1
|
Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
Collapse
Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
2
|
Michino M, Beautrait A, Boyles NA, Nadupalli A, Dementiev A, Sun S, Ginn J, Baxt L, Suto R, Bryk R, Jerome SV, Huggins DJ, Vendome J. Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors. ACS BIO & MED CHEM AU 2023; 3:507-515. [PMID: 38144256 PMCID: PMC10739260 DOI: 10.1021/acsbiomedchemau.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 12/26/2023]
Abstract
Lpd (lipoamide dehydrogenase) in Mycobacterium tuberculosis (Mtb) is required for virulence and is a genetically validated tuberculosis (TB) target. Numerous screens have been performed over the last decade, yet only two inhibitor series have been identified. Recent advances in large-scale virtual screening methods combined with make-on-demand compound libraries have shown the potential for finding novel hits. In this study, the Enamine REAL library consisting of ∼1.12 billion compounds was efficiently screened using the GPU Shape screen method against Mtb Lpd to find additional chemical matter that would expand on the known sulfonamide inhibitor series. We identified six new inhibitors with IC50 in the range of 5-100 μM. While these compounds remained chemically close to the already known sulfonamide series inhibitors, some diversity was found in the cores of the hits. The two most potent hits were further validated by one-step potency optimization to submicromolar levels. The co-crystal structure of optimized analogue TDI-13537 provided new insights into the potency determinants of the series.
Collapse
Affiliation(s)
- Mayako Michino
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States
| | - Alexandre Beautrait
- Schrödinger,
Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Nicholas A. Boyles
- Schrödinger,
Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Aparna Nadupalli
- Schrödinger,
Inc., 12 Michigan Dr., Natick, Massachusetts 01760, United States
| | - Alexey Dementiev
- Schrödinger,
Inc., 12 Michigan Dr., Natick, Massachusetts 01760, United States
| | - Shan Sun
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States
| | - John Ginn
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States
| | - Leigh Baxt
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States
| | - Robert Suto
- Schrödinger,
Inc., 12 Michigan Dr., Natick, Massachusetts 01760, United States
| | - Ruslana Bryk
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10065, United States
| | - Steven V. Jerome
- Schrödinger,
Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - David J. Huggins
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Jeremie Vendome
- Schrödinger,
Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| |
Collapse
|
3
|
Prussia GA, Gauss GH, Mus F, Conner L, DuBois JL, Peters JW. Substitution of a conserved catalytic dyad into 2‐
KPCC
causes loss of carboxylation activity. FEBS Lett 2016; 590:2991-6. [DOI: 10.1002/1873-3468.12325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Gregory A. Prussia
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| | - George H. Gauss
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| | - Florence Mus
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| | - Leah Conner
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| | - John W. Peters
- Department of Chemistry and Biochemistry Montana State University Bozeman MT USA
| |
Collapse
|
4
|
Arenas FA, Leal CA, Pinto CA, Arenas-Salinas MA, Morales WA, Cornejo FA, Díaz-Vásquez WA, Vásquez CC. On the mechanism underlying tellurite reduction by Aeromonas caviae ST dihydrolipoamide dehydrogenase. Biochimie 2014; 102:174-82. [PMID: 24680738 DOI: 10.1016/j.biochi.2014.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
The dihydrolipoamide dehydrogenase (LpdA) from the tellurite-resistant bacterium Aeromonas caviae ST reduces tellurite to elemental tellurium. To characterize this NADH-dependent activity, the A. caviae lpdA gene was subjected to site-directed mutagenesis and genes containing C45A, H322Y and E354K substitutions were individually transformed into Escherichia coli Δlpd. Cells expressing the modified genes exhibited decreased pyruvate dehydrogenase, dihydrolipoamide dehydrogenase and TR activity regarding that observed with the wild type A. caviae lpdA gene. In addition, cells expressing the altered lpdA genes showed increased oxidative stress levels and tellurite sensitivity than those carrying the wild type counterpart. The involvement of Cys residues in LpdA's TR activity was analyzed using specific inhibitors that interact with catalytic cysteines and/or disulfide bridges such as aurothiomalate, zinc or nickel. TR activity of purified LpdA was drastically affected by these compounds. Since LpdA belongs to the flavoprotein family, the involvement of the FAD/NAD(P)(+)-binding domain in TR activity was determined. FAD removal from purified LpdA results in loss of TR activity, which was restored with exogenously added FAD. Substitutions in E354, involved in FAD/NADH binding, resulted in low TR activity because of flavin loss. Finally, changing H322 (involved in NAD(+)/NADH binding) by tyrosine also resulted in altered TR activity.
