TY - JOUR AU - Szimler, Tamás AU - Gráczer, Éva Laura AU - Györffy, Dániel AU - Végh, Barbara AU - Szilágyi, András AU - Hajdú, István AU - Závodszky, Péter AU - Kazinczyné Vas, Mária TI - New type of interaction between the SARAH domain of the tumour suppressor RASSF1A and its mitotic kinase Aurora A JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 9 PY - 2019 PG - 12 SN - 2045-2322 DO - 10.1038/s41598-019-41972-x UR - https://m2.mtmt.hu/api/publication/30625253 ID - 30625253 LA - English DB - MTMT ER - TY - JOUR AU - Gráczer, Éva Laura AU - Szimler, Tamás AU - Garamszegi, A AU - Konarev, PV AU - Krezinger, Anikó AU - Oláh, Julianna AU - Pallo, A AU - Svergun, DI AU - Merli, A AU - Závodszky, Péter AU - Weiss, MS AU - Kazinczyné Vas, Mária TI - Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure. JF - BIOCHEMISTRY J2 - BIOCHEMISTRY-US VL - 55 PY - 2016 IS - 3 SP - 560 EP - 574 PG - 15 SN - 0006-2960 DO - 10.1021/acs.biochem.5b00839 UR - https://m2.mtmt.hu/api/publication/3023735 ID - 3023735 AB - The key active site residues K185, Y139, D217, D241, D245, and N102 of Thermus thermophilus 3-isopropylmalate dehydrogenase (Tt-IPMDH) have been replaced, one by one, with Ala. A drastic decrease in the kcat value (0.06% compared to that of the wild-type enzyme) has been observed for the K185A and D241A mutants. Similarly, the catalytic interactions (Km values) of these two mutants with the substrate IPM are weakened by more than 1 order of magnitude. The other mutants retained some (1-13%) of the catalytic activity of the wild-type enzyme and do not exhibit appreciable changes in the substrate Km values. The pH dependence of the wild-type enzyme activity (pK = 7.4) is shifted toward higher values for mutants K185A and D241A (pK values of 8.4 and 8.5, respectively). For the other mutants, smaller changes have been observed. Consequently, K185 and D241 may constitute a proton relay system that can assist in the abstraction of a proton from the OH group of IPM during catalysis. Molecular dynamics simulations provide strong support for the neutral character of K185 in the resting state of the enzyme, which implies that K185 abstracts the proton from the substrate and D241 assists the process via electrostatic interactions with K185. Quantum mechanics/molecular mechanics calculations revealed a significant increase in the activation energy of the hydride transfer of the redox step for both D217A and D241A mutants. Crystal structure analysis of the molecular contacts of the investigated residues in the enzyme-substrate complex revealed their additional importance (in particular that of K185, D217, and D241) in stabilizing the domain-closed active conformation. In accordance with this, small-angle X-ray scattering measurements indicated the complete absence of domain closure in the cases of D217A and D241A mutants, while only partial domain closure could be detected for the other mutants. This suggests that the same residues that are important for catalysis are also essential for inducing domain closure. LA - English DB - MTMT ER - TY - JOUR AU - Gráczer, Éva Laura AU - Palló, Anna AU - Oláh, Julianna AU - Szimler, Tamás AU - Konarev, Petr V AU - Svergun, Dmitri I AU - Merli, Angelo AU - Závodszky, Péter AU - Weiss, Manfred S AU - Kazinczyné Vas, Mária TI - Glutamate 270 plays an essential role in K+-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase JF - FEBS LETTERS J2 - FEBS LETT VL - 589 PY - 2015 IS - 2 SP - 240 EP - 245 PG - 6 SN - 0014-5793 DO - 10.1016/j.febslet.2014.12.005 UR - https://m2.mtmt.hu/api/publication/2807961 ID - 2807961 LA - English DB - MTMT ER - TY - JOUR AU - Palló, A AU - Oláh, Julianna AU - Gráczer, Éva Laura AU - Merli, A AU - Závodszky, Péter AU - Weiss, MS AU - Kazinczyné Vas, Mária TI - Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis JF - FEBS JOURNAL J2 - FEBS J VL - 281 PY - 2014 IS - 22 SP - 5063 EP - 5076 PG - 14 SN - 1742-464X DO - 10.1111/febs.13044 UR - https://m2.mtmt.hu/api/publication/2785761 ID - 2785761 N1 - Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, H-1117, Hungary Dipartimento di Bioscienze, Universitá Degli Studi di Parma, Parma, Italy Helmholtz Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert Einstein Straße 15, Berlin, D-12489, Germany Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Brussels, B-1050, Belgium Brussels Center for Redox Biology, Brussels, B-1050, Belgium Structural Biology Brussels Laboratory, Vrije Universiteit Brussel, Brussels, B-1050, Belgium Cited By :12 Export Date: 15 April 2021 CODEN: FJEOA Correspondence Address: Weiss, M.S.; Helmholtz Zentrum Berlin für Materialien und Energie, Albert Einstein Straße 15, Germany; email: manfred.weiss@helmholtz-berlin.de Chemicals/CAS: 3 isopropylmalate dehydrogenase, 9030-97-1; magnesium, 7439-95-4; manganese, 16397-91-4, 7439-96-5; nicotinamide adenine