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Zhou Y, Chen J, Pu W, Cai N, Che B, Yang J, Wang M, Zhong S, Zuo X, Wang D, Wang Y, Zheng P, Sun J. Development of a growth-coupled selection platform for directed evolution of heme biosynthetic enzymes in Corynebacterium glutamicum. Front Bioeng Biotechnol 2023; 11:1236118. [PMID: 37654705 PMCID: PMC10465345 DOI: 10.3389/fbioe.2023.1236118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Heme is an important tetrapyrrole compound, and has been widely applied in food and medicine industries. Although microbial production of heme has been developed with metabolic engineering strategies during the past 20 years, the production levels are relatively low due to the multistep enzymatic processes and complicated regulatory mechanisms of microbes. Previous studies mainly adopted the strategies of strengthening precursor supply and product transportation to engineer microbes for improving heme biosynthesis. Few studies focused on the engineering and screening of efficient enzymes involved in heme biosynthesis. Herein, a growth-coupled, high-throughput selection platform based on the detoxification of Zinc-protoporphyrin IX (an analogue of heme) was developed and applied to directed evolution of coproporphyrin ferrochelatase, catalyzing the insertion of metal ions into porphyrin ring to generate heme or other tetrapyrrole compounds. A mutant with 3.03-fold increase in k cat/K M was selected. Finally, growth-coupled directed evolution of another three key enzymes involved in heme biosynthesis was tested by using this selection platform. The growth-coupled selection platform developed here can be a simple and effective strategy for directed evolution of the enzymes involved in the biosynthesis of heme or other tetrapyrrole compounds.
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Affiliation(s)
- Yingyu Zhou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ningyun Cai
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jinxing Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mengmeng Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shasha Zhong
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xingtao Zuo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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Shan X, Fu J, Li X, Peng X, Chen L. Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals. J Proteomics 2022; 251:104408. [PMID: 34737110 DOI: 10.1016/j.jprot.2021.104408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/12/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. In this study, we determined virulence-associated genes, cross-resistance between antibiotics and heavy metals, and genome fingerprinting profiles of non O1/O139 V. cholerae isolates (n = 20) recovered from 16 species of consumable aquatic animals. Secretomes and proteomes of V. cholerae with distinct genotypes and phenotypes were obtained by using two-dimensional gel electrophoresis (2D-GE) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analysis revealed 4 common and 45 differential extracellular proteins among 20 V. cholerae strains, including 13 virulence- and 8 resistance-associated proteins. A total of 21,972 intracellular proteins were identified, and comparative proteomic analysis revealed 215 common and 913 differential intracellular proteins, including 22 virulence- and 8 resistance-associated proteins. Additionally, different secretomes and proteomes were observed between V. cholerae isolates of fish and shellfish origins. A number of novel proteins with unknown function and strain-specific proteins were also discovered in the V. cholerae isolates. SIGNIFICANCE: V. cholerae can cause pandemic cholera in humans. The bacterium is distributed in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. Non-O1/O139 V. cholerae has been reported to cause sporadic cholera-like diarrhea and bacteremia diseases, which indicates virulence factors rather than the major cholera toxin (CT) exist. This study for the first time investigated proteomes and secretomes of non-O1/O139 V. cholerae originating from aquatic animals. This resulted in the identification of a number of virulence and coresistance-related factors, as well as novel proteins and strain-specific proteins in V. cholerae isolates recovered from 16 species of consumable aquatic animals. These results fill gaps for better understanding of pathogenesis and resistance of V. cholerae, and also support the increasing need for novel diagnosis and vaccine targets against the leading waterborne pathogen worldwide.
