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Diamanti R, Srinivas V, Johansson A, Nordström A, Griese JJ, Lebrette H, Högbom M. Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase. FEBS Lett 2022; 596:1600-1610. [PMID: 35175627 PMCID: PMC9314684 DOI: 10.1002/1873-3468.14319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/11/2022]
Abstract
R2‐like ligand‐binding oxidase (R2lox) is a ferritin‐like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross‐link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry‐based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.
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Affiliation(s)
- Riccardo Diamanti
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | | | | | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.,Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
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Aerobic oxidation of alcohol by model complexes relevant to metal site galactose oxidase: role of copper(I) intermediate, evidence for the generation of end-on copper(II)–OOH species and catalytic promiscuity for oxidation of benzyl alcohol, catechol and o-aminophenol. TRANSIT METAL CHEM 2020. [DOI: 10.1007/s11243-019-00367-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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New mixed-ligand 8-hydroxyquinolinato iron(III) complexes of dimethylethylenediamine-based aminophenol ligands. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.01.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Safaei E, Hajikhanmirzaei L, Karimi B, Wojtczak A, Cotič P, Lee YI. TEMPO-mediated aerobic oxidation of alcohols using copper(II) complex of bis(phenol) di-amine ligand as biomimetic model for Galactose oxidase enzyme. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ravikiran B, Mahalakshmi R. Unusual post-translational protein modifications: the benefits of sophistication. RSC Adv 2014. [DOI: 10.1039/c4ra04694c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.
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Affiliation(s)
- Boddepalli Ravikiran
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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Zhou Q, Hu M, Zhang W, Jiang L, Perrett S, Zhou J, Wang J. Probing the function of the Tyr-Cys cross-link in metalloenzymes by the genetic incorporation of 3-methylthiotyrosine. Angew Chem Int Ed Engl 2012. [PMID: 23197358 DOI: 10.1002/anie.201207229] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qing Zhou
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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Zhou Q, Hu M, Zhang W, Jiang L, Perrett S, Zhou J, Wang J. Probing the Function of the Tyr-Cys Cross-Link in Metalloenzymes by the Genetic Incorporation of 3-Methylthiotyrosine. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Cooley RB, Rhoads TW, Arp DJ, Karplus PA. A diiron protein autogenerates a valine-phenylalanine cross-link. Science 2011; 332:929. [PMID: 21596985 DOI: 10.1126/science.1205687] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
All known internal covalent cross-links in proteins involve functionalized groups having oxygen, nitrogen, or sulfur atoms present to facilitate their formation. Here, we report a carbon-carbon cross-link between two unfunctionalized side chains. This valine-phenyalanine cross-link, produced in an oxygen-dependent reaction, is generated by its own carboxylate-bridged diiron center and serves to stabilize the metallocenter. This finding opens the door to new types of posttranslational modifications, and it demonstrates new catalytic potential of diiron centers.
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Affiliation(s)
- Richard B Cooley
- Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
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10
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Tabuchi K, Ertem MZ, Sugimoto H, Kunishita A, Tano T, Fujieda N, Cramer CJ, Itoh S. Reactions of Copper(II)-Phenol Systems with O2: Models for TPQ Biosynthesis in Copper Amine Oxidases. Inorg Chem 2011; 50:1633-47. [DOI: 10.1021/ic101832c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kae Tabuchi
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Mehmed Z. Ertem
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Sugimoto
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Atsushi Kunishita
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tetsuro Tano
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Nobutaka Fujieda
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Shinobu Itoh
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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Affiliation(s)
- J Martin Bollinger
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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Heuts DPHM, Scrutton NS, McIntire WS, Fraaije MW. What's in a covalent bond? On the role and formation of covalently bound flavin cofactors. FEBS J 2009; 276:3405-27. [PMID: 19438712 DOI: 10.1111/j.1742-4658.2009.07053.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many enzymes use one or more cofactors, such as biotin, heme, or flavin. These cofactors may be bound to the enzyme in a noncovalent or covalent manner. Although most flavoproteins contain a noncovalently bound flavin cofactor (FMN or FAD), a large number have these cofactors covalently linked to the polypeptide chain. Most covalent flavin-protein linkages involve a single cofactor attachment via a histidyl, tyrosyl, cysteinyl or threonyl linkage. However, some flavoproteins contain a flavin that is tethered to two amino acids. In the last decade, many studies have focused on elucidating the mechanism(s) of covalent flavin incorporation (flavinylation) and the possible role(s) of covalent protein-flavin bonds. These endeavors have revealed that covalent flavinylation is a post-translational and self-catalytic process. This review presents an overview of the known types of covalent flavin bonds and the proposed mechanisms and roles of covalent flavinylation.
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Affiliation(s)
- Dominic P H M Heuts
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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Phanerochaete chrysosporium Genomics. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1874-5334(05)80016-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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