vitro/in vivo strategy for the rapid and effective identification of bioactive small molecules, chosen among a chemical library hosting approved drugs and phytochemicals, to be used after harvest. The molecular target of our analysis was the GMC oxidoreductase from Penicillium expansum involved in the biosynthesis of patulin, a mycotoxin that can contaminate many foods, especially fruits and fruit-based products. The employed in silico/in vitro/in vivo assays described in our study proved the effectiveness of our strategy and in particular of two small molecules, 6-hydroxycoumarin (structurally related to umbelliferon, an already characterized patulin synthase inhibitor) and meticrane (an already approved drug) in reducing patulin accumulation. Our findings highly recommend the mentioned ligands to be subjected to further analysis for being used in the next future in place of other more toxic compounds, in postharvest treatments based on dipping or drenching methods. Abstract Flavine adenine dinucleotide (FAD) dependent glucose methanol choline oxidoreductase (GMC oxidoreductase) is the terminal key enzyme of the patulin biosynthetic pathway. GMC oxidoreductase catalyzes the oxidative ring closure of (E)-ascladiol to patulin. Currently, no protein involved in the patulin biosynthesis in Penicillium expansum has been experimentally characterized or solved by X-ray diffraction. Consequently, nothing is known about P. expansum GMC oxidoreductase substrate-binding site and mode of action. In the present investigation, a 3D comparative model for P. expansum GMC oxidoreductase has been described. Furthermore, a multistep computational approach was used to identify P. expansum GMC oxidoreductase residues involved in the FAD binding and in substrate recognition. Notably, the obtained 3D comparative model of P. expansum GMC oxidoreductase was used for performing a virtual screening of a chemical/drug library, which allowed to predict new GMC oxidoreductase high affinity ligands to be tested in in vitro/in vivo assays. In vitro assays performed in presence of 6-hydroxycoumarin and meticrane, among the highly affinity predicted binders, confirmed a dose-dependent inhibition (17–81%) of patulin production by 6-hydroxycoumarin (10 µM–1 mM concentration range), whereas the approved drug meticrane inhibited patulin production by 43% already at 10 µM. Furthermore, 6-hydroxycoumarin and meticrane caused a 60 and 41% reduction of patulin production, respectively, in vivo on apples at 100 µg/wound.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy;
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Maria Maddalena Cavalluzzi
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Annamaria Mincuzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Giovanni Lentini
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Simona Marianna Sanzani
- CIHEAM Bari, Via Ceglie 9, 70010 Valenzano (BA), Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
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Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R, Ben-Tal N, Tawfik DS. On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment. eLife 2020; 9:e64415. [PMID: 33295875 PMCID: PMC7758060 DOI: 10.7554/elife.64415] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous and diverse enzyme lineages. Despite similarities in their overall architecture and phosphate binding motif, a lack of sequence identity and some fundamental structural differences currently designates them as independent emergences. We systematically searched for structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ motif of both lineages, including the phosphate binding loop and a conserved aspartate at the tip of β2. The latter ligates the catalytic metal in P-loop NTPases, while in Rossmanns it binds the nucleotide's ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. While convergence cannot be completely ruled out, we show that both lineages likely emerged from a common βαβ segment that comprises the core of these enzyme families to this very day.
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Affiliation(s)
- Liam M Longo
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Jagoda Jabłońska
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Pratik Vyas
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Manil Kanade
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Rachel Kolodny
- University of Haifa, Department of Computer ScienceHaifaIsrael
| | - Nir Ben-Tal
- Tel Aviv University, George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular BiologyTel AvivIsrael
| | - Dan S Tawfik
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
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13
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Gupta A, Sharma P, Singh TP, Sharma S. Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140566. [PMID: 33271445 DOI: 10.1016/j.bbapap.2020.140566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/11/2023]
Abstract
Phosphopantetheine Adenylyltransferase (PPAT) is an enzyme that catalyzes the penultimate step in the biosynthesis of Coenzyme A (CoA), which is the active and physiologically functional form of dietary Vitamin B5. CoA serves as a cofactor for numerous metabolic reactions which makes it essential for cellular survival. This enzyme is also subject to feedback inhibition by CoA to maintain its cellular concentration. The steps of the CoA biosynthesis pathway remain conserved from prokaryotes to eukaryotes, with humans and pathogenic micro-organisms showing significant diversity on a sequence, structure and mechanistic level. This suggests that the development of selective inhibitors of microbial CoA biosynthesis should be possible using these enzymes as targets for drug development. Bacterial PPAT shows significant mechanistic difference from its human counterpart CoA synthase, which is a dual protein carrying the activity of both PPAT and next step in the pathway catalyzed by the enzyme Dephospho CoA kinase (DPCK). This review covers the detailed description of the mechanistic, structural and functional aspects of this enzyme. Also, all the attempts to design high efficiency inhibitors of this enzyme using the approach of structure based drug design have been discussed in detail. This comprehensive structural and functional discussion of PPAT will help in further exploiting it as a drug target.
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Affiliation(s)
- Akshita Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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14
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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15
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Setny P. Conserved internal hydration motifs in protein kinases. Proteins 2020; 88:1578-1591. [DOI: 10.1002/prot.25977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/18/2020] [Accepted: 07/05/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Piotr Setny
- Centre of New Technologies University of Warsaw Warsaw Poland
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16
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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. PLoS Comput Biol 2020; 16:e1007904. [PMID: 32453784 PMCID: PMC7319350 DOI: 10.1371/journal.pcbi.1007904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 06/26/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors—angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water. The topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design.
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17
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Stolarczyk K, Rogalski J, Bilewicz R. NAD(P)-dependent glucose dehydrogenase: Applications for biosensors, bioelectrodes, and biofuel cells. Bioelectrochemistry 2020; 135:107574. [PMID: 32498025 DOI: 10.1016/j.bioelechem.2020.107574] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
This review discusses the physical and chemical properties of nicotinamide redox cofactor dependent glucose dehydrogenase (NAD(P) dependent GDH) and its extensive application in biosensors and bio-fuel cells. GDHs from different organisms show diverse biochemical properties (e.g., activity and stability) and preferences towards cofactors, such as nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). The (NAD(P)+) play important roles in biological electron transfer, however, there are some difficulties related to their application in devices that originate from their chemical properties and labile binding to the GDH enzyme. This review discusses the electrode modifications aimed at immobilising NAD+ or NADP+ cofactors and GDH at electrodes. Binding of the enzyme was achieved by appropriate protein engineering techniques, including polymerisation, hydrophobisation or hydrophilisation processes. Various enzyme-modified electrodes applied in biosensors, enzymatic fuel cells, and biobatteries are compared. Importantly, GDH can operate alone or as part of an enzymatic cascade, which often improves the functional parameters of the biofuel cell or simply allows use of cheaper fuels. Overall, this review explores how NAD(P)-dependent GDH has recently demonstrated high potential for use in various systems to generate electricity from biological sources for applications in implantable biomedical devices, wireless sensors, and portable electronic devices.
