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Pederick JL, Thompson AP, Bell SG, Bruning JB. d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J Biol Chem 2020; 295:7894-7904. [PMID: 32335509 DOI: 10.1074/jbc.ra120.012936] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, d-alanine-d-alanine ligase (Ddl), catalyzes ATP-dependent formation of the d-alanyl-d-alanine dipeptide essential for bacterial cell wall biosynthesis and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K+, but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize MVC activation. We found that TtDdl is a type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ∼20-fold in the presence of activating MVCs, and it was maximally activated by K+ and Rb+ ions. A strict dependence on ionic radius of the MVC was observed, with Li+ and Na+ providing little to no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K+, Rb+, or Cs+ Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew P Thompson
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen G Bell
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia .,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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Sethna SS, Gander JE, Rathbun WB. Glutathione synthetase of bovine lens: Anomalies of the enzyme-catalyzed formation of ophthalmic acid. Curr Eye Res 2009; 3:923-8. [PMID: 6547896 DOI: 10.3109/02713688409167209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The activity of glutathione synthetase from bovine lens was examined as a functions of the concentration of L-gamma-glutamyl-L-alpha-aminobutyrate, the dipeptide substrate required in the formation of ophthalmic acid. Several significant anomalies of the glutathione synthetase-catalyzed formation of ophthalmic acid were found. Curvilinearity of double reciprocal plots occurred with this substrate; this curvilinearity shows substrate activation of the reaction which is likely a result of negative cooperativity. Both ATP4- and, to a lesser extent Mg2+ inhibited the reaction, whereas MgATP2- is the substrate; maximum activity occurred with 2 mM Mg2+ in excess of the concentration of added ATP. This investigation shows that it is necessary to establish a defined set of conditions for reporting enzyme activity and that the usual practice of using very large concentrations of Mg2+ relative to ATP, and 5- to 20-fold excess of the dipeptide will give less than optimum activity. The unit of enzyme activity is suggested to be that activity in ml using 2 mM ATP, 4 mM Mg2+, 30 mM glycine and 15 mM L-gamma-glutamyl-alpha-aminobutyrate, which results in the formation of 1 nmole/minute of ADP or P(i). In this study, 5'-AMP was for the first time, shown to be an inhibitor of the reaction with a K(i) of 0.9 mM.
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Frendo P, Jiménez MJ, Mathieu C, Duret L, Gallesi D, Van de Sype G, Hérouart D, Puppo A. A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication. PLANT PHYSIOLOGY 2001; 126:1706-15. [PMID: 11500568 PMCID: PMC117169 DOI: 10.1104/pp.126.4.1706] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2001] [Revised: 04/03/2001] [Accepted: 05/04/2001] [Indexed: 05/19/2023]
Abstract
Glutathione (GSH) and homo-GSH (hGSH) are the major low-molecular weight thiols synthesized in Medicago truncatula. Two M. truncatula cDNAs (gshs1 and gshs2) corresponding to a putative GSH synthetase (GSHS) and a putative hGSH synthetase (hGSHS) were characterized. Heterologous expression of gshs1 and gshs2 cDNAs in an Escherichia coli strain deficient in GSHS activity showed that GSHS1 and GSHS2 are a GSHS and an hGSHS, respectively. Leucine-534 and proline-535 present in hGSHS were substituted by alanines that are conserved in plant GSHS. These substitutions resulted in a strongly stimulated GSH accumulation in the transformed E. coli strain showing that these residues play a crucial role in the differential recognition of beta-alanine and glycine by hGSHS. Phylogenetic analysis of GSHS2 and GSHS1 with other eukaryotic GSHS sequences indicated that gshs2 and gshs1 are the result of a gene duplication that occurred after the divergence between Fabales, Solanales, and Brassicales. Analysis of the structure of gshs1 and gshs2 genes shows they are both present in a cluster and in the same orientation in the M. truncatula genome, suggesting that the duplication of gshs1 and gshs2 occurred via a tandem duplication.
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Affiliation(s)
- P Frendo
- Laboratoire de Biologie Végétale et Microbiologie, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 2294, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Nice cedex 2, France.
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Gali RR, Board PG. Identification of an essential cysteine residue in human glutathione synthase. Biochem J 1997; 321 ( Pt 1):207-10. [PMID: 9003420 PMCID: PMC1218055 DOI: 10.1042/bj3210207] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glutathione is essential for a variety of cellular functions, and is synthesized from gamma-glutamylcysteine and glycine by the action of glutathione synthase (EC 6.3.2.3). Human glutathione synthase is a dimer of two identical subunits, each composed of 474 amino acids. Little is known about the structure-function relationships of mammalian glutathione synthases and, in order to gain a greater understanding of this critical enzyme, we have probed the role of cysteine residues by chemical modification and site-directed mutagenesis. Preincubation with thiol reagents such as p-chloromercuribenzoate, N-ethylmaleimide, iodoacetate and 5,5'-dithiobis-(2-nitrobenzoate) resulted in significant inhibition of recombinant human glutathione synthase. Each subunit contains cysteine residues at positions 294, 409 and 422, and we have prepared four different mutants by replacing individual cysteine residues, or all of the cysteine residues, with alanine. The C294A and C409A cysteine mutants retained significant residual activity, indicating that these two cysteine residues are not essential for activity. In contrast, substantial decreases in enzymic activity were detected with the C422A and cysteine-free mutants. This suggests that Cys-422 may play a significant structural or functional role in human glutathione synthase.