dinucleotide, 53-84-9; potassium, 7440-09-7; 3-Isopropylmalate Dehydrogenase; Bacterial Proteins; Magnesium; Malates; Manganese; NAD; Potassium Funding details: Hungarian Scientific Research Fund, OTKA, 108642 AB - The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn2+, its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K+ ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD+ is easily possible, with an activation energy of approximately 15 kcal·mol-1. The activation energy increases by approximately 4-6 kcal·mol-1 when the K+ ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule. LA - English DB - MTMT ER - TY - JOUR AU - Gráczer, Éva Laura AU - Bacsó, András AU - Kónya, Dénes AU - Kazi, A AU - Soós, Tibor AU - Molnár, Laura AU - Szimler, Tamás AU - Beinrohr, László AU - Szilágyi, András AU - Závodszky, Péter AU - Kazinczyné Vas, Mária TI - Drugs Against Mycobacterium Tuberculosis 3-Isopropylmalate Dehydrogenase Can be Developed using Homologous Enzymes as Surrogate Targets JF - PROTEIN AND PEPTIDE LETTERS J2 - PROTEIN PEPTIDE LETT VL - 21 PY - 2014 IS - 12 SP - 1295 EP - 1307 PG - 13 SN - 0929-8665 UR - https://m2.mtmt.hu/api/publication/2604041 ID - 2604041 N1 - Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, Budapest, H-1519, Hungary Cited By :2 Export Date: 3 October 2022 CODEN: PPELE Correspondence Address: Vas, M.; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Hungary AB - 3-Isopropylmalate dehydrogenase (IPMDH) from Mycobacterium tuberculosis (Mtb) may be a target for specific drugs against this pathogenic bacterium. We have expressed and purified Mtb IPMDH and determined its physical-chemical and enzymological properties. Size-exclusion chromatography and dynamic light scattering measurements (DLS) suggest a tetrameric structure for Mtb IPMDH, in contrast to the dimeric structure of most IPMDHs. The kinetic properties (kcat and Km values) of Mtb IPMDH and the pH-dependence of kcat are very similar to both Escherichia coli (Ec) and Thermus thermophilus (Tt) IPMDHs. The stability of Mtb IPMDH in 8 M urea is close to that of the mesophilic counterpart, Ec IPMDH, both of them being much less stable than the thermophilic (Tt) enzyme. Two known IPMDH inhibitors, O-methyl oxalohydroxamate and 3-methylmercaptomalate, have been synthesised. Their inhibitory effects were found to be independent of the origin of IPMDHs. Thus, experiments with either Ec or Tt IPMDH would be equally relevant for designing specific inhibitory drugs against Mtb IPMDH. LA - English DB - MTMT ER - TY - CHAP AU - Bowler, MW AU - Kazinczyné Vas, Mária ED - Kazinczyné Vas, Mária TI - Structural-Temporal Description of the Reaction Cycle T2 - Phosphoglycerate Kinase: A Hinge-Bending Enzyme PB - Nova Science Publishers CY - New York, New York SN - 9781628088380 T3 - Molecular Anatomy and Physiology of Proteins PY - 2014 SP - 223 EP - 229 PG - 7 UR - https://m2.mtmt.hu/api/publication/2573753 ID - 2573753 LA - English DB - MTMT ER - TY - CHAP AU - JP, Waltho AU - M W, Bowler AU - M J, Cliff AU - Kazinczyné Vas, Mária ED - Kazinczyné Vas, Mária TI - Architecture of the Active Site and the Importance of Charge Balance in Catalysis T2 - Phosphoglycerate Kinase: A Hinge-Bending Enzyme PB - Nova Science Publishers CY - New York, New York SN - 9781628088380 T3 - Molecular Anatomy and Physiology of Proteins PY - 2014 SP - 203 EP - 210 PG - 8 UR - https://m2.mtmt.hu/api/publication/2573745 ID - 2573745 LA - English DB - MTMT ER - TY - CHAP AU - Matkovicsné Varga, Andrea AU - Kazinczyné Vas, Mária ED - Kazinczyné Vas, Mária TI - Physiological and Non-Physiological Functions of PGK and Its Abundance T2 - Phosphoglycerate Kinase: A Hinge-Bending Enzyme PB - Nova Science Publishers CY - New York, New York SN - 9781628088380 T3 - Molecular Anatomy and Physiology of Proteins PY - 2014 SP - 143 EP - 153 PG - 11 UR - https://m2.mtmt.hu/api/publication/2573725 ID - 2573725 LA - English DB - MTMT ER - TY - CHAP AU - Kazinczyné Vas, Mária ED - Kazinczyné Vas, Mária TI - Substrate-Assisted Cooperative Interaction of the Two Domains: Mechanism of Domain Closure at the Level of Atomic Interactions T2 - Phosphoglycerate Kinase: A Hinge-Bending Enzyme PB - Nova Science Publishers CY - New York, New York SN - 9781628088380 T3 - Molecular Anatomy and Physiology of Proteins PY - 2014 SP - 211 EP - 221 PG - 11 UR - https://m2.mtmt.hu/api/publication/2573721 ID - 2573721 LA - English DB - MTMT ER - TY - CHAP AU - Kazinczyné Vas, Mária ED - Kazinczyné Vas, Mária TI - Role of the Metal-Ion in Nucleotide Binding and in the Catalysis T2 - Phosphoglycerate Kinase: A Hinge-Bending Enzyme PB - Nova Science Publishers CY - New York, New York SN - 9781628088380 T3 - Molecular Anatomy and Physiology of Proteins PY - 2014 SP - 195 EP - 200 PG - 6 UR - https://m2.mtmt.hu/api/publication/2573696 ID - 2573696 LA - English DB - MTMT ER -