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Affiliation(s)
- Krzysztof Stolarczyk
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland
| | - Jerzy Rogalski
- Department of Biochemistry and Biotechnology, Maria Curie-Sklodowska University, Akademicka Str. 19, 20-031 Lublin, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland.
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18
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Laciak AR, Korasick DA, Gates KS, Tanner JJ. Structural analysis of pathogenic mutations targeting Glu427 of ALDH7A1, the hot spot residue of pyridoxine-dependent epilepsy. J Inherit Metab Dis 2020; 43:635-644. [PMID: 31652343 PMCID: PMC7182499 DOI: 10.1002/jimd.12184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022]
Abstract
Certain loss-of-function mutations in the gene encoding the lysine catabolic enzyme aldehyde dehydrogenase 7A1 (ALDH7A1) cause pyridoxine-dependent epilepsy (PDE). Missense mutations of Glu427, especially Glu427Gln, account for ~30% of the mutated alleles in PDE patients, and thus Glu427 has been referred to as a mutation hot spot of PDE. Glu427 is invariant in the ALDH superfamily and forms ionic hydrogen bonds with the nicotinamide ribose of the NAD+ cofactor. Here we report the first crystal structures of ALDH7A1 containing pathogenic mutations targeting Glu427. The mutant enzymes E427Q, Glu427Asp, and Glu427Gly were expressed in Escherichia coli and purified. The recombinant enzymes displayed negligible catalytic activity compared to the wild-type enzyme. The crystal structures of the mutant enzymes complexed with NAD+ were determined to understand how the mutations impact NAD+ binding. In the E427Q and E427G structures, the nicotinamide mononucleotide is highly flexible and lacks a defined binding pose. In E427D, the bound NAD+ adopts a "retracted" conformation in which the nicotinamide ring is too far from the catalytic Cys residue for hydride transfer. Thus, the structures revealed a shared mechanism for loss of function: none of the variants are able to stabilise the nicotinamide of NAD+ in the pose required for catalysis. We also show that these mutations reduce the amount of active tetrameric ALDH7A1 at the concentration of NAD+ tested. Altogether, our results provide the three-dimensional molecular structural basis of the most common pathogenic variants of PDE and implicate strong (ionic) hydrogen bonds in the aetiology of a human disease.
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Affiliation(s)
- Adrian R. Laciak
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - David A. Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - John J. Tanner
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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19
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Peng F, Su HH, Ou XY, Ni ZF, Zong MH, Lou WY. Immobilization of Cofactor Self-Sufficient Recombinant Escherichia coli for Enantioselective Biosynthesis of ( R)-1-Phenyl-1,2-Ethanediol. Front Bioeng Biotechnol 2020; 8:17. [PMID: 32154222 PMCID: PMC7046757 DOI: 10.3389/fbioe.2020.00017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/09/2020] [Indexed: 11/18/2022] Open
Abstract
(R)-1-phenyl-1,2-ethanediol is an important synthon for the preparation of β-adrenergic blocking agents. This study identified a (2R,3R)-butanediol dehydrogenase (KgBDH) from Kurthia gibsonii SC0312, which showed high enantioselectivity for production of (R)-1-phenyl-1,2-ethanediol by reduction of 2-hydroxyacetophenone. KgBDH was expressed in a recombinant engineered strain, purified, and characterized. It showed good catalytic activity at pH 6–8 and better stability in alkaline (pH 7.5–8) than an acidic environment (pH 6.0–7.0), providing approximately 73 and 88% of residual activity after 96 h at pH 7.5 and 8.0, respectively. The maximum catalytic activity was obtained at 45°C; nevertheless, poor thermal stability was observed at >30°C. Additionally, the examined metal ions did not activate the catalytic activity of KgBDH. A recombinant Escherichia coli strain coexpressing KgBDH and glucose dehydrogenase (GHD) was constructed and immobilized via entrapment with a mixture of activated carbon and calcium alginate via entrapment. The immobilized cells had 1.8-fold higher catalytic activity than that of cells immobilized by calcium alginate alone. The maximum catalytic activity of the immobilized cells was achieved at pH 7.5, and favorable pH stability was observed at pH 6.0–9.0. Moreover, the immobilized cells showed favorable thermal stability at 25–30°C and better operational stability than free cells, retaining approximately 55% of the initial catalytic activity after four cycles. Finally, 81% yields (195 mM product) and >99% enantiomeric excess (ee) of (R)-1-phenyl-1,2-ethanediol were produced within 12 h through a fed-batch strategy with the immobilized cells (25 mg/ml wet cells) at 35°C and 180 rpm, with a productivity of approximately 54 g/L per day.
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Affiliation(s)
- Fei Peng
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hui-Hui Su
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Xiao-Yang Ou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Zi-Fu Ni
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Min-Hua Zong
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Wen-Yong Lou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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20
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Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proc Natl Acad Sci U S A 2020; 117:5310-5318. [PMID: 32079722 DOI: 10.1073/pnas.1911742117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ubiquity of phospho-ligands suggests that phosphate binding emerged at the earliest stage of protein evolution. To evaluate this hypothesis and unravel its details, we identified all phosphate-binding protein lineages in the Evolutionary Classification of Protein Domains database. We found at least 250 independent evolutionary lineages that bind small molecule cofactors and metabolites with phosphate moieties. For many lineages, phosphate binding emerged later as a niche functionality, but for the oldest protein lineages, phosphate binding was the founding function. Across some 4 billion y of protein evolution, side-chain binding, in which the phosphate moiety does not interact with the backbone at all, emerged most frequently. However, in the oldest lineages, and most characteristically in αβα sandwich enzyme domains, N-helix binding sites dominate, where the phosphate moiety sits atop the N terminus of an α-helix. This discrepancy is explained by the observation that N-helix binding is uniquely realized by short, contiguous sequences with reduced amino acid diversity, foremost Gly, Ser, and Thr. The latter two amino acids preferentially interact with both the backbone amide and the side-chain hydroxyl (bidentate interaction) to promote binding by short sequences. We conclude that the first αβα sandwich domains emerged from shorter and simpler polypeptides that bound phospho-ligands via N-helix sites.
