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New Insights into the Determinants of Specificity in Human Type I Arginase: Generation of a Mutant That Is Only Active with Agmatine as Substrate. Int J Mol Sci 2022; 23:ijms23126438. [PMID: 35742891 PMCID: PMC9224512 DOI: 10.3390/ijms23126438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/25/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea. This enzyme has several analogies with agmatinase, which catalyzes the hydrolysis of agmatine into putrescine and urea. However, this contrasts with the highlighted specificity that each one presents for their respective substrate. A comparison of available crystal structures for arginases reveals an important difference in the extension of two loops located in the entrance of the active site. The first, denominated loop A (I129-L140) contains the residues that interact with the alpha carboxyl group or arginine of arginase, and the loop B (D181-P184) contains the residues that interact with the alpha amino group of arginine. In this work, to determine the importance of these loops in the specificity of arginase, single, double, and triple arginase mutants in these loops were constructed, as well as chimeras between type I human arginase and E. coli agmatinase. In previous studies, the substitution of N130D in arginase (in loop A) generated a species capable of hydrolyzing arginine and agmatine. Now, the specificity of arginase is completely altered, generating a chimeric species that is only active with agmatine as a substrate, by substituting I129T, N130Y, and T131A together with the elimination of residues P132, L133, and T134. In addition, Quantum Mechanic/Molecular Mechanic (QM/MM) calculations were carried out to study the accommodation of the substrates in in the active site of this chimera. With these results it is concluded that this loop is decisive to discriminate the type of substrate susceptible to be hydrolyzed by arginase. Evidence was also obtained to define the loop B as a structural determinant for substrate affinity. Concretely, the double mutation D181T and V182E generate an enzyme with an essentially unaltered kcat value, but with a significantly increased Km value for arginine and a significant decrease in affinity for its product ornithine.
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2
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Chitrakar I, Ahmed SF, Torelli AT, French JB. Structure of the E. coli agmatinase, SPEB. PLoS One 2021; 16:e0248991. [PMID: 33857156 PMCID: PMC8049259 DOI: 10.1371/journal.pone.0248991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023] Open
Abstract
Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E. coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P31 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/Rfree values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.
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Affiliation(s)
- Iva Chitrakar
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, United States of America
| | - Syed Fardin Ahmed
- Department of Chemistry, Ithaca College, Ithaca, NY, United States of America
| | - Andrew T. Torelli
- Department of Chemistry, Ithaca College, Ithaca, NY, United States of America
| | - Jarrod B. French
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- Chemistry Department, Stony Brook University, Stony Brook, NY, United States of America
- Hormel Institute, University of Minnesota, Austin, MN, United States of America
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3
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A Computational Method to Predict Effects of Residue Mutations on the Catalytic Efficiency of Hydrolases. Catalysts 2021. [DOI: 10.3390/catal11020286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
With scientific and technological advances, growing research has focused on engineering enzymes that acquire enhanced efficiency and activity. Thereinto, computer-based enzyme modification makes up for the time-consuming and labor-intensive experimental methods and plays a significant role. In this study, for the first time, we collected and manually curated a data set for hydrolases mutation, including structural information of enzyme-substrate complexes, mutated sites and Kcat/Km obtained from vitro assay. We further constructed a classification model using the random forest algorithm to predict the effects of residue mutations on catalytic efficiency (increase or decrease) of hydrolases. This method has achieved impressive performance on a blind test set with the area under the receiver operating characteristic curve of 0.86 and the Matthews Correlation Coefficient of 0.659. Our results demonstrate that computational mutagenesis has an instructive effect on enzyme modification, which may expedite the design of engineering hydrolases.