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Affiliation(s)
- R R Gali
- Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Gali RR, Board PG. Sequencing and expression of a cDNA for human glutathione synthetase. Biochem J 1995; 310 ( Pt 1):353-8. [PMID: 7646467 PMCID: PMC1135895 DOI: 10.1042/bj3100353] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A human brain cDNA clone encoding glutathione synthetase (EC 6.3.2.3) has been sequenced and expressed in Escherichia coli. The protein is 474 amino acids in length with a subunit molecular mass of 52,352 Da. The recombinant protein exhibits glutathione synthetase activity and occurs as a homodimer. The recombinant glutathione synthetase was purified to homogeneity and had a specific activity of 1.73 mumol/min per mg of protein, an isoelectric point of 5.35 and a pH optimum between 7.0 and 7.5. Southern blots of human genomic DNA hybridized with the glutathione synthetase cDNA revealed a relatively simple pattern of strongly hybridizing fragments, indicating the absence of a large gene family and suggesting that there may be only one glutathione synthetase gene in the human genome.
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Affiliation(s)
- R R Gali
- Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra ACT
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Rathbun WB, Holleschau AM, Alterman L. Glutathione metabolism in primate lenses: A phylogenetic study of glutathione synthesis and glutathione redox cycle enzyme activities. Am J Primatol 1994; 33:101-120. [DOI: 10.1002/ajp.1350330205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/1993] [Revised: 01/12/1994] [Indexed: 11/07/2022]
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Dickerson JE, Lou MF. A new mixed disulfide species in human cataractous and aged lenses. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1157:141-6. [PMID: 8507650 DOI: 10.1016/0304-4165(93)90057-f] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The process of ageing in the normal human eye lens is unique among tissues due to the absence of turnover in the structural proteins. These proteins accumulate a variety of modifications throughout their lifetime. Significantly, the cysteine residues are subject to disulfide formation with the low molecular weight thiol compounds present in the lens. It has been shown that accumulation of glutathione and cysteine mixed disulfides in the proteins of normal human lens is a function of age. In this report a third mixed disulfide species gamma-glutamylcysteine (gamma-Glu-Cys), has been identified by comparison with standards which were produced through two distinct methods. This new mixed disulfide is only prominent in old lenses (> 60 years) and cataractous lenses. In these situations its level may approach those of cysteine mixed disulfide. The appearance of gamma-Glu-Cys may be coincident with biochemical abnormalities preceding cataract formation. This protein modification may be a result of changes in the GSH biosynthetic pathway within the lens.
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Affiliation(s)
- J E Dickerson
- Cataract Research Group, Alcon Laboratories, Inc., Fort Worth, TX 76134
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Rathbun WB, Murray DL. Age-related cysteine uptake as rate-limiting in glutathione synthesis and glutathione half-life in the cultured human lens. Exp Eye Res 1991; 53:205-12. [PMID: 1915676 DOI: 10.1016/0014-4835(91)90075-p] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study included human lenses of ages ranging from newborn to 92 years. Protein-free reduced glutathione decreased 14-fold, whereas protein-free oxidized glutathione increased 2.6-fold with increasing age. L-Cyst(e)ine uptake g-1 lens of very old cultured lenses decreased 70% from that exhibited in newborn lenses, demonstrating a marked decline of L-cyst(e)ine uptake as a function of age. In these same lenses the synthesis of reduced glutathione (mumol g-1 lens) decreased 73% with age. It was concluded that the glutathione decrease observed in the aging human lens was associated with decreased uptake of L-cyst(e)ine, decreased glutathione synthesis and possibly an increase in protein-free oxidized glutathione. The high correlation of L-cyst(e)ine uptake and glutathione synthesis supports the hypothesis that L-cyst(e)ine uptake is a rate-limiting factor of glutathione synthesis in the intact human lens. By the use of buthionine sulfoximine, the half-life of glutathione was estimated to be 90 hr in the cultured human lens.