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21
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Fan J, Liao G, Ludwig-Radtke L, Yin WB, Li SM. Formation of Terrestric Acid in Penicillium crustosum Requires Redox-Assisted Decarboxylation and Stereoisomerization. Org Lett 2019; 22:88-92. [DOI: 10.1021/acs.orglett.9b04002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jie Fan
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Ge Liao
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Lena Ludwig-Radtke
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
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22
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Palaka BK, Velmurugan Ilavarasi A, Sapam TD, Kotapati KV, Nallala VS, Khan MB, Ampasala DR. Molecular cloning, gene expression analysis, and in silico characterization of UDP-N-acetylglucosamine pyrophosphorylase from Bombyx mori. Biotechnol Appl Biochem 2019; 66:880-899. [PMID: 31397000 DOI: 10.1002/bab.1802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
The present study was aimed to explore the molecular and structural features of UDP-N-acetylglucosamine pyrophosphorylase of Bombyx mori (BmUAP), an essential enzyme for chitin synthesis in insects. The BmUAP cDNA sequence was cloned and expression profiles were monitored during the molting and feeding stages of silkworm larvae. The effect of 20-hydroxyecdysone (20E) on BmUAP expression, and on silkworm molting was studied, which revealed that 20E regulates its expression. Multiple sequence alignment of various pyrophosphorylases revealed that the residues N223, G290, N327, and K407 of human UAP (PDB ID: 1JV1) were found to be highly conserved in BmUAP and all other eukaryotic UAPs considered for the study. Phylogenetic analysis inferred that the UAPs possess discrete variations in primary structure among different insect Orders while sharing good identity between species of the Order. The structure of BmUAP was predicted and its interactions with uridine triphosphate, N-acetylglucosamine-1-phosphate, and UDP-N-acetylglucosamine were analyzed. Virtual screening with a library of natural compounds resulted in five potential hits with good binding affinities. On further analysis, these five hits were found to be mimicking substrate and product, in inducing conformational changes in the active site. This work provides crucial information on molecular interactions and structural dynamics of insect UAPs.
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Affiliation(s)
- Bhagath Kumar Palaka
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Tuleshwori Devi Sapam
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Kasi Viswanath Kotapati
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Venkata Satyanarayana Nallala
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mohd Babu Khan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Dinakara Rao Ampasala
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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23
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Nguyen T, Kim T, Ta HM, Yeo WS, Choi J, Mizar P, Lee SS, Bae T, Chaurasia AK, Kim KK. Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus. mBio 2019; 10:e02660-18. [PMID: 31289190 PMCID: PMC6623548 DOI: 10.1128/mbio.02660-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/05/2019] [Indexed: 11/22/2022] Open
Abstract
Mannitol-1-phosphate dehydrogenase (M1PDH) is a key enzyme in Staphylococcus aureus mannitol metabolism, but its roles in pathophysiological settings have not been established. We performed comprehensive structure-function analysis of M1PDH from S. aureus USA300, a strain of community-associated methicillin-resistant S. aureus, to evaluate its roles in cell viability and virulence under pathophysiological conditions. On the basis of our results, we propose M1PDH as a potential antibacterial target. In vitro cell viability assessment of ΔmtlD knockout and complemented strains confirmed that M1PDH is essential to endure pH, high-salt, and oxidative stress and thus that M1PDH is required for preventing osmotic burst by regulating pressure potential imposed by mannitol. The mouse infection model also verified that M1PDH is essential for bacterial survival during infection. To further support the use of M1PDH as an antibacterial target, we identified dihydrocelastrol (DHCL) as a competitive inhibitor of S. aureus M1PDH (SaM1PDH) and confirmed that DHCL effectively reduces bacterial cell viability during host infection. To explain physiological functions of SaM1PDH at the atomic level, the crystal structure of SaM1PDH was determined at 1.7-Å resolution. Structure-based mutation analyses and DHCL molecular docking to the SaM1PDH active site followed by functional assay identified key residues in the active site and provided the action mechanism of DHCL. Collectively, we propose SaM1PDH as a target for antibiotic development based on its physiological roles with the goals of expanding the repertory of antibiotic targets to fight antimicrobial resistance and providing essential knowledge for developing potent inhibitors of SaM1PDH based on structure-function studies.IMPORTANCE Due to the shortage of effective antibiotics against drug-resistant Staphylococcus aureus, new targets are urgently required to develop next-generation antibiotics. We investigated mannitol-1-phosphate dehydrogenase of S. aureus USA300 (SaM1PDH), a key enzyme regulating intracellular mannitol levels, and explored the possibility of using SaM1PDH as a target for developing antibiotic. Since mannitol is necessary for maintaining the cellular redox and osmotic potential, the homeostatic imbalance caused by treatment with a SaM1PDH inhibitor or knockout of the gene encoding SaM1PDH results in bacterial cell death through oxidative and/or mannitol-dependent cytolysis. We elucidated the molecular mechanism of SaM1PDH and the structural basis of substrate and inhibitor recognition by enzymatic and structural analyses of SaM1PDH. Our results strongly support the concept that targeting of SaM1PDH represents an alternative strategy for developing a new class of antibiotics that cause bacterial cell death not by blocking key cellular machinery but by inducing cytolysis and reducing stress tolerance through inhibition of the mannitol pathway.