Collapse
Affiliation(s)
- F A Arenas
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C A Leal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C A Pinto
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - M A Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - W A Morales
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - F A Cornejo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - W A Díaz-Vásquez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile; Facultad de Ciencia, Universidad San Sebastián, Santiago, Chile
| | - C C Vásquez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
| |
Collapse
|
5
|
Kollman PA, Daggett V, Dang LX. The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme. CIBA FOUNDATION SYMPOSIUM 2007; 161:91-103; discussion 103-7. [PMID: 1814699 DOI: 10.1002/9780470514146.ch7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.
Collapse
Affiliation(s)
- P A Kollman
- Department of Pharmaceutical Chemistry, UCSF 94143
| | | | | |
Collapse
|
6
|
Håkansson AP, Smith AW. Enzymatic characterization of dihydrolipoamide dehydrogenase from Streptococcus pneumoniae harboring its own substrate. J Biol Chem 2007; 282:29521-30. [PMID: 17690105 DOI: 10.1074/jbc.m703144200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study describes the enzymatic characterization of dihydrolipoamide dehydrogenase (DLDH) from Streptococcus pneumoniae and is the first characterization of a DLDH that carries its own substrate (a lipoic acid covalently attached to a lipoyl protein domain) within its own sequence. Full-length recombinant DLDH (rDLDH) was expressed and compared with enzyme expressed in the absence of lipoic acid (rDLDH(-LA)) or with enzyme lacking the first 112 amino acids constituting the lipoyl protein domain (rDLDH(-LIPOYL)). All three proteins contained 1 mol of FAD/mol of protein, had a higher activity for the conversion of NAD(+) to NADH than for the reaction in the reverse direction, and were unable to use NADP(+) and NADPH as substrates. The enzymes had similar substrate specificities, with the K(m) for NAD(+) being approximately 20 times higher than that for dihydrolipoamide. The kinetic pattern suggested a Ping Pong Bi Bi mechanism, which was verified by product inhibition studies. The protein expressed without lipoic acid was indistinguishable from the wild-type protein in all analyses. On the other hand, the protein without a lipoyl protein domain had a 2-3-fold higher turnover number, a lower K(I) for NADH, and a higher K(I) for lipoamide compared with the other two enzymes. The results suggest that the lipoyl protein domain (but not lipoic acid alone) plays a regulatory role in the enzymatic characteristics of pneumococcal DLDH.
Collapse
Affiliation(s)
- Anders P Håkansson
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA.
