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Shi J, Guo X, Liu C, Wang Y, Chen X, Wu G, Ding J, Zhang T. Molecular insight into the potential functional role of pseudoenzyme GFOD1 via interaction with NKIRAS2. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38946427 DOI: 10.3724/abbs.2024105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
The glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family includes a variety of oxidoreductases with a wide range of substrates that utilize NAD or NADP as redox cofactor. Human contains two members of this family, namely glucose-fructose oxidoreductase domain-containing protein 1 and 2 (GFOD1 and GFOD2). While GFOD1 exhibits low tissue specificity, it is notably expressed in the brain, potentially linked to psychiatric disorders and severe diseases. Nevertheless, the specific function, cofactor preference, and enzymatic activity of GFOD1 remain largely unknown. In this work, we find that GFOD1 does not bind to either NAD or NADP. Crystal structure analysis unveils that GFOD1 exists as a typical homodimer resembling other family members, but lacks essential residues required for cofactor binding, suggesting that it may function as a pseudoenzyme. Exploration of GFOD1-interacting partners in proteomic database identifies NK-κB inhibitor-interacting Ras-like 2 (NKIRAS2) as one potential candidate. Co-immunoprecipitation (co-IP) analysis indicates that GFOD1 interacts with both GTP- and GDP-bound forms of NKIRAS2. The predicted structural model of the GFOD1-NKIRAS2 complex is validated in cells using point mutants and shows that GFOD1 selectively recognizes the interswitch region of NKIRAS2. These findings reveal the distinct structural properties of GFOD1 and shed light on its potential functional role in cellular processes.
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Affiliation(s)
- Jiawen Shi
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Xinyi Guo
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Chan Liu
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Yilun Wang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Xiaobao Chen
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Guihua Wu
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Tianlong Zhang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
- China-Japan Friendship Medical Research Institute, Shanghai University, Shanghai 200444, China
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de Araújo NC, Bury PDS, Tavares MT, Huang F, Parise-Filho R, Leadlay P, Dias MVB. Crystal Structure of GenD2, an NAD-Dependent Oxidoreductase Involved in the Biosynthesis of Gentamicin. ACS Chem Biol 2019; 14:925-933. [PMID: 30995396 DOI: 10.1021/acschembio.9b00115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Gentamicins are clinically relevant aminoglycoside antibiotics produced by several Micromonospora species. Gentamicins are highly methylated and functionalized molecules, and their biosynthesis include glycosyltransferases, dehydratase/oxidoreductases, aminotransferases, and methyltransferases. The biosynthesis of gentamicin A from gentamicin A2 involves three enzymatic steps that modify the hydroxyl group at position 3″ of the unusual garosamine sugar to provide its substitution for an amino group, followed by an N-methylation. The first of these reactions is catalyzed by GenD2, an oxidoreductase from the Gfo/Idh/MocA protein family, which reduces the hydroxyl at the C3″ of gentamicin A to produce 3''-dehydro-3''-oxo-gentamicin A2 (DOA2). In this work, we solved the structure of GenD2 in complex with NAD+. Although the structure of GenD2 has a similar fold to other members of the Gfo/Idh/MocA family, this enzyme has several new features, including a 3D-domain swapping of two β-strands that are involved in a novel oligomerization interface for this protein family. In addition, the active site of this enzyme also has several specialties which are possibly involved in the substrate specificity, including a number of aromatic residues and a negatively charged region, which is complementary to the polycationic aminoglycoside-substrate. Therefore, docking simulations provided insights into the recognition of gentamicin A2 and into the catalytic mechanism of GenD2. This is the first report describing the structure of an oxidoreductase involved in aminoglycoside biosynthesis and could open perspectives into producing new aminoglycoside derivatives by protein engineering.