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Affiliation(s)
- Thanh Nguyen
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Truc Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Hai Minh Ta
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Won Sik Yeo
- Department of Microbiology and Immunology, Indiana University School of Medicine Northwest, Gary, Indiana, USA
| | - Jongkeun Choi
- Department of Chemical Engineering, Chungwoon University, Incheon, South Korea
| | - Pushpak Mizar
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Seung Seo Lee
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine Northwest, Gary, Indiana, USA
| | - Akhilesh Kumar Chaurasia
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
- Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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24
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Yang L, Yang Q, Wang M, Jia R, Chen S, Zhu D, Liu M, Wu Y, Zhao X, Zhang S, Liu Y, Yu Y, Zhang L, Chen X, Cheng A. Terminase Large Subunit Provides a New Drug Target for Herpesvirus Treatment. Viruses 2019; 11:v11030219. [PMID: 30841485 PMCID: PMC6466031 DOI: 10.3390/v11030219] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 12/26/2022] Open
Abstract
Herpesvirus infection is an orderly, regulated process. Among these viruses, the encapsidation of viral DNA is a noteworthy link; the entire process requires a powered motor that binds to viral DNA and carries it into the preformed capsid. Studies have shown that this power motor is a complex composed of a large subunit, a small subunit, and a third subunit, which are collectively known as terminase. The terminase large subunit is highly conserved in herpesvirus. It mainly includes two domains: the C-terminal nuclease domain, which cuts the viral concatemeric DNA into a monomeric genome, and the N-terminal ATPase domain, which hydrolyzes ATP to provide energy for the genome cutting and transfer activities. Because this process is not present in eukaryotic cells, it provides a reliable theoretical basis for the development of safe and effective anti-herpesvirus drugs. This article reviews the genetic characteristics, protein structure, and function of the herpesvirus terminase large subunit, as well as the antiviral drugs that target the terminase large subunit. We hope to provide a theoretical basis for the prevention and treatment of herpesvirus.
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Affiliation(s)
- Linlin Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Xiaoyue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
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25
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Abstract
SIGNIFICANCE Proline catabolism refers to the 4-electron oxidation of proline to glutamate catalyzed by the enzymes proline dehydrogenase (PRODH) and l-glutamate γ-semialdehyde dehydrogenase (GSALDH, or ALDH4A1). These enzymes and the intermediate metabolites of the pathway have been implicated in tumor growth and suppression, metastasis, hyperprolinemia metabolic disorders, schizophrenia susceptibility, life span extension, and pathogen virulence and survival. In some bacteria, PRODH and GSALDH are combined into a bifunctional enzyme known as proline utilization A (PutA). PutAs are not only virulence factors in some pathogenic bacteria but also fascinating systems for studying the coordination of metabolic enzymes via substrate channeling. Recent Advances: The past decade has seen an explosion of structural data for proline catabolic enzymes. This review surveys these structures, emphasizing protein folds, substrate recognition, oligomerization, kinetic mechanisms, and substrate channeling in PutA. CRITICAL ISSUES Major unsolved structural targets include eukaryotic PRODH, the complex between monofunctional PRODH and monofunctional GSALDH, and the largest of all PutAs, trifunctional PutA. The structural basis of PutA-membrane association is poorly understood. Fundamental aspects of substrate channeling in PutA remain unknown, such as the identity of the channeled intermediate, how the tunnel system is activated, and the roles of ancillary tunnels. FUTURE DIRECTIONS New approaches are needed to study the molecular and in vivo mechanisms of substrate channeling. With the discovery of the proline cycle driving tumor growth and metastasis, the development of inhibitors of proline metabolic enzymes has emerged as an exciting new direction. Structural biology will be important in these endeavors.
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Affiliation(s)
- John J Tanner
- 1 Department of Biochemistry and University of Missouri-Columbia , Columbia, Missouri.,2 Department of Chemistry, University of Missouri-Columbia , Columbia, Missouri
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26
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Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants. J Mol Biol 2018; 431:576-592. [PMID: 30580036 DOI: 10.1016/j.jmb.2018.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022]
Abstract
Heterokonts, Alveolata protists, green algae from Charophyta and Chlorophyta divisions, and all Embryophyta plants possess an aldehyde dehydrogenase (ALDH) gene named ALDH12. Here, we provide a biochemical characterization of two ALDH12 family members from the lower plant Physcomitrella patens and higher plant Zea mays. We show that ALDH12 encodes an NAD+-dependent glutamate γ-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate γ-semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate. Sedimentation equilibrium and small-angle X-ray scattering analyses reveal that in solution both plant GSALDHs exist as equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer. Plant GSALDHs share very low-sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nevertheless, the crystal structure of ZmALDH12 at 2.2-Å resolution shows that nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants. Finally, ALDH12 expression in maize and moss is downregulated in response to salt and drought stresses, possibly to maintain proline levels. Taken together, these results provide molecular insight into the biological roles of the plant ALDH12 family.
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The Pseudoalteromonas luteoviolacea L-amino Acid Oxidase with Antimicrobial Activity Is a Flavoenzyme. Mar Drugs 2018; 16:md16120499. [PMID: 30545033 PMCID: PMC6316408 DOI: 10.3390/md16120499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022] Open
Abstract
The marine environment is a rich source of antimicrobial compounds with promising pharmaceutical and biotechnological applications. The Pseudoalteromonas genus harbors one of the highest proportions of bacterial species producing antimicrobial molecules. For decades, the presence of proteins with L-amino acid oxidase (LAAO) and antimicrobial activity in Pseudoalteromonas luteoviolacea has been known. Here, we present for the first time the identification, cloning, characterization and phylogenetic analysis of Pl-LAAO, the enzyme responsible for both LAAO and antimicrobial activity in P. luteoviolacea strain CPMOR-2. Pl-LAAO is a flavoprotein of a broad substrate range, in which the hydrogen peroxide generated in the LAAO reaction is responsible for the antimicrobial activity. So far, no protein with a sequence similarity to Pl-LAAO has been cloned or characterized, with this being the first report on a flavin adenine dinucleotide (FAD)-containing LAAO with antimicrobial activity from a marine microorganism. Our results revealed that 20.4% of the sequenced Pseudoalteromonas strains (specifically, 66.6% of P. luteoviolacea strains) contain Pl-laao similar genes, which constitutes a well-defined phylogenetic group. In summary, this work provides insights into the biological significance of antimicrobial LAAOs in the Pseudoalteromonas genus and shows an effective approach for the detection of novel LAAOs, whose study may be useful for biotechnological applications.
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28
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Zachos I, Nowak C, Sieber V. Biomimetic cofactors and methods for their recycling. Curr Opin Chem Biol 2018; 49:59-66. [PMID: 30336443 DOI: 10.1016/j.cbpa.2018.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022]
Abstract
Nicotinamide cofactor biomimetics (NCBs) belong to a class of compounds that, as the name suggests, mimic the structures and functions of natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide and nicotinamide adenine dinucleotide phosphate and their corresponding reduced forms. The first set of NCBs was discovered in the 1930s; these were initially used to study the chemical properties of this class of cofactors as well as understand nicotinamide binding of oxidoreductases. Since then, various NCBs, enzymes, and recycling systems have evolved and lately, new NCBs have been developed and used to run biocatalytic reactions.