| | | |
Collapse
|
7
|
McMillan PJ, Stimmler LM, Foth BJ, McFadden GI, Müller S. The human malaria parasite Plasmodium falciparum possesses two distinct dihydrolipoamide dehydrogenases. Mol Microbiol 2004; 55:27-38. [PMID: 15612914 DOI: 10.1111/j.1365-2958.2004.04398.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Plasmodium falciparum genome contains genes encoding three alpha-ketoacid dehydrogenase multienzyme complexes (KADHs) that have central metabolic functions. The parasites possess two distinct genes encoding dihydrolipoamide dehydrogenases (LipDH), which are indispensable subunits of KADHs. This situation is reminiscent of that in plants, where two distinct LipDHs are found in mitochondria and chloroplasts, respectively, that are part of the organelle-specific KADHs. In this study, we show by reverse transcription polymerase chain reaction (RT-PCR) that the genes encoding subunits of all three KADHs, including both LipDHs, are transcribed during the erythrocytic development of P. falciparum. Protein expression of mitochondrial LipDH and mitochondrial branched chain alpha-ketoacid dihydrolipoamide transacylase in these parasite stages was confirmed by Western blotting. The localization of the two LipDHs to the parasite's apicoplast and mitochondrion, respectively, was shown by expressing the LipDH N-terminal presequences fused to green fluorescent protein in erythrocytic stages of P. falciparum and by immunofluorescent colocalization with organelle-specific markers. Biochemical characterization of recombinantly expressed mitochondrial LipDH revealed that the protein has kinetic and physicochemical characteristics typical of these flavo disulphide oxidoreductases. We propose that the mitochondrial LipDH is part of the mitochondrial alpha-ketoglutarate dehydrogenase and branched chain alpha-ketoacid dehydrogenase complexes and that the apicoplast LipDH is an integral part of the pyruvate dehydrogenase complex which occurs only in the apicoplast in P. falciparum.
Collapse
Affiliation(s)
- Paul J McMillan
- Institute of Biomedical and Life Sciences, Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | | |
Collapse
|
8
|
Lindsay H, Beaumont E, Richards SD, Kelly SM, Sanderson SJ, Price NC, Lindsay JG. FAD insertion is essential for attaining the assembly competence of the dihydrolipoamide dehydrogenase (E3) monomer from Escherichia coli. J Biol Chem 2000; 275:36665-70. [PMID: 10970889 DOI: 10.1074/jbc.m004777200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydrolipoamide dehydrogenase (E3) from Escherichia coli, an FAD-linked homodimer, can be fully reconstituted in vitro following denaturation in 6 m guanidinium chloride. Complete restoration of activity occurs within 1-2 h in the presence of FAD, dithiothreitol, and bovine serum albumin. In the absence of FAD, the dihydrolipoamide dehydrogenase monomer forms a stable folding intermediate, which is incapable of dimerization. This intermediate displays a similar tryptic resistance to the native enzyme but is less heat-stable, because its ability to form native E3 is lost after incubation at 65 degrees C for 15 min. The presence of FAD promotes slow, additional conformational rearrangements of the E3 subunit as observed by cofactor-dependent decreases in intrinsic tryptophan fluorescence. However, after 2 h, the tryptophan fluorescence spectrum and far UV CD spectrum of E3, refolded in the absence of FAD, are similar to that of the native enzyme, and full activity can still be recovered on addition of FAD. Cross-linking studies show that FAD insertion is necessary for the monomeric folding intermediate to attain an assembly competent state leading to dimerization. Thus cofactor insertion represents a key step in the assembly of this enzyme, although its initial presence appears not to be required to promote the correct folding pathway.
Collapse
Affiliation(s)
- H Lindsay
- Division of Biochemistry and Molecular Biology, Davidson Building, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | | | | | | | | | | | | |
Collapse
|
9
|
Bunik V, Raddatz G, Lemaire S, Meyer Y, Jacquot JP, Bisswanger H. Interaction of thioredoxins with target proteins: role of particular structural elements and electrostatic properties of thioredoxins in their interplay with 2-oxoacid dehydrogenase complexes. Protein Sci 1999; 8:65-74. [PMID: 10210184 PMCID: PMC2144114 DOI: 10.1110/ps.8.1.65] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The thioredoxin action upon the 2-oxoacid dehydrogenase complexes is investigated by using different thioredoxins, both wild-type and mutated. The attacking cysteine residue of thioredoxin is established to be essential for the thioredoxin-dependent activation of the complexes. Mutation of the buried cysteine residue to serine is not crucial for the activation, but prevents inhibition of the complexes, exhibited by the Clamydomonas reinhardtii thioredoxin m disulfide. Site-directed mutagenesis of D26, W31, F/W12, and Y/A70 (the Escherichia coli thioredoxin numbering is employed for all the thioredoxins studied) indicates that both the active site and remote residues of thioredoxin are involved in its interplay with the 2-oxoacid dehydrogenase complexes. Sequences of 11 thioredoxin species tested biochemically are aligned. The thioredoxin residues at the contact between the alpha3/3(10) and alpha1 helices, the length of the alpha1 helix and the charges in the alpha2-beta3 and beta4-beta5 linkers are found to correlate with the protein influence on the 2-oxoacid dehydrogenase complexes (the secondary structural elements of thioredoxin are defined according to Eklund H et al., 1991, Proteins 11:13-28). The distribution of the charges on the surface of the thioredoxin molecules is analyzed. The analysis reveals the species specific polarization of the thioredoxin active site surroundings, which corresponds to the efficiency of the thioredoxin interplay with the 2-oxoacid dehydrogenase systems. The most effective mitochondrial thioredoxin is characterized by the strongest polarization of this area and the highest value of the electrostatic dipole vector of the molecule. Not only the magnitude, but also the orientation of the dipole vector show correlation with the thioredoxin action. The dipole direction is found to be significantly influenced by the charges of the residues 13/14, 51, and 83/85, which distinguish the activating and inhibiting thioredoxin disulfides.