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Affiliation(s)
- Natalia Cerrone de Araújo
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil
| | - Priscila Dos Santos Bury
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil
| | - Maurício Temotheo Tavares
- Department of Pharmacy, Faculty of Pharmaceutical Sciences , University of São Paulo , Prof. Lineu Prestes Avenue 580 , 05508-900 São Paulo , Brazil
| | - Fanglu Huang
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , U.K
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences , University of São Paulo , Prof. Lineu Prestes Avenue 580 , 05508-900 São Paulo , Brazil
| | - Peter Leadlay
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , U.K
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science , University of São Paulo , Avenida Prof. Lineu Prestes 1374 , 05508-900 São Paulo , Brazil.,Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
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Taberman H, Parkkinen T, Rouvinen J. Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases. Protein Sci 2016; 25:778-86. [PMID: 26749496 DOI: 10.1002/pro.2877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
The Gfo/Idh/MocA protein family contains a number of different proteins, which almost exclusively consist of NAD(P)-dependent oxidoreductases that have a diverse set of substrates, typically pyranoses. In this study, to clarify common structural features that would contribute to their function, the available crystal structures of the members of this family have been analyzed. Despite a very low sequence identity, the central features of the three-dimensional structures of the proteins are surprisingly similar. The members of the protein family have a two-domain structure consisting of a N-terminal nucleotide-binding domain and a C-terminal α/β-domain. The C-terminal domain contributes to the substrate binding and catalysis, and contains a βα-motif with a central α-helix carrying common essential amino acid residues. The β-sheet of the α/β-domain contributes to the oligomerization in most of the proteins in the family.
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Affiliation(s)
- Helena Taberman
- Department of Chemistry, University of Eastern Finland, PO Box 111, Joensuu, 80101, Finland
| | - Tarja Parkkinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, Joensuu, 80101, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, Joensuu, 80101, Finland
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Structure and function of Caulobacter crescentus aldose–aldose oxidoreductase. Biochem J 2015; 472:297-307. [DOI: 10.1042/bj20150681] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/05/2015] [Indexed: 11/17/2022]
Abstract
We solved the crystal structures of Caulobacter crescentus aldose–aldose oxidoreductase complexed with its NADP(H) cofactor, different saccharides and sugar alcohols. The structures demonstrate the molecular basis for substrate binding and allowed us to present a reaction mechanism for the enzyme.
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Characterization of a unique Caulobacter crescentus aldose-aldose oxidoreductase having dual activities. Appl Microbiol Biotechnol 2015; 100:673-85. [PMID: 26428243 DOI: 10.1007/s00253-015-7011-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/04/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
Abstract
We describe here the characterization of a novel enzyme called aldose-aldose oxidoreductase (Cc AAOR; EC 1.1.99) from Caulobacter crescentus. The Cc AAOR exists in solution as a dimer, belongs to the Gfo/Idh/MocA family and shows homology with the glucose-fructose oxidoreductase from Zymomonas mobilis. However, unlike other known members of this protein family, Cc AAOR is specific for aldose sugars and can be in the same catalytic cycle both oxidise and reduce a panel of monosaccharides at the C1 position, producing in each case the corresponding aldonolactone and alditol, respectively. Cc AAOR contains a tightly-bound nicotinamide cofactor, which is regenerated in this oxidation-reduction cycle. The highest oxidation activity was detected on D-glucose but significant activity was also observed on D-xylose, L-arabinose and D-galactose, revealing that both hexose and pentose sugars are accepted as substrates by Cc AAOR. The configuration at the C2 and C3 positions of the saccharides was shown to be especially important for the substrate binding. Interestingly, besides monosaccharides, Cc AAOR can also oxidise a range of 1,4-linked oligosaccharides having aldose unit at the reducing end, such as lactose, malto- and cello-oligosaccharides as well as xylotetraose. (1)H NMR used to monitor the oxidation and reduction reaction simultaneously, demonstrated that although D-glucose has the highest affinity and is also oxidised most efficiently by Cc AAOR, the reduction of D-glucose is clearly not as efficient. For the overall reaction catalysed by Cc AAOR, the L-arabinose, D-xylose and D-galactose were the most potent substrates.
