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Seo D. The Role of the si-Face Tyrosine of a Homodimeric Ferredoxin-NADP + Oxidoreductase from Bacillus subtilis during Complex Formation and Redox Equivalent Transfer with NADP +/H and Ferredoxin. Antioxidants (Basel) 2023; 12:1741. [PMID: 37760044 PMCID: PMC10526003 DOI: 10.3390/antiox12091741] [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: 07/18/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
In the crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (BsFNR), Tyr50 stacks on the si-face of the isoalloxazine ring portion of the FAD prosthetic group. This configuration is highly conserved among the homodimeric ferredoxin-NAD(P)+ oxidoreductases (FNR) from Gram-positive bacteria and photosynthetic bacteria. In this report, pre-steady state reactions of Tyr50 variants with NADP+/NADPH and ferredoxin from B. subtilis (BsFd) were examined with stopped-flow spectrophotometry to assess the effects of the mutation on the formation of FNR-substrate complexes and following redox equivalent transfer. Mixing oxidized BsFNRs with NADPH resulted in a rapid complex formation followed by a rate-limiting hydride transfer. The substitution substantially modulated the intensity of the charge transfer absorption band and decreased the observed hydride transfer rates compared to the wild type. Reduction of the Y50W mutant by NADPH proceeded in a monophasic manner, while the Y50G and Y50S mutants did in biphasic phases. The reduced Tyr50 mutants hardly promoted the reduction of NADP+. Mixing oxidized BsFNRs with reduced BsFd resulted in the reduction of the FNRs. The observed FNR reduction rates of the three variants were comparable, but in the Y50G and Y50S mutants, the amount of the reduced FNR at the rapid phase was decreased, and a slow FNR reduction phase was observed. The obtained results suggest that the replacements of Tyr50 with Gly and Ser permitted the conformational change in the reduced form, which induced an asymmetric kinetic behavior between the protomers of the homodimeric BsFNR.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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Hammerstad M, Rugtveit AK, Dahlen S, Andersen HK, Hersleth HP. Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Antioxidants (Basel) 2023; 12:1224. [PMID: 37371954 DOI: 10.3390/antiox12061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. Bacillus cereus (Bc) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. Bc FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The Bc IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Anne Kristine Rugtveit
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Sondov Dahlen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hilde Kristin Andersen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
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Shoor M, Gudim I, Hersleth HP, Hammerstad M. Thioredoxin reductase from Bacillus cereus exhibits distinct reduction and NADPH-binding properties. FEBS Open Bio 2021; 11:3019-3031. [PMID: 34492167 PMCID: PMC8564101 DOI: 10.1002/2211-5463.13289] [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: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/23/2022] Open
Abstract
Low‐molecular‐weight (low Mr) thioredoxin reductases (TrxRs) are homodimeric NADPH‐dependent dithiol flavoenzymes that reduce thioredoxins (Trxs) or Trx‐like proteins involved in the activation networks of enzymes, such as the bacterial class Ib ribonucleotide reductase (RNR). During the last few decades, TrxR‐like ferredoxin/flavodoxin NADP+ oxidoreductases (FNRs) have been discovered and characterized in several types of bacteria, including those not encoding the canonical plant‐type FNR. In Bacillus cereus, a TrxR‐like FNR has been shown to reduce the flavodoxin‐like protein NrdI in the activation of class Ib RNR. However, some species only encode TrxR and lack the homologous TrxR‐like FNR. Due to the structural similarity between TrxRs and TrxR‐like FNRs, as well as variations in their occurrence in different microorganisms, we hypothesized that low Mr TrxR may be able to replace TrxR‐like FNR in, for example, the reduction of NrdI. In this study, characterization of TrxR from B. cereus has revealed a weak FNR activity toward NrdI reduction. Additionally, the crystal structure shows that only one out of two binding sites of the B. cereus TrxR homodimer is occupied with NADPH, indicating a possible asymmetric co‐substrate binding in TrxR.
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Affiliation(s)
- Marita Shoor
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
| | - Ingvild Gudim
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway.,Department of Chemistry, Section for Chemical Life Sciences, University of Oslo, Norway
| | - Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
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Alqurashi A, Alfs L, Swann J, Butt JN, Kelly DJ. The flavodoxin FldA activates the class Ia ribonucleotide reductase of Campylobacter jejuni. Mol Microbiol 2021; 116:343-358. [PMID: 33721378 DOI: 10.1111/mmi.14715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/11/2021] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a microaerophilic zoonotic pathogen with an atypical respiratory Complex I that oxidizes a flavodoxin (FldA) instead of NADH. FldA is essential for viability and is reduced via pyruvate and 2-oxoglutarate oxidoreductases (POR/OOR). Here, we show that FldA can also be reduced by FqrB (Cj0559), an NADPH:FldA reductase. An fqrB deletion mutant was viable but displayed a significant growth defect. FqrB is related to flavoprotein reductases from Gram-positive bacteria that can reduce NrdI, a specialized flavodoxin that is needed for tyrosyl radical formation in NrdF, the beta subunit of class 1b-type (Mn) ribonucleotide reductase (RNR). However, C. jejuni possesses a single class Ia-type (Fe) RNR (NrdAB) that would be expected to be ferredoxin dependent. We show that CjFldA is an unusually high potential flavodoxin unrelated to NrdI, yet growth of the fqrB mutant, but not the wild-type or a complemented strain, was stimulated by low deoxyribonucleoside (dRNS) concentrations, suggesting FldA links FqrB and RNR activity. Using purified proteins, we confirmed the NrdB tyrosyl radical could be regenerated in an NADPH, FqrB, and FldA dependent manner, as evidenced by both optical and electron paramagnetic resonance (EPR) spectroscopy. Thus, FldA activates RNR in C. jejuni, partly explaining its essentiality.