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Velázquez-Libera JL, Caballero J, Tuñón I, Hernández-Rodríguez EW, Ruiz-Pernía JJ. On the Nature of the Enzyme–Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Velázquez-Libera
- Doctorado en Ciencias Aplicadas, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - Erix W. Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile
| | - J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
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5
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Dadová J, Wu KJ, Isenegger PG, Errey JC, Bernardes GL, Chalker JM, Raich L, Rovira C, Davis BG. Precise Probing of Residue Roles by Post-Translational β,γ-C,N Aza-Michael Mutagenesis in Enzyme Active Sites. ACS CENTRAL SCIENCE 2017; 3:1168-1173. [PMID: 29202018 PMCID: PMC5704290 DOI: 10.1021/acscentsci.7b00341] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Biomimicry valuably allows the understanding of the essential chemical components required to recapitulate biological function, yet direct strategies for evaluating the roles of amino acids in proteins can be limited by access to suitable, subtly-altered unnatural variants. Here we describe a strategy for dissecting the role of histidine residues in enzyme active sites using unprecedented, chemical, post-translational side-chain-β,γ C-N bond formation. Installation of dehydroalanine (as a "tag") allowed the testing of nitrogen conjugate nucleophiles in "aza-Michael"-1,4-additions (to "modify"). This allowed the creation of a regioisomer of His (iso-His, Hisiso) linked instead through its pros-Nπ atom rather than naturally linked via C4, as well as an aza-altered variant aza-Hisiso. The site-selective generation of these unnatural amino acids was successfully applied to probe the contributing roles (e.g., size, H-bonding) of His residues toward activity in the model enzymes subtilisin protease from Bacillus lentus and Mycobacterium tuberculosis pantothenate synthetase.
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Affiliation(s)
- Jitka Dadová
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kuan-Jung Wu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Patrick G. Isenegger
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James C. Errey
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Gonçalo
J. L. Bernardes
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Justin M. Chalker
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Benjamin G. Davis
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
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Pudlo M, Demougeot C, Girard-Thernier C. Arginase Inhibitors: A Rational Approach Over One Century. Med Res Rev 2016; 37:475-513. [DOI: 10.1002/med.21419] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/14/2016] [Accepted: 09/22/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marc Pudlo
- PEPITE - EA4267; University Bourgogne Franche-Comté; Besançon France
| | - Céline Demougeot
- PEPITE - EA4267; University Bourgogne Franche-Comté; Besançon France
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7
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D'Antonio EL, Hai Y, Christianson DW. Structure and function of non-native metal clusters in human arginase I. Biochemistry 2012; 51:8399-409. [PMID: 23061982 DOI: 10.1021/bi301145n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Various binuclear metal ion clusters and complexes have been reconstituted in crystalline human arginase I by removing the Mn(2+)(2) cluster of the wild-type enzyme with metal chelators and subsequently soaking the crystalline apoenzyme in buffer solutions containing NiCl(2) or ZnCl(2). X-ray crystal structures of these metal ion variants are correlated with catalytic activity measurements that reveal differences resulting from metal ion substitution. Additionally, treatment of crystalline Mn(2+)(2)-human arginase I with Zn(2+) reveals for the first time the structural basis for inhibition by Zn(2+), which forms a carboxylate-histidine-Zn(2+) triad with H141 and E277. The imidazole side chain of H141 is known to be hyper-reactive, and its chemical modification or mutagenesis is known to similarly compromise catalysis. The reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH) binds as a tetrahedral boronate anion to Mn(2+)(2), Co(2+)(2), Ni(2+)(2), and Zn(2+)(2) clusters in human arginase I, and it can be stabilized by a third inhibitory Zn(2+) ion coordinated by H141. Because ABH binds as an analogue of the tetrahedral intermediate and its flanking transition states in catalysis, this implies that the various metallo-substituted enzymes are capable of some level of catalysis with an actual substrate. Accordingly, we establish the following trend for turnover number (k(cat)) and catalytic efficiency (k(cat)/K(M)): Mn(2+) > Ni(2+) ≈ Co(2+) ≫ Zn(2+). Therefore, Mn(2+) is required for optimal catalysis by human arginase I.
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Affiliation(s)
- Edward L D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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8
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Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry 2012; 51:7525-32. [PMID: 22970849 DOI: 10.1021/bi300472n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PchB is an isochorismate-pyruvate lyase from Pseudomonas aeruginosa. A positively charged lysine residue is located in a flexible loop that behaves as a lid to the active site, and the lysine residue is required for efficient production of salicylate. A variant of PchB that lacks the lysine at residue 42 has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Construction of a lysine isosteric residue bearing a positive charge at the appropriate position leads to the recovery of 2.5-2.7 kcal/mol (about 60%) of the 4.4 kcal/mol by chemical rescue. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity (0.180 kcal/mol, roughly 7% rescue), whereas addition of propylamine caused an additional modest loss in catalytic power (0.056 kcal/mol, or 2% loss). This is consistent with the view that (a) the lysine-42 residue is required in a specific conformation to stabilize the transition state and (b) the correct conformation is achieved for a lysine-mimetic side chain at site 42 in the course of loop closure, as expected for transition-state stabilization by the side chain ammonio function. That the positive charge is the main effector of transition state stabilization is shown by the construction of a lysine-isosteric residue capable of exerting steric effects and hydrogen bonding but not electrostatic effects, leading to a modest increase of catalytic power (0.267-0.505 kcal/mol of catalytic free energy, or roughly 6-11% rescue).