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Meneely KM, Lamb AL. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry 2012; 51:9002-13. [PMID: 23066849 DOI: 10.1021/bi3011016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The thiazolinyl imine reductase from Yersinia enterocolitica (Irp3) catalyzes the NADPH-dependent reduction of a thiazoline ring in an intermediate for the formation of the siderophore yersiniabactin. Two structures of Irp3 were determined in the apo (1.85 Å) and NADP(+)-bound (2.31 Å) forms. Irp3 is structurally homologous to sugar oxidoreductases such as glucose-fructose oxidoreductase and 1,5-anhydro-d-fructose reductase, as well as to biliverdin reductase. A homology model of the thiazolinyl imine reductase from Pseudomonas aeruginosa (PchG) was generated. Extensive loop insertions are observed in the C-terminal domain that are unique to Irp3 and PchG and not found in the structural homologues that recognize small molecular substrates. These loops are hypothesized to be important for binding of the nonribosomal peptide synthetase modules (found in HMWP1 and PchF, respectively) to which the substrate of the reductase is covalently attached. A catalytic mechanism for the donation of a proton from a general acid (either histidine 101 or tyrosine 128) and the donation of a hydride from C4 of nicotinamide of the NADPH cofactor is proposed for reduction of the carbon-nitrogen double bond of the thiazoline.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
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Pedruzzi I, Borges da Silva EA, Rodrigues AE. Production of lactobionic acid and sorbitol from lactose/fructose substrate using GFOR/GL enzymes from Zymomonas mobilis cells: A kinetic study. Enzyme Microb Technol 2011; 49:183-91. [DOI: 10.1016/j.enzmictec.2011.04.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 11/30/2022]
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Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification. Biochem J 2010; 432:237-47. [PMID: 20809899 DOI: 10.1042/bj20101079] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Inositol dehydrogenase from Bacillus subtilis (BsIDH) is a NAD+-dependent enzyme that catalyses the oxidation of the axial hydroxy group of myo-inositol to form scyllo-inosose. We have determined the crystal structures of wild-type BsIDH and of the inactive K97V mutant in apo-, holo- and ternary complexes with inositol and inosose. BsIDH is a tetramer, with a novel arrangement consisting of two long continuous β-sheets, formed from all four monomers, in which the two central strands are crossed over to form the core of the tetramer. Each subunit in the tetramer consists of two domains: an N-terminal Rossmann fold domain containing the cofactor-binding site, and a C-terminal domain containing the inositol-binding site. Structural analysis allowed us to determine residues important in cofactor and substrate binding. Lys97, Asp172 and His176 are the catalytic triad involved in the catalytic mechanism of BsIDH, similar to what has been proposed for related enzymes and short-chain dehydrogenases. Furthermore, a conformational change in the nicotinamide ring was observed in some ternary complexes, suggesting hydride transfer to the si-face of NAD+. Finally, comparison of the structure and sequence of BsIDH with other putative inositol dehydrogenases allowed us to differentiate these enzymes into four subfamilies based on six consensus sequence motifs defining the cofactor- and substrate-binding sites.
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Hayes JM, Mantle TJ. The effect of pH on the initial rate kinetics of the dimeric biliverdin-IXalpha reductase from the cyanobacterium Synechocystis PCC6803. FEBS J 2009; 276:4414-25. [PMID: 19614741 DOI: 10.1111/j.1742-4658.2009.07149.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biliverdin-IXalpha reductase from Synechocystis PCC6803 (sBVR-A) is a stable dimer and this behaviour is observed under a range of conditions. This is in contrast to all other forms of BVR-A, which have been reported to behave as monomers, and places sBVR-A in the dihydrodiol dehydrogenase/N-terminally truncated glucose-fructose oxidoreductase structural family of dimers. The cyanobacterial enzyme obeys an ordered steady-state kinetic mechanism at pH 5, with NADPH being the first to bind and NADP(+) the last to dissociate. An analysis of the effect of pH on k(cat) with NADPH as cofactor reveals a pK of 5.4 that must be protonated for effective catalysis. Analysis of the effect of pH on k(cat)/K(m)(NADPH) identifies pK values of 5.1 and 6.1 in the free enzyme. Similar pK values are identified for biliverdin binding to the enzyme-NADPH complex. The lower pK values in the free enzyme (pK 5.1) and enzyme-NADPH complex (pK 4.9) are not evident when NADH is the cofactor, suggesting that this ionizable group may interact with the 2'-phosphate of NADPH. His84 is implicated as a crucial residue for sBVR-A activity because the H84A mutant has less than 1% of the activity of the wild-type and exhibits small but significant changes in the protein CD spectrum. Binding of biliverdin to sBVR-A is conveniently monitored by following the induced CD spectrum for biliverdin. Binding of biliverdin to wild-type sBVR-A induces a P-type spectrum. The H84A mutant shows evidence for weak binding of biliverdin and appears to bind a variant of the P-configuration. Intriguingly, the Y102A mutant, which is catalytically active, binds biliverdin in the M-configuration.
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Affiliation(s)
- Jerrard M Hayes
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland.