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Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Claudia Nowak
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Current address: Dr. Ebeling & Assoc. GmbH, Hamburg, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Catalysis Research Center, Technical University of Munich, Garching, Germany; Fraunhofer Institute of InterfacialBiotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, Australia.
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29
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Abstract
Interest in how proline contributes to cancer biology is expanding because of the emerging role of a novel proline metabolic cycle in cancer cell survival, proliferation, and metastasis. Proline biosynthesis and degradation involve the shared intermediate Δ1-pyrroline-5-carboxylate (P5C), which forms l-glutamate-γ-semialdehyde (GSAL) in a reversible non-enzymatic reaction. Proline is synthesized from glutamate or ornithine through GSAL/P5C, which is reduced to proline by P5C reductase (PYCR) in a NAD(P)H-dependent reaction. The degradation of proline occurs in the mitochondrion and involves two oxidative steps catalyzed by proline dehydrogenase (PRODH) and GSAL dehydrogenase (GSALDH). PRODH is a flavin-dependent enzyme that couples proline oxidation with reduction of membrane-bound quinone, while GSALDH catalyzes the NAD+-dependent oxidation of GSAL to glutamate. PRODH and PYCR form a metabolic relationship known as the proline-P5C cycle, a novel pathway that impacts cellular growth and death pathways. The proline-P5C cycle has been implicated in supporting ATP production, protein and nucleotide synthesis, anaplerosis, and redox homeostasis in cancer cells. This Perspective details the structures and reaction mechanisms of PRODH and PYCR and the role of the proline-P5C cycle in cancer metabolism. A major challenge in the field is to discover inhibitors that specifically target PRODH and PYCR isoforms for use as tools for studying proline metabolism and the functions of the proline-P5C cycle in cancer. These molecular probes could also serve as lead compounds in cancer drug discovery targeting the proline-P5C cycle.
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Affiliation(s)
- John J. Tanner
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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30
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Dey P, Bairagya HR, Roy A. Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases. J Biosci 2018; 43:339-349. [PMID: 29872022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fungal endo-1,4-beta-xylanases (EC3.2.1.8), because of their widespread industrial applications have become one of the most researched industrial enzymes in recent times. Despite its significance, the role of conserved water molecules in the catalytic activities and structural stability of these enzymes from the fungi have not been studied to a great extent. Our computational structural bioinformatics and MD simulation studies have identified the existence of seven invariant water molecules (IW1- IW7) and reveals the stereo-chemical and electronic consequences of those conserved water molecules in G-xylanase enzyme from eight different fungi. The buried water molecules IW1 and IW2 may have decisive roles in catalysis and may also be associated with ligand binding process of the enzyme, whereas IW3, IW4, IW5, IW6 and IW7 may be involved in stabilizing the important (H144/R145) residues through H-bonds. Possibly they are also involved in the stabilization of secondary structures and anchor to maintain its stereo-chemical architecture. Moreover, a distorted 'W' shaped signature geometry that is observed at the surface of the enzyme can be used to identify the hydrophilic centers in the electron density map of other unknown members of the family G xylanases. The results from this computational investigation could be of interest to a large number of researchers working with the xylanases.
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Affiliation(s)
- Protyusha Dey
- Department of Biotechnology, Visva-Bharati University, Santiniketan, West Bengal 731 235, India
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31
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Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases. J Biosci 2018. [DOI: 10.1007/s12038-018-9752-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Shi L, Cao S, Chen X, Chen W, Zheng Y, Yang Z. Proanthocyanidin Synthesis in Chinese Bayberry ( Myrica rubra Sieb. et Zucc.) Fruits. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 29541082 PMCID: PMC5835688 DOI: 10.3389/fpls.2018.00212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Proanthocyanidins (PAs) are distributed widely in Chinese bayberry fruit and have been associated with human health benefits, but molecular and biochemical characterization of PA biosynthesis remains unclear. Here, two genes encoding key PA biosynthetic enzymes, anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR) were isolated in bayberry fruit. MrANR was highly expressed at the early stage of fruit development when soluble PAs accumulated at high levels. Meanwhile, the transcript abundance of both MrANR and MrLAR observed at the late stage was paralleled with the high amounts of insoluble PAs. LC-MS/MS showed that PAs in developing Chinese bayberry fruits were comprised predominantly of epigallocatechin-3-O-gallate terminal subunits, while the extension subunits were a mixture of epigallocatechin-3-O-gallate, epigallocatechin and catechin. Recombinant MrANR protein converted cyanidin to a mixture of epicatechin and catechin, and delphinidin to a mixture of epigallocatechin and gallocatechin in vitro. Recombinant MrLAR was active with leucocyanidin as substrate to produce catechin. Ectopic expression of MrANR in tobacco reduced anthocyanin levels but increased PA accumulation. The catechin and epicatechin contents in transgenic flowers overexpressed MrANR were significantly higher than those of wild-type. However, overexpression of MrLAR in tobacco led to an increase in catechin levels but had no impact on PA contents. Quantitative real time PCR revealed that the loss of anthocyanin in transgenic flowers overexpressed MrANR or MrLAR is probably attributed to decreased expression of tobacco chalcone isomerase (CHI) gene. Our results not only reveal in vivo and in vitro functions for ANR and LAR but also provide a resource for understanding the mechanism of PA biosynthesis in Chinese bayberry fruit.
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Affiliation(s)
- Liyu Shi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shifeng Cao
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Xin Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Wei Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Yonghua Zheng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Yonghua Zheng
| | - Zhenfeng Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Zhenfeng Yang
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33
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Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
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34
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Sellés Vidal L, Kelly CL, Mordaka PM, Heap JT. Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:327-347. [PMID: 29129662 DOI: 10.1016/j.bbapap.2017.11.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 11/27/2022]
Abstract
NAD(P)H-dependent oxidoreductases catalyze the reduction or oxidation of a substrate coupled to the oxidation or reduction, respectively, of a nicotinamide adenine dinucleotide cofactor NAD(P)H or NAD(P)+. NAD(P)H-dependent oxidoreductases catalyze a large variety of reactions and play a pivotal role in many central metabolic pathways. Due to the high activity, regiospecificity and stereospecificity with which they catalyze redox reactions, they have been used as key components in a wide range of applications, including substrate utilization, the synthesis of chemicals, biodegradation and detoxification. There is great interest in tailoring NAD(P)H-dependent oxidoreductases to make them more suitable for particular applications. Here, we review the main properties and classes of NAD(P)H-dependent oxidoreductases, the types of reactions they catalyze, some of the main protein engineering techniques used to modify their properties and some interesting examples of their modification and application.