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Affiliation(s)
- Abdulmajeed Alqurashi
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Laura Alfs
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Jordan Swann
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Julea N Butt
- School of Chemistry, University of East Anglia, Norwich, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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Overview of structurally homologous flavoprotein oxidoreductases containing the low M r thioredoxin reductase-like fold - A functionally diverse group. Arch Biochem Biophys 2021; 702:108826. [PMID: 33684359 DOI: 10.1016/j.abb.2021.108826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023]
Abstract
Structural studies show that enzymes have a limited number of unique folds, although structurally related enzymes have evolved to perform a large variety of functions. In this review, we have focused on enzymes containing the low molecular weight thioredoxin reductase (low Mr TrxR) fold. This fold consists of two domains, both containing a three-layer ββα sandwich Rossmann-like fold, serving as flavin adenine dinucleotide (FAD) and, in most cases, pyridine nucleotide (NAD(P)H) binding-domains. Based on a search of the Protein Data Bank for all published structures containing the low Mr TrxR-like fold, we here present a comprehensive overview of enzymes with this structural architecture. These range from TrxR-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases, through glutathione reductase, to NADH peroxidase. Some enzymes are solely composed of the low Mr TrxR-like fold, while others contain one or two additional domains. In this review, we give a detailed description of selected enzymes containing only the low Mr TrxR-like fold, however, catalyzing a diversity of chemical reactions. Our overview of this structurally similar, yet functionally distinct group of flavoprotein oxidoreductases highlights the fascinating and increasing number of studies describing the diversity among these enzymes, especially during the last decade(s).
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Hammerstad M, Gudim I, Hersleth HP. The Crystal Structures of Bacillithiol Disulfide Reductase Bdr (YpdA) Provide Structural and Functional Insight into a New Type of FAD-Containing NADPH-Dependent Oxidoreductase. Biochemistry 2020; 59:4793-4798. [PMID: 33326741 PMCID: PMC7774306 DOI: 10.1021/acs.biochem.0c00745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Low
G+C Gram-positive Firmicutes, such as the clinically important
pathogens Staphylococcus aureus and Bacillus
cereus, use the low-molecular weight thiol bacillithiol (BSH)
as a defense mechanism to buffer the intracellular redox environment
and counteract oxidative stress encountered by human neutrophils during
infections. The protein YpdA has recently been shown to function as
an essential NADPH-dependent reductase of oxidized bacillithiol disulfide
(BSSB) resulting from stress responses and is crucial for maintaining
the reduced pool of BSH and cellular redox balance. In this work,
we present the first crystallographic structures of YpdAs, namely,
those from S. aureus and B. cereus. Our analyses reveal a uniquely organized biological tetramer; however,
the structure of the monomeric subunit is highly similar to those
of other flavoprotein disulfide reductases. The absence of a redox
active cysteine in the vicinity of the FAD isoalloxazine ring implies
a new direct disulfide reduction mechanism, which is backed by the
presence of a potentially gated channel, serving as a putative binding
site for BSSB in the proximity of the FAD cofactor. We also report
enzymatic activities for both YpdAs, which along with the structures
presented in this work provide important structural and functional
insight into a new class of FAD-containing NADPH-dependent oxidoreductases,
related to the emerging fight against pathogenic bacteria.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, University of Oslo, Section for Biochemistry and Molecular Biology, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Ingvild Gudim
- Department of Biosciences, University of Oslo, Section for Biochemistry and Molecular Biology, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, University of Oslo, Section for Biochemistry and Molecular Biology, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway.,Department of Chemistry, University of Oslo, Section for Chemical Life Sciences, P.O. Box 1033, Blindern, NO-0315 Oslo, Norway
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Seo D, Muraki N, Kurisu G. Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP + oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP +/NADPH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148140. [PMID: 31838096 DOI: 10.1016/j.bbabio.2019.148140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/08/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]
Abstract
Among the thioredoxin reductase-type ferredoxin-NAD(P)+ oxidoreductase (FNR) family, FNR from photosynthetic purple non‑sulfur bacterium Rhodopseudomonas palustris (RpFNR) is distinctive because the predicted residue on the re-face of the isoalloxazine ring portion of the FAD prosthetic group is a tyrosine. Here, we report the crystal structure of wild type RpFNR and kinetic analyses of the reaction of wild type, and Y328F, Y328H and Y328S mutants with NADP+/NADPH using steady state and pre-steady state kinetic approaches. The obtained crystal structure of wild type RpFNR confirmed the presence of Tyr328 on the re-face of the isoalloxazine ring of the FAD prosthetic group through the unique hydrogen bonding of its hydroxyl group. In the steady state assays, the substitution results in the decrease of Kd for NADP+ and KM for NADPH in the diaphorase assay; however, the kcat values also decreased significantly. In the stopped-flow spectrophotometry, mixing oxidized RpFNRs with NADPH and reduced RpFNRs with NADP+ resulted in rapid charge transfer complex formation followed by hydride transfer. The observed rate constants for the hydride transfer in both directions were comparable (>400 s-1). The substitution did not drastically affect the rate of hydride transfer, but substantially slowed down the subsequent release and re-association of NADP+/NADPH in both directions. The obtained results suggest that Tyr328 stabilizes the stacking of C-terminal residues on the isoalloxazine ring portion of the FAD prosthetic group, which impedes the access of NADP+/NADPH on the isoalloxazine ring portions, in turn, enhancing the release of the NADP+/NADPH and/or reaction with electron transfer proteins.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
| | - Norifumi Muraki
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan; Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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