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Anders A, Lilie H, Franke K, Kapp L, Stelling J, Gilles ED, Breunig KD. The Galactose Switch in Kluyveromyces lactis Depends on Nuclear Competition between Gal4 and Gal1 for Gal80 Binding. J Biol Chem 2006; 281:29337-48. [PMID: 16867978 DOI: 10.1074/jbc.m604271200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Gal4 protein represents a universally functional transcription activator, which in yeast is regulated by protein-protein interaction of its transcription activation domain with the inhibitor Gal80. Gal80 inhibition is relieved via galactose-mediated Gal80-Gal1-Gal3 interaction. The Gal4-Gal80-Gal1/3 regulatory module is conserved between Saccharomyces cerevisiae and Kluyveromyces lactis. Here we demonstrate that K. lactis Gal80 (KlGal80) is a nuclear protein independent of the Gal4 activity status, whereas KlGal1 is detected throughout the entire cell, which implies that KlGal80 and KlGal1 interact in the nucleus. Consistently KlGal1 accumulates in the nucleus upon KlGAL80 overexpression. Furthermore, we show that the KlGal80-KlGal1 interaction blocks the galactokinase activity of KlGal1 and is incompatible with KlGal80-KlGal4-AD interaction. Thus, we propose that dissociation of KlGal80 from the AD forms the basis of KlGal4 activation in K. lactis. Quantitation of the dissociation constants for the KlGal80 complexes gives a much lower affinity for KlGal1 as compared with Gal4. Mathematical modeling shows that with these affinities a switch based on competition between Gal1 and Gal4 for Gal80 binding is nevertheless efficient provided two monomeric Gal1 molecules interact with dimeric Gal80. Consistent with such a mechanism, analysis of the sedimentation behavior by analytical ultracentrifugation demonstrates the formation of a heterotetrameric KlGal80-KlGal1 complex of 2:2 stoichiometry.
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Affiliation(s)
- Alexander Anders
- Institut für Genetik and Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle, Germany
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Watanabe S, Kodaki T, Kodak T, Makino K. Cloning, Expression, and Characterization of Bacterial l-Arabinose 1-Dehydrogenase Involved in an Alternative Pathway of l-Arabinose Metabolism. J Biol Chem 2006; 281:2612-23. [PMID: 16326697 DOI: 10.1074/jbc.m506477200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azospirillum brasiliense converts L-arabinose to alpha-ketoglutarate via five hypothetical enzymatic steps. We purified and characterized L-arabinose 1-dehydrogenase (EC 1.1.1.46), catalyzing the conversion of L-arabinose to L-arabino-gamma-lactone as an enzyme responsible for the first step of this alternative pathway of L-arabinose metabolism. The purified enzyme preferred NADP+ to NAD+ as a coenzyme. Kinetic analysis revealed that the enzyme had high catalytic efficiency for both L-arabinose and D-galactose. The gene encoding L-arabinose 1-dehydrogenase was cloned using a partial peptide sequence of the purified enzyme and was overexpressed in Escherichia coli as a fully active enzyme. The enzyme consists of 308 amino acids and has a calculated molecular mass of 33,663.92 Da. The deduced amino acid sequence had some similarity to glucose-fructose oxidoreductase, D-xylose 1-dehydrogenase, and D-galactose 1-dehydrogenase. Site-directed mutagenesis revealed that the enzyme possesses unique catalytic amino acid residues. Northern blot analysis showed that this gene was induced by L-arabinose but not by D-galactose. Furthermore, a disruptant of the L-arabinose 1-dehydrogenase gene did not grow on L-arabinose but grew on D-galactose at the same growth rate as the wild-type strain. There was a partial gene for L-arabinose transport in the flanking region of the L-arabinose 1-dehydrogenase gene. These results indicated that the enzyme is involved in the metabolism of L-arabinose but not D-galactose. This is the first identification of a gene involved in an alternative pathway of L-arabinose metabolism in bacterium.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Engineering, Kyoto University, Kyotodaigakukatsura, Saikyo-ku, Kyoto 615-8530
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Abstract
The Saccharomyces cerevisiae Gal80 protein has two binding partners: Gal4 and Gal3. In the absence of galactose, Gal80 binds to and inhibits the transcriptional activation domain (AD) of the GAL gene activator, Gal4, preventing GAL gene expression. Galactose triggers an association between Gal3 and Gal80, relieving Gal80 inhibition of Gal4. We selected for GAL80 mutants with impaired capacity of Gal80 to bind to Gal3 or Gal4AD. Most Gal80 variants selected for impaired binding to Gal4AD retained their capacity to bind to Gal3 and to self-associate, whereas most of those selected for impaired binding to Gal3 lost their ability to bind to Gal4AD and self-associate. Thus, some Gal80 amino acids are determinants for both the Gal80-Gal3 association and the Gal80 self-association, and Gal80 self-association may be required for binding to Gal4AD. We propose that the binding of Gal3 to the Gal80 monomer competes with Gal80 self-association, reducing the amount of the Gal80 dimer available for inhibition of Gal4.
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Affiliation(s)
- Vepkhia Pilauri
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, 17033, USA
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