Collapse
Affiliation(s)
- V Bunik
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | | | | | | | | | | |
Collapse
|
10
|
de Kok A, Hengeveld AF, Martin A, Westphal AH. The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:353-66. [PMID: 9655933 DOI: 10.1016/s0167-4838(98)00079-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate dehydrogenase multi-enzyme complexes from Gram-negative bacteria consists of three enzymes, pyruvate dehydrogenase/decarboxylase (E1p), dihydrolipoyl acetyltransferase (E2p) and dihydrolipoyl dehydrogenase (E3). The acetyltransferase harbors all properties required for multi-enzyme catalysis: it forms a large core of 24 subunits, it contains multiple binding sites for the E1p and E3 components, the acetyltransferase catalytic site and mobile substrate carrying lipoyl domains that visit the active sites. Today, the Azotobacter vinelandii complex is the best understood oxo acid dehydrogenase complex with respect to structural details. A description of multi-enzyme catalysis starts with the structural and catalytic properties of the individual components of the complex. Integration of the individual properties is obtained by a description of how the many copies of the individual enzymes are arranged in the complex and how the lipoyl domains couple the activities of the respective active sites by way of flexible linkers. These latter aspects are the most difficult to study and future research need to be aimed at these properties.
Collapse
Affiliation(s)
- A de Kok
- Department of Biomolecular Sciences, Laboratory of Biochemistry, Wageningen Agricultural University, Dreijenlaan 3, 6703 HA Wageningen, Netherlands.
| | | | | | | |
Collapse
|
11
|
Maeda-Yorita K, Russell GC, Guest JR, Massey V, Williams CH. Modulation of the oxidation-reduction potential of the flavin in lipoamide dehydrogenase from Escherichia coli by alteration of a nearby charged residue, K53R. Biochemistry 1994; 33:6213-20. [PMID: 8193135 DOI: 10.1021/bi00186a022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The epsilon-amino group of a lysine residue occupies a position within bonding distance of the flavin N5 and the bound NADPH pyridinium C4' in glutathione reductase, and it has been suggested that this positive charge influences the redox potential of the FAD [Pai & Schulz (1983) J. Biol. Chem. 258, 1752]. A conserved lysine residue occupies a similar position in lipoamide dehydrogenase. This residue has been replaced by an arginine in lipoamide dehydrogenase from Escherichia coli to give K53R. The spectral and redox properties of the FAD in K53R as well as the interaction of the flavin with bound NAD+ are profoundly affected by the change. K53R does not catalyze either the dihydrolipoamide-NAD+ or the NADH-lipoamide reactions except at very low concentrations of the reducing substrate. The absorbance spectrum of K53R in the visible and near-ultraviolet is little changed from that of wild-type enzyme, but in contrast, the spectrum of K53R is sensitive to pH with an apparent pKa = 7.0. Unlike the wild-type enzyme, the binding of beta-NAD+ to K53R alters the spectrum and indicates an apparent Kd = 7.0 microM at pH 7.6. The flavin fluorescence is partially quenched, and the visible and near-ultraviolet circular dichroism spectrum is changed by beta-NAD+. K53R is extensively reduced (mostly EH4) by 2 equiv of dihydrolipoamide/FAD while the wild-type enzyme is only partially reduced (mostly EH2). The rate of this reduction is lowered by approximately 3-fold relative to the wild-type enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- K Maeda-Yorita
- Department of Biological Chemistry, University of Michigan, Ann Arbor 48109