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Affiliation(s)
- W B Rathbun
- Ophthalmology Department, University of Minnesota, Minneapolis 55455
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Pau H, Graf P, Sies H. Glutathione levels in human lens: regional distribution in different forms of cataract. Exp Eye Res 1990; 50:17-20. [PMID: 2307192 DOI: 10.1016/0014-4835(90)90005-f] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The content of glutathione is high in the anterior lens cortex (plus epithelium) and the posterior lens cortex, whereas it is substantially lower in the lens nucleus. A decrease of glutathione in the lens cortex does not occur with lenses from adults up to the highest age. The glutathione content is highest in the cortex of clear fresh lenses and shows a decrease with deep supranuclear cataract, primary nuclear cataract (cataracta brunescens nigra) and clear lenses post-mortem (approximately 20 hr). The subcapsular cataract, especially with additional secondary nuclear cataract, with cataracta matura or intumescens, shows a rapid and pronounced progressive decrease in the glutathione content.
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Affiliation(s)
- H Pau
- Department of Ophthalmology, University of Düsseldorf, F.R.G
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Abstract
Six factors were analyzed which may be involved in the decline of glutathione synthesis in the aging lens and cataract, with special emphasis placed upon the human lens. The factors included: 1) lability of gamma-glutamylcysteine synthetase, 2) paucity of gamma-glutamylcysteine synthetase in primate lenses as compared to other mammalian lenses, 3) enzyme activity reduction with age in the human lens, 4) rate control by reactant scarcity, especially of cysteine and magnesium ion, 5) rate control by inhibition using 5'-AMP, 5'-ADP and glutathione, and 6) possible dissociation of the multi-enzyme complex. It was concluded that decline of the glutathione synthetic capacity in vivo would be most likely caused by reduction of gamma-glutamylcysteine synthetase activity rather than of glutathione synthetase activity.
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Rathbun WB, Sethna SS, Skelnik DL, Bistner SI. Glutathione metabolism in lenses of dogs and rabbits: activities of five enzymes. Exp Eye Res 1983; 36:845-58. [PMID: 6134632 DOI: 10.1016/0014-4835(83)90038-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Several biochemical parameters were examined in clear dog and rabbit lenses as functions of age, and in posterior subcapsular cataracts in the Alaskan malamute. Tabulated data include soluble protein, reduced sulfhydryl content of soluble protein, reduced glutathione, water, and activity of five enzymes of glutathione metabolism. The enzymes include the glutathione biosynthesis system consisting of gamma-glutamylcysteine synthetase and glutathione synthetase, as well as glutathione peroxidase, glutathione reductase and glutathione-S-transferase. Each enzyme, acting last in a sequential reaction of either two or three reactions, was in excess activity over the preceding enzyme(s) in every case but one. In the exception, the ratio of glutathione reductase to glutathione peroxidase activity was about 1:600 and 1:155 in the dog and rabbit lens, respectively.
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Sethna SS, Holleschau AM, Rathbun WB. Activity of glutathione synthesis enzymes in human lens related to age. Curr Eye Res 1982; 2:735-42. [PMID: 6138216 DOI: 10.3109/02713688209020005] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The high levels of both enzymes of glutathione synthesis found in the infant human lens rapidly reached lower levels by age 10, and thereafter the rate of decrease diminished. Glutathione synthetase activity in the 6 month old lens was six-fold (units/g lens), four-fold (units/mg soluble protein) and two-fold (units/lens) higher than that in the 83 year old, clear human lens. gamma-Glutamylcysteine synthetase activity in the 6 month old lens was sixteen-fold (units/g lens), ten-fold (units/mg soluble protein) and six-fold (units/lens) higher than that in the 83 year old, clear human lens. When lenses from the young adult beagle, rabbit, bovine, and humans are compared, glutathione synthetase activity (units/g lens) varies by about two-fold. gamma-Glutamylcysteine synthetase activity (units/g lens) is quite similar in the first three species, whereas the enzyme activity is more than a magnitude less in young adult human lenses, and becomes much less with increasing age and in a high proportion of life-support system organ donors. The enzyme activity was undetectable in a few of the latter lenses. Loss of activity was not due to increased susceptibility to heat denaturation. The low levels of the enzyme, and total loss in some situations, suggest that gamma-glutamylcysteine synthetase may be an Achilles' Heel of human lens metabolism.
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van Buskirk GE, Gander JE, Rathbun WB. Bovine lenticular gamma-glutamylcysteine synthetase: reaction sequence. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 85:589-97. [PMID: 25775 DOI: 10.1111/j.1432-1033.1978.tb12274.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The sequence of substrate addition and product release during the reaction catalyzed by gamma-glutamylcysteine synthetase was investigated with purified enzyme from bovine lens. Thermal inactivation and kinetic studies suggest that L-glutamate is the first substrate to bind to the enzyme. L-beta-Chloroalanine was used as the L-cysteine analogue. Utilizing substrate activation and product inhibition studies, the following reaction sequence was determined: L-glutamate binding. ATP binding, ADP release, L-beta-chloroalanine binding, followed by inorganic phosphate and then dipeptide release. The implications of this mechanism with regard to control of the enzyme in situ and its importance in glutathione synthesis are discussed.
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