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Affiliation(s)
- Xinying Shan
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Junfeng Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaohui Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
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Bustad HJ, Kallio JP, Laitaoja M, Toska K, Kursula I, Martinez A, Jänis J. Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism. iScience 2021; 24:102152. [PMID: 33665570 PMCID: PMC7907807 DOI: 10.1016/j.isci.2021.102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Porphobilinogen deaminase (PBGD), the third enzyme in the heme biosynthesis, catalyzes the sequential coupling of four porphobilinogen (PBG) molecules into a heme precursor. Mutations in PBGD are associated with acute intermittent porphyria (AIP), a rare metabolic disorder. We used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to demonstrate that wild-type PBGD and AIP-associated mutant R167W both existed as holoenzymes (Eholo) covalently attached to the dipyrromethane cofactor, and three intermediate complexes, ES, ES2, and ES3, where S represents PBG. In contrast, only ES2 was detected in AIP-associated mutant R173W, indicating that the formation of ES3 is inhibited. The R173W crystal structure in the ES2-state revealed major rearrangements of the loops around the active site, compared to wild-type PBGD in the Eholo-state. These results contribute to elucidating the structural pathogenesis of two common AIP-associated mutations and reveal the important structural role of Arg173 in the polypyrrole elongation mechanism.
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Affiliation(s)
- Helene J Bustad
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, 80130 Joensuu, Finland
| | - Karen Toska
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, 80130 Joensuu, Finland
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Sato H, Sugishima M, Tsukaguchi M, Masuko T, Iijima M, Takano M, Omata Y, Hirabayashi K, Wada K, Hisaeda Y, Yamamoto K. Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps. Biochem J 2021; 478:1023-1042. [PMID: 33600566 PMCID: PMC7959689 DOI: 10.1042/bcj20200996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/30/2022]
Abstract
Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Å resolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.
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Affiliation(s)
- Hideaki Sato
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Mai Tsukaguchi
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
| | - Takahiro Masuko
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mikuru Iijima
- Department of Pure and Applied Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshiaki Omata
- Department of Molecular Biology, Faculty of Pharmaceutical Science, Yokohama University of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Kei Hirabayashi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yoshio Hisaeda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan
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Antibiotic Susceptibility Testing (AST) Reports: A Basis for Environmental/Epidemiological Surveillance and Infection Control Amongst Environmental Vibrio cholerae. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17165685. [PMID: 32781601 PMCID: PMC7460427 DOI: 10.3390/ijerph17165685] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Distribution, investigation, surveillance and control (DISC) of cholera outbreaks in endemic/non-endemic regions has been a concerted approach towards the management of the causal pathogen. Relevant organization, government, health systems and the public have implemented several steps towards controlling the menace, yet pathogen continues to occur with diverse phenotypes/genotypes of high clinical and epidemiological relevance. The study determines antibiotic susceptibility/resistance pattern of Vibrio cholerae isolates retrieved from six domestic water sources between March and August 2018. Serological and molecular typing methods (polymerase chain reaction or PCR) were used to confirm the isolates identity. Antibiotic susceptibility testing was conducted using six commonly employed antibiotics of V. cholerae according to the recommendation of Clinical Laboratory Standard and European Committee for Antimicrobial Susceptibility Testing with other relevant antibiotics of investigative epidemiology and infection control, employing both disc diffusion test and PCR gene detection. Samples presumptive counts ranged between 1.10 to 7.91 log10 CFU/mL. Amongst the 759 presumptive isolates retrieved, sixty-one were confirmed as V. cholerae which were further serogrouped as Non-O1/Non-O139 V. cholerae. Various V. cholerae resistant phenotypes/genoytypes were detected vis: carbapenemase (CR-Vc; 31.1%/5.3%). New Delhi Metallobetalactamase (NDM-1-Vc; 23.0%/42.5%), extended spectrum betalactamase (ESBL-Vc; 42.6%/blaTEM:86,7%), chloramphenicol resistance (62.3%/Flor: 46.2%}, tetracycline resistance (70.5%/46.7%), AmpC resistance (21.0 (34.4%/56.7%)) and various other resistant genotypes/phenotypes. It was observed that more than 50% of the confirmed V. cholerae isolates possess resistance to two or more antibiotic classes/groups with multiple antibiotic resistance index (MARI) ranging from 0.031 to 0.5. This observation provides necessary information and updates for surveillance, planning and implementation of control strategies for cholera. It would also encourage decision making, formulation of policy by the government and cholera control authorities.