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Affiliation(s)
- José Olucha
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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9
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Leopoldini M, Russo N, Toscano M. Determination of the Catalytic Pathway of a Manganese Arginase Enzyme Through Density Functional Investigation. Chemistry 2009; 15:8026-8036. [DOI: 10.1002/chem.200802252] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW. Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 2009; 47:13554-63. [PMID: 19053282 DOI: 10.1021/bi801610c] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metal-dependent histone deacetylases (HDACs) require Zn(2+) or Fe(2+) to regulate the acetylation of lysine residues in histones and other proteins in eukaryotic cells. Isozyme HDAC8 is perhaps the archetypical member of the class I HDAC family and serves as a paradigm for studying structure-function relationships. Here, we report the structures of HDAC8 complexes with trichostatin A and 3-(1-methyl-4-phenylacetyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide (APHA) in a new crystal form. The structure of the APHA complex reveals that the hydroxamate CO group accepts a hydrogen bond from Y306 but does not coordinate to Zn(2+) with favorable geometry, perhaps due to the constraints of its extended pi system. Additionally, since APHA binds to only two of the three protein molecules in the asymmetric unit of this complex, the structure of the third monomer represents the first structure of HDAC8 in the unliganded state. Comparison of unliganded and liganded structures illustrates ligand-induced conformational changes in the L2 loop that likely accompany substrate binding and catalysis. Furthermore, these structures, along with those of the D101N, D101E, D101A, and D101L variants, support the proposal that D101 is critical for the function of the L2 loop. However, amino acid substitutions for D101 can also trigger conformational changes of Y111 and W141 that perturb the substrate binding site. Finally, the structure of H143A HDAC8 complexed with an intact acetylated tetrapeptide substrate molecule confirms the importance of D101 for substrate binding and reveals how Y306 and the active site zinc ion together bind and activate the scissile amide linkage of acetyllysine.
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Affiliation(s)
- Daniel P Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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11
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Reisner HM, Lundblad RL. Identifying residues in antigenic determinants by chemical modification. Methods Mol Biol 2009; 524:103-117. [PMID: 19377940 DOI: 10.1007/978-1-59745-450-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical modification of the side chains of amino acid residues was one of the first methods developed to investigate epitopes in protein antigens. The principle of the method is that alteration of the structure of a key residue of an epitope by a chemical modification will alter reactivity with antibody by affecting either specificity or avidity or both. Chemical modification has the advantage that it can be applied to discontinuous as well as continuous epitopes and may be of value in identifying cryptic epitopes. We consider here the several recent studies that have applied site-specific chemical modification to the identification of epitopes on antigens, including the use of formaldehyde, glutaraldehyde, and acid anhydrides, to produce allergoids where determinants important to reaction with IgE are modified but the ability to elicit an IgG response is retained. It is noteworthy that modification of amino groups with charge reversal appears to be the most useful approach. The approach to the use of site-specific chemical modification as a tool for the study of protein function is discussed, and emphasis is placed on the necessity to (1) validate the specificity of modification and (2) assess potential conformational change that may occur secondary to modification. Finally, a list of chemical reagents used for protein modification is presented, together with properties and references to use.
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Affiliation(s)
- Howard M Reisner
- Department of Pathology and Laboratory Medicine, University of North Carolina, PO Box 16695, Chapel Hill, NC 27516, USA
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12
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Ikeda H, Yukawa M, Niiya T. Ab Initio Molecular Orbital Study of the Reactivity of Active Alkyl Groups. VII. Solvent Effects on the Formation of Enolate Isomers from 2-Butanone with Methoxide Anion in Methanol. Chem Pharm Bull (Tokyo) 2006; 54:731-4. [PMID: 16651780 DOI: 10.1248/cpb.54.731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mechanism of the deprotonation of 2-butanone (1) with methoxide anion (2) was studied by ab initio molecular orbital (MO) methods. Calculations of the thermodynamic stabilities of each complex and the regioselectivity of the reaction were performed using a static isodensity surface polarized continuum model (IPCM) which takes the solvent effect into consideration. The calculated energies of the complexes lead ultimately to the conclusion that the major deprotonation pathway in protic solvents is dependent upon thermodynamically stable complexes with small activation energies under equilibrium control.
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Affiliation(s)
- Hirohito Ikeda
- Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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