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Affiliation(s)
- Lara Sellés Vidal
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ciarán L Kelly
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Paweł M Mordaka
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - John T Heap
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
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35
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Ashraf R, Rashid N, Kanai T, Imanaka T, Akhtar M. Pcal_1311, an alcohol dehydrogenase homologue from Pyrobaculum calidifontis, displays NADH-dependent high aldehyde reductase activity. Extremophiles 2017; 21:1101-1110. [PMID: 29022135 DOI: 10.1007/s00792-017-0970-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
Abstract
Genome sequence of Pyrobaculum calidifontis, a hyperthermophilic archaeon, harbors three open-reading frames annotated as alcohol dehydrogenases. One of them, Pcal_1311, does not display a significantly high homology with any of the characterized alcohol dehydrogenases. Highest homology of 38% was found with the characterized counterpart from Geobacillus stearothermophilus. To examine the biochemical properties of Pcal_1311, we have cloned and functionally expressed the gene in Escherichia coli. Purified recombinant Pcal_1311 catalyzed the NAD(H)-dependent oxidation of various alcohols and reduction of aldehydes, with a marked preference for substrates with functional group at the terminal carbon. Highest activity for the oxidation reaction (3 μmol min-1 mg-1) was found with 1,4-butanediol and for the reduction reaction (150 μmol min-1 mg-1) with glutaraldehyde. Both the oxidation and reduction activities increased with the increase in temperature up to 80 °C. Recombinant Pcal_1311 was highly stable and retained more than 90% activity even after incubation of 180 min at 90 °C. In addition to the thermostabilty, Pcal_1311 was highly stable in the presence of known denaturants including urea and guanidine hydrochloride. The high stability, particularly thermostability, and the NADH-dependent aldehyde reduction activity make Pcal_1311 a unique member in the alcohol dehydrogenase family.
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Affiliation(s)
- Raza Ashraf
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Tadayuki Imanaka
- The Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan.,School of Biological Sciences, University of Southampton, Southampton, SO16 7PX, UK
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36
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Srivastava VK, Yadav R, Watanabe N, Tomar P, Mukherjee M, Gourinath S, Nakada-Tsukui K, Nozaki T, Datta S. Structural and thermodynamic characterization of metal binding in Vps29 from Entamoeba histolytica: implication in retromer function. Mol Microbiol 2017; 106:562-581. [PMID: 28898487 DOI: 10.1111/mmi.13836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2017] [Indexed: 11/28/2022]
Abstract
Vps29 is the smallest subunit of retromer complex with metallo-phosphatase fold. Although the role of metal in Vps29 is in quest, its metal binding mutants has been reported to affect the localization of the retromer complex in human cells. In this study, we report the structural and thermodynamic consequences of these mutations in Vps29 from the protozoan parasite, Entamoeba histolytica (EhVps29). EhVps29 is a zinc binding protein as revealed by X-ray crystallography and isothermal titration calorimetry. The metal binding pocket of EhVps29 exhibits marked differences in its 3-dimensional architecture and metal coordination in comparison to its human homologs and other metallo-phosphatases. Alanine substitutions of the metal-coordinating residues showed significant alteration in the binding affinity of EhVps29 for zinc. We also determined the crystal structures of metal binding defective mutants (D62A and D62A/H86A) of EhVps29. Based on our results, we propose that the metal atoms or the bound water molecules in the metal binding site are important for maintaining the structural integrity of the protein. Further cellular studies in the amoebic trophozoites showed that the overexpression of wild type EhVps29 leads to reduction in intracellular cysteine protease activity suggesting its crucial role in secretion of the proteases.
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Affiliation(s)
- Vijay Kumar Srivastava
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.,Amity Institute of Biotechnology, Amity University Jaipur, Rajasthan 303002, India
| | - Rupali Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Natsuki Watanabe
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan.,Department of Biologikal Science, Graduate school of live and Environmental science, University of Tsukuba, Japan
| | - Priya Tomar
- Structural Biology Laboratory, School of Life Sciences (JNU), New Delhi 110067, India
| | - Madhumita Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences (JNU), New Delhi 110067, India
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
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37
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Liu LK, Becker DF, Tanner JJ. Structure, function, and mechanism of proline utilization A (PutA). Arch Biochem Biophys 2017; 632:142-157. [PMID: 28712849 DOI: 10.1016/j.abb.2017.07.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/13/2023]
Abstract
Proline has important roles in multiple biological processes such as cellular bioenergetics, cell growth, oxidative and osmotic stress response, protein folding and stability, and redox signaling. The proline catabolic pathway, which forms glutamate, enables organisms to utilize proline as a carbon, nitrogen, and energy source. FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent glutamate semialdehyde dehydrogenase (GSALDH) convert proline to glutamate in two sequential oxidative steps. Depletion of PRODH and GSALDH in humans leads to hyperprolinemia, which is associated with mental disorders such as schizophrenia. Also, some pathogens require proline catabolism for virulence. A unique aspect of proline catabolism is the multifunctional proline utilization A (PutA) enzyme found in Gram-negative bacteria. PutA is a large (>1000 residues) bifunctional enzyme that combines PRODH and GSALDH activities into one polypeptide chain. In addition, some PutAs function as a DNA-binding transcriptional repressor of proline utilization genes. This review describes several attributes of PutA that make it a remarkable flavoenzyme: (1) diversity of oligomeric state and quaternary structure; (2) substrate channeling and enzyme hysteresis; (3) DNA-binding activity and transcriptional repressor function; and (4) flavin redox dependent changes in subcellular location and function in response to proline (functional switching).
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Affiliation(s)
- Li-Kai Liu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, United States.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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Christensen EM, Patel SM, Korasick DA, Campbell AC, Krause KL, Becker DF, Tanner JJ. Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. J Biol Chem 2017; 292:7233-7243. [PMID: 28258219 PMCID: PMC5409489 DOI: 10.1074/jbc.m117.780288] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 02/27/2017] [Indexed: 01/22/2023] Open
Abstract
Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation-velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition. We see NADPH bound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination.