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Biophysical research in Hokkaido University, Japan. Biophys Rev 2020; 12:233-236. [PMID: 32347462 DOI: 10.1007/s12551-020-00649-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 10/24/2022] Open
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Nishitani Y, Okutani H, Takeda Y, Uchida T, Iwai K, Ishimori K. Specific heme binding to heme regulatory motifs in iron regulatory proteins and its functional significance. J Inorg Biochem 2019; 198:110726. [PMID: 31220756 DOI: 10.1016/j.jinorgbio.2019.110726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022]
Abstract
Iron regulatory proteins (IRPs) control iron metabolism in mammalian cells by binding to the iron-responsive element (IRE) in the target mRNA. Heme regulatory motifs (HRMs) are conserved in the two IRP homologues IRP1 and IRP2 that specifically bind to two and three heme equivalents, respectively; however, only the heme binding to the iron-dependent degradation (IDD) domain of IRP2 causes heme-mediated oxidation, which does not occur in IRP1. Therefore, the functional significance of conserved HRMs outside the IDD domain is yet unclear. In this study, spectroscopic heme titration with IRP mutants confirmed heme binding to each HRM in IRPs, and the effect of heme binding to HRMs on IRE binding was examined. Native polyacrylamide gel electrophoresis analysis revealed that heme binding to HRMs near the IRE binding site inhibits complex formation between IRPs and IRE without oxidative modification, indicating that the function of HRMs varies outside and within the IDD domain. However, the formation of a typical reactive oxygen species (ROS), hydrogen peroxide, was spectroscopically detected in both heme-bound IRPs. Comparing the heme environmental structures surrounding HRMs, the flexible conformation and many amino acid residues sensitive to ROS of the IDD domain were suggested to promote specific oxidation by the generated hydrogen peroxide. Thus, heme binding to HRM near the IRE binding site sterically interferes with IRE binding, while HRM in the IDD domain facilitates specific heme-mediated oxidation of the protein moiety and the protein degradation via the ubiquitin-proteasome system, resulting in the inhibition of IRE binding.
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Affiliation(s)
- Yudai Nishitani
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hirotaka Okutani
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yukiko Takeda
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuhiro Iwai
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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Bung N, Roy A, Priyakumar UD, Bulusu G. Computational modeling of the catalytic mechanism of hydroxymethylbilane synthase. Phys Chem Chem Phys 2019; 21:7932-7940. [DOI: 10.1039/c9cp00196d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthesis pathway, catalyzes the formation of 1-hydroxymethylbilane (HMB) by a stepwise polymerization of four molecules of porphobilinogen (PBG) using the dipyrromethane (DPM) cofactor.
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Affiliation(s)
- Navneet Bung
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
- Center for Computational Natural Sciences and Bioinformatics
| | - Arijit Roy
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500032
- India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs – Hyderabad (Life Sciences Division)
- Tata Consultancy Services Limited
- Hyderabad 500081
- India
- Center for Computational Natural Sciences and Bioinformatics
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Shimizu T, Lengalova A, Martínek V, Martínková M. Heme: emergent roles of heme in signal transduction, functional regulation and as catalytic centres. Chem Soc Rev 2019; 48:5624-5657. [DOI: 10.1039/c9cs00268e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular mechanisms of unprecedented functions of exchangeable/labile heme and heme proteins including transcription, DNA binding, protein kinase activity, K+ channel functions, cis–trans isomerization, N–N bond formation, and other functions are described.
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Affiliation(s)
- Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Václav Martínek
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
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Pluta P, Roversi P, Bernardo-Seisdedos G, Rojas AL, Cooper JB, Gu S, Pickersgill RW, Millet O. Structural basis of pyrrole polymerization in human porphobilinogen deaminase. Biochim Biophys Acta Gen Subj 2018; 1862:1948-1955. [PMID: 29908816 DOI: 10.1016/j.bbagen.2018.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 01/27/2023]
Abstract
Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.
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Affiliation(s)
- Paula Pluta
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Dept. of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, England, UK
| | | | - Adriana L Rojas
- Structural Biology Unit, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Jonathan B Cooper
- Department of Biological Sciences, Birkbeck, London WC1E 7HX, UK; Division of Medicine, University College London, London WC1E 6BT, UK
| | - Shuang Gu
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain.
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