| | | | | | | | | |
Collapse
|
12
|
Benen J, van Berkel W, Dieteren N, Arscott D, Williams C, Veeger C, de Kok A. Lipoamide dehydrogenase from Azotobacter vinelandii: site-directed mutagenesis of the His450-Glu455 diad. Kinetics of wild-type and mutated enzymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 207:487-97. [PMID: 1633804 DOI: 10.1111/j.1432-1033.1992.tb17075.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Three amino acid residues in the active site of lipoamide dehydrogenase from Azotobacter vinelandii were replaced with other residues. His450, the active-site base, was replaced with Ser, Tyr or Phe. Pro451, from X-ray analysis found to be in cis conformation positioning the backbone carbonyl of His450 close to N3 of the flavin, was changed to Ala. Glu455, from X-ray analysis expected to be involved in modulating the pKa of the base (His450), was replaced with Asp and Gln. The general conclusion is that mutation of the His-Glu diad impairs intramolecular electron transfer between the disulfide/dithiol and the FADH-/FAD. The wild-type enzyme functions according to a ping-pong mechanism in the physiological reaction in which the formation of NADH is rate-limiting. Above pH 8.0 the enzyme is strongly inhibited by the product NADH. The pH dependence of the steady-state kinetics using the NAD+ analog 3-acetylpyridine adenine dinucleotide (AcPyAde+) reveals a pKa of 8.1 in the pKm AcPyAde+ plot indicating that this pKa is related to the deprotonation of His450 [Benen, J., Berkel van, W., Zak, Z., Visser, T., Veeger, C. & Kok de, A. (1991) Eur. J. Biochem. 202, 863-872] and to the inhibition by NADH. The mutations considerably affect turnover. Enzymes with the mutations Pro451----Ala, His450----Phe and His450----Tyr appear to be almost inactive in both directions. Enzyme His450----Ser is minimally active, V at the pH optimum being 0.5% of wild-type activity in the physiological reaction. Rapid reaction kinetics show that for the His450-mutated enzymes the reductive half reaction using reduced 6,8-thioctic acid amide [Lip(SH)2] is rate-limiting and extremely slow when compared using reduced 6,8-thioctic acid amide [Lip(SH)2] is rate-limiting and extremely slow when compared to the wild-type enzyme. For enzyme Pro451----Ala it is concluded that the loss of activity is due to over-reduction by Lip(SH)2 and NADH. The Glu455-mutated enzymes are catalytically competent but show strong inhibition by the product NADH (enzyme Glu455----Asp more than Glu455----Gln). The inhibition can largely be overcome by using AcPyAde+ instead of NAD+ in the physiological reaction. The rapid reaction kinetics obtained for enzymes Glu455----Asp and Glu455----Gln deviate from the wild-type enzyme. It is concluded that this difference is due to cooperativity between the active sites in this dimeric enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)
Collapse
Affiliation(s)
- J Benen
- Department of Biochemistry, Agricultural University, Wageningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
13
|
Characterization of two site-specifically mutated human dihydrolipoamide dehydrogenases (His-452—-Gln and Glu-457—-Gln). J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42740-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
14
|
Guest JR, Russell GC. Complexes and complexities of the citric acid cycle in Escherichia coli. CURRENT TOPICS IN CELLULAR REGULATION 1992; 33:231-47. [PMID: 1499335 DOI: 10.1016/b978-0-12-152833-1.50018-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- J R Guest
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, England
| | | |
Collapse
|