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Affiliation(s)
| | - Sagar M Patel
- the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | | | | | - Kurt L Krause
- the Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand, and
| | - Donald F Becker
- the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - John J Tanner
- From the Departments of Chemistry and
- Biochemistry University of Missouri, Columbia, Missouri 65211
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A new source of resistance to 2-furaldehyde from Scheffersomyces (Pichia) stipitis for sustainable lignocellulose-to-biofuel conversion. Appl Microbiol Biotechnol 2017; 101:4981-4993. [PMID: 28357544 DOI: 10.1007/s00253-017-8208-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/15/2017] [Accepted: 02/18/2017] [Indexed: 10/19/2022]
Abstract
Aldehyde inhibitory compounds derived from lignocellulosic biomass pretreatment have been identified as a major class of toxic chemicals that interfere with microbial growth and subsequent fermentation for advanced biofuel production. Development of robust next-generation biocatalyst is a key for a low-cost biofuel production industry. Scheffersomyces (Pichia) stipitis is a naturally occurring C-5 sugar utilization yeast; however, little is known about the genetic background underlying its potential tolerance to biomass conversion inhibitors. We investigated and identified five uncharacterized putative aryl-alcohol dehydrogenase genes (SsAADs) from this yeast as a new source of resistance against biomass fermentation inhibitor 2-furaldehyde (furfural) by gene expression, gene cloning, and direct enzyme assay analysis using partially purified proteins. All five proteins from S. stipitis showed furfural reduction using cofactor NADH. An optimum active temperature was observed at 40 °C for SsAad1p; 30 °C for SsAad3p, SsAad4p, and SsAad5p; and 20 °C for SsAad2p. SsAad2p, SsAad3p, and SsAad4p showed tolerance to a wide range of pH from 4.5 to 8, but SsAad1p and SsAad5p were sensitive to pH changes beyond 7. Genes SsAAD2, SsAAD3, and SsAAD4 displayed significantly enhanced higher levels of expression in response to the challenge of furfural. Their encoding proteins also showed higher levels of specific activity toward furfural and were suggested as core functional enzymes contributing aldehyde resistance in S. stipitis.
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40
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Ashraf R, Rashid N, Basheer S, Aziz I, Akhtar M. Glutathione-Dependent Formaldehyde Dehydrogenase Homolog from Bacillus subtilis Strain R5 is a Propanol-Preferring Alcohol Dehydrogenase. BIOCHEMISTRY (MOSCOW) 2017; 82:13-23. [PMID: 28320283 DOI: 10.1134/s0006297917010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genome search of Bacillus subtilis revealed the presence of an open reading frame annotated as glutathione-dependent formaldehyde dehydrogenase/alcohol dehydrogenase. The open reading frame consists of 1137 nucleotides corresponding to a polypeptide of 378 amino acids. To examine whether the encoded protein is glutathione-dependent formaldehyde dehydrogenase or alcohol dehydrogenase, we cloned and characterized the gene product. Enzyme activity assays revealed that the enzyme exhibits a metal ion-dependent alcohol dehydrogenase activity but no glutathione-dependent formaldehyde dehydrogenase or aldehyde dismutase activity. Although the protein is of mesophilic origin, optimal temperature for the enzyme activity is 60°C. Thermostability analysis by circular dichroism spectroscopy revealed that the protein is stable up to 60°C. Presence or absence of metal ions in the reaction mixture did not affect the enzyme activity. However, metal ions were necessary at the time of protein production and folding. There was a marked difference in the enzyme activity and CD spectra of the proteins produced in the presence and absence of metal ions. The experimental results obtained in this study demonstrate that the enzyme is a bona-fide alcohol dehydrogenase and not a glutathione-dependent formaldehyde dehydrogenase.
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Affiliation(s)
- Raza Ashraf
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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41
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Zeng Z, Bernstein ER. Photoelectron spectroscopy and density functional theory studies of (fructose + (H 2O) n) − ( n = 1–5) anionic clusters. Phys Chem Chem Phys 2017; 19:31121-31137. [DOI: 10.1039/c7cp06625b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
(Fructose + (H2O)n)− (n = 1–5) cluster anions mainly exist as open chain structures. Some cyclic structures of (fructose + (H2O)n)− (n = 3, 4) are present too.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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Urban MO, Vašek J, Klíma M, Krtková J, Kosová K, Prášil IT, Vítámvás P. Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy. J Proteomics 2016; 152:188-205. [PMID: 27838467 DOI: 10.1016/j.jprot.2016.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level. SIGNIFICANCE Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.
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Affiliation(s)
- Milan Oldřich Urban
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic; Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic.
| | - Jakub Vašek
- Czech University of Life Sciences Prague, Department of Genetics and Breeding, Kamýcká 129, Prague, Czech Republic
| | - Miroslav Klíma
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Jana Krtková
- Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic
| | - Klára Kosová
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Ilja Tom Prášil
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Pavel Vítámvás
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
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Small RNA transcriptomes of mangroves evolve adaptively in extreme environments. Sci Rep 2016; 6:27551. [PMID: 27278626 PMCID: PMC4899726 DOI: 10.1038/srep27551] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/20/2016] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are key players in plant stress responses. Here, we present the sRNA transcriptomes of mangroves Bruguiera gymnorrhiza and Kandelia candel. Comparative computational analyses and target predictions revealed that mangroves exhibit distinct sRNA regulatory networks that differ from those of glycophytes. A total of 32 known and three novel miRNA families were identified. Conserved and mangrove-specific miRNA targets were predicted; the latter were widely involved in stress responses. The known miRNAs showed differential expression between the mangroves and glycophytes, reminiscent of the adaptive stress-responsive changes in Arabidopsis. B. gymnorrhiza possessed highly abundant but less conserved TAS3 trans-acting siRNAs (tasiRNAs) in addition to tasiR-ARFs, with expanded potential targets. Our results indicate that the evolutionary alteration of sRNA expression levels and the rewiring of sRNA-regulatory networks are important mechanisms underlying stress adaptation. We also identified sRNAs that are involved in salt and/or drought tolerance and nutrient homeostasis as possible contributors to mangrove success in stressful environments.
