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Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J. Structural and mutational characterization of a malate racemase from the LarA superfamily. Biometals 2023; 36:303-313. [PMID: 35182264 PMCID: PMC9388697 DOI: 10.1007/s10534-022-00372-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/07/2022] [Indexed: 01/13/2023]
Abstract
The LarA superfamily consists of nickel-dependent enzymes catalyzing racemization/epimerization reactions using a variety of α-hydroxy acids. The first-characterized LarA, a lactate racemase from Lactobacillus plantarum, led to the discovery of the nickel-pincer nucleotide (NPN) cofactor that is utilized by family members with alternative substrates, including malate racemase from Thermoanaerobacterium thermosaccharolyticum (Mar2). In this work, a higher resolution crystal structure of Mar2 was obtained with better data quality that revealed new structural and dynamic characteristics of the protein. A model of the Mar2 structure with bound cofactor and substrate was generated to uncover the common and the unique features among two distinct subgroups in the LarA superfamily. In addition, structure-guided mutational studies were used to examine the importance of residues that are modeled to interact with NPN and to explore which residues were critical for conferring specificity for malate. In particular, substitution of two residues involved in substrate binding in Mar2 to match the corresponding residues in LarA led to the acquisition of low levels of lactate racemase activity. Of additional interest, the substrate spectrum was expanded to include tartrate, an analog of malate. These new findings will help to better understand structure-function relationships of many other LarA homologs that are broadly distributed in bacterial and archaeal species.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Julian Urdiain-Arraiza
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Benoît Desguin
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
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2
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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3
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Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem J 2021; 478:3265-3279. [PMID: 34409984 PMCID: PMC8454699 DOI: 10.1042/bcj20210565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.
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Nickel as a virulence factor in the Class I bacterial carcinogen, Helicobacter pylori. Semin Cancer Biol 2021; 76:143-155. [PMID: 33865991 DOI: 10.1016/j.semcancer.2021.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 01/16/2023]
Abstract
Helicobacter pylori is a human bacterial pathogen that causes peptic ulcers and has been designated a Class I carcinogen by the International Agency for Research on Cancer (IARC). Its ability to survive in the acid environment of the stomach, to colonize the stomach mucosa, and to cause cancer, are linked to two enzymes that require nickel-urease and hydrogenase. Thus, nickel is an important virulence factor and the proteins involved in nickel trafficking are potential antibiotic targets. This review summarizes the nickel biochemistry of H. pylori with a focus on the roles of nickel in virulence, nickel homeostasis, maturation of urease and hydrogenase, and the unique nickel trafficking that occurs between the hydrogenase maturation pathway and urease nickel incorporation that is mediated by the metallochaperone HypA and its partner, HypB.
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Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P. Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases. Sci Rep 2020; 10:18123. [PMID: 33093595 PMCID: PMC7583248 DOI: 10.1038/s41598-020-74802-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.
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Affiliation(s)
- Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium.
| | - Julian Urdiain-Arraiza
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | | | - Matthias Fellner
- Biochemistry, University of Otago, PO Box 56, Dunedin, Otago, 9054, New Zealand.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Tom Desmet
- Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
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Choi MY, Shin KC, Ho TH, Park H, Nguyen DQ, Park YS, Kim DW, Oh DK, Kang LW. Fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi has a versatile TIM-barrel scaffold suitable for a sugar metabolizing biocatalyst. Int J Biol Macromol 2020; 163:1369-1374. [PMID: 32758598 DOI: 10.1016/j.ijbiomac.2020.07.285] [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: 04/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
Abstract
Xylan and pectin are major structural components of plant cell walls. There are two independent catabolic pathways for xylan and pectin. UxaE bridges these two pathways by reversibly epimerizing D-fructuronate and D-tagaturonate. The crystal structure of UxaE from Cohnella laeviribosi (ClUxaE) shows a core scaffold of TIM-barrel with a position-changing divalent metal cofactor. ClUxaE has the flexible metal-coordination loop to allow the metal shift and the extra domains to bind a phosphate ion in the active site, which are important for catalysis and substrate specificity. Elucidation of the structure and mechanism of ClUxaE will assist in understanding the catalytic mechanism of UxaE family members, which are useful for processing both xylan and pectin-derived carbohydrates for practical and industrial purposes, including the transformation of agricultural wastes into numerous valuable products.
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Affiliation(s)
- Moon Young Choi
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Kyung-Chul Shin
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dae Wook Kim
- Forest Plant Industry Department, Baekdudaegan National Arboretum, Bonghwa 36209, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea.
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7
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Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep 2020; 10:5830. [PMID: 32242052 PMCID: PMC7118094 DOI: 10.1038/s41598-020-62847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/20/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
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Shi R, Wodrich MD, Pan H, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Matthew D. Wodrich
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
- Laboratory for Computational Molecular DesignInstitute of Chemical Science and EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL) Lausanne 1015 Switzerland
| | - Hui‐Jie Pan
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
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9
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Shi R, Wodrich MD, Pan HJ, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019; 58:16869-16872. [PMID: 31535787 DOI: 10.1002/anie.201910490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Indexed: 11/06/2022]
Abstract
A novel nickel pincer cofactor was recently discovered in lactate racemase. Reported here are three synthetic nickel pincer complexes that are both structural and functional models of the pincer cofactor in lactate racemase. DFT computations suggest the ipso-carbon atom of the pyridinium pincer ligands act as a hydride acceptor for lactate isomerization, whereas an organometallic pathway involving nickel-mediated β-hydride elimination is less favored.
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Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Matthew D Wodrich
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland.,Laboratory for Computational Molecular Design, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Hui-Jie Pan
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
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Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum. Biochemistry 2018; 57:5513-5523. [PMID: 30157639 DOI: 10.1021/acs.biochem.8b00601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LarE from Lactobacillus plantarum is an ATP-dependent sulfur transferase that sacrifices its Cys176 sulfur atom to form a dehydroalanine (Dha) side chain during biosynthesis of the covalently linked nickel-pincer nucleotide (NPN) cofactor (pyridinium 3-thioamide-5-thiocarboxylic acid mononucleotide) of lactate racemase. Coenzyme A (CoA) stabilizes LarE and forms a CoA-Cys176 mixed disulfide with the protein. This study presents the crystal structure of the LarE/CoA complex, revealing protein interactions with CoA that mimic those for binding ATP. CoA weakly inhibits LarE activity, and the persulfide of CoA is capable of partially regenerating functional LarE from the Dha176 form of the protein. The physiological relevance of this cycling reaction is unclear. A new form of LarE was discovered, an NPN-LarE covalent adduct, explaining prior results in which activation of the lactate racemase apoprotein required only the isolated LarE. The crystal structure of the inactive C176A variant revealed a fold essentially identical to that of wild-type LarE. Additional active site variants of LarE were created and their activities characterized, with all LarE variants analyzed in terms of the structure. Finally, the L. plantarum LarE structure was compared to a homology model of Thermoanaerobacterium thermosaccharolyticum LarE, predicted to contain three cysteine residues at the active site, and to other proteins with a similar fold and multiple active site cysteine residues. These findings suggest that some LarE orthologs may not be sacrificial but instead may catalyze sulfur transfer by using a persulfide mechanism or from a labile site on a [4Fe-4S] cluster at this position.
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Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Benoît Desguin
- Institute of Life Sciences , Université catholique de Louvain , B-1348 Louvain-La-Neuve , Belgium
| | - Jian Hu
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Microbiology and Molecular Genetics , Michigan State University , East Lansing , Michigan 48824 , United States
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