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44
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Kanteev M, Bregman-Cohen A, Deri B, Shahar A, Adir N, Fishman A. A crystal structure of 2-hydroxybiphenyl 3-monooxygenase with bound substrate provides insights into the enzymatic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1906-1913. [PMID: 26275805 DOI: 10.1016/j.bbapap.2015.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 11/16/2022]
Abstract
2-Hydroxybiphenyl 3-monooxygenase (HbpA) is an FAD dependent monooxygenase which catalyzes the ortho-hydroxylation of a broad range of 2-substituted phenols in the presence of NADH and molecular oxygen. We have determined the structure of HbpA from the soil bacterium Pseudomonas azelaica HBP1 with bound 2-hydroxybiphenyl, as well as several variants, at a resolution of 2.3-2.5Å to investigate structure function correlations of the enzyme. An observed hydrogen bond between 2-hydroxybiphenyl and His48 in the active site confirmed the previously suggested role of this residue in substrate deprotonation. The entrance to the active site was confirmed by generating variant G255F which exhibited only 7% of the wild-type's specific activity of product formation, suggesting inhibition of substrate entrance into the active site by the large aromatic residue. Residue Arg242 is suggested to facilitate FAD movement and reduction as was previously reported in studies on the homologous protein para-hydroxybenzoate hydroxylase. In addition, it is suggested that Trp225, which is located in the active site, facilitates proper substrate entrance into the binding pocket in contrast to aklavinone-11-hydroxylase and para-hydroxybenzoate hydroxylase in which a residue at a similar position is responsible for substrate deprotonation. Structure function correlations described in this work will aid in the design of variants with improved activity and altered selectivity for potential industrial applications.
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Affiliation(s)
- Margarita Kanteev
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Almog Bregman-Cohen
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Batel Deri
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center (MCRC), Department of Life Sciences & NIBN, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
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Forlani G, Makarova KS, Ruszkowski M, Bertazzini M, Nocek B. Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:567. [PMID: 26284089 PMCID: PMC4522605 DOI: 10.3389/fpls.2015.00567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/09/2015] [Indexed: 05/23/2023]
Abstract
Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ(1)-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughout evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We also attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.
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Affiliation(s)
- Giuseppe Forlani
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, BethesdaMD, USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, ArgonneIL, USA
| | - Michele Bertazzini
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Boguslaw Nocek
- The Bioscience Division, Argonne National Laboratory, ArgonneIL, USA
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Son HF, Kim IK, Kim KJ. Structural insights into domain movement and cofactor specificity of glutamate dehydrogenase from Corynebacterium glutamicum. Biochem Biophys Res Commun 2015; 459:387-92. [PMID: 25727019 DOI: 10.1016/j.bbrc.2015.02.109] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
Glutamate dehydrogenase (GDH) is an enzyme involved in the synthesis of amino acids by converting glutamate to α-ketoglutarate, and vice versa. To investigate the molecular mechanism of GDH, we determined a crystal structure of the Corynebacterium glutamicum-derived GDH (CgGDH) in complex with its NADP cofactor and α-ketoglutarate substrate. CgGDH functions as a hexamer, and each CgGDH monomer comprises 2 separate domains; a Rossmann fold cofactor-binding domain and a substrate-binding domain. The structural comparison between the apo- and cofactor/substrate-binding forms revealed that the CgGDH enzyme undergoes a domain movement during catalysis. In the apo-form, CgGDH exists as an open state, and upon binding of the substrate and cofactor the protein undergoes a conformation change to a closed state. Our structural study also revealed that CgGDH has cofactor specificity for NADP, but not NAD, and this was confirmed by GDH activity measurements. Residues involved in the stabilization of the NADP cofactor and the α-ketoglutarate substrate were identified, and their roles in substrate/cofactor binding were confirmed by site-directed mutagenesis experiments.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Il-Kwon Kim
- Paik Kwang Industrial Company Ltd., 57 Oehang-4 Gil, Gunsan, Jellabuk-do 573-879, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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48
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Wu MM, Huang HD, Li GQ, Zhou JF, Ma T. Biochemical characterization and functional analysis of Udp-glucose dehydrogenase, in the synthesis of biopolymer Ss from Sphingomonas sanxanigenens NX02. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683815010160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Tu IF, Liao JH, Yang FL, Lin NT, Chan HL, Wu SH. Lon protease affects the RdxA nitroreductase activity and metronidazole susceptibility in Helicobacter pylori. Helicobacter 2014; 19:356-66. [PMID: 24834789 DOI: 10.1111/hel.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The lon gene of Helicobacter pylori strains is constitutively expressed during growth. However, virtually nothing is understood concerning the role of Lon in H. pylori. This study examined the function and physiological role of Lon in H. pylori (HpLon) using a trapping approach to identify putative Lon binding partners in the bacterium. MATERIALS AND METHODS Protease-deficient Lon was expressed and served as the bait in trapping approach to capture the interacting partners in H. pylori. The antibiotic susceptibility of wild-type and lon derivative mutants was determined by the E test trips and the disc diffusion assay. The effect of HpLon on RdxA activity was detected the change in NADPH oxidation and metronidazole reduction by spectrophotometer. RESULTS Lon in Helicobacter pylori (HpLon) interacting partners are mostly associated with metronidazole activation. lon mutant presents more susceptible to metronidazole than that of the wild type, and this phenotype is recovered by complementation of the wild-type Lon. We found that the ATPases associated with a variety of cellular activities (AAA(+) ) module of HpLon causes a decrease in both NADPH oxidase and Mtz reductase activity in RdxA, a major Mtz-activating enzyme in H. pylori. CONCLUSION Metronidazole resistance of H. pylori causes the serious medical problem worldwide. In this study, HpLon is involved in metronidazole susceptibility among H. pylori strains. We provide the evidence that HpLon alters RdxA activity in vitro. The decrease in metronidazole activation caused by HpLon is possibly prior to accumulate mutation in rdxA gene before the metronidazole-resistant strains to be occurred.
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Affiliation(s)
- I-Fan Tu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
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50
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Raj S, Ramaswamy S, Plapp BV. Yeast alcohol dehydrogenase structure and catalysis. Biochemistry 2014; 53:5791-803. [PMID: 25157460 PMCID: PMC4165444 DOI: 10.1021/bi5006442] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/22/2014] [Indexed: 11/30/2022]
Abstract
Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.
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Affiliation(s)
| | | | - Bryce V. Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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