1
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Walker RM, Zhang M, Burnap RL. Elucidating the role of primary and secondary sphere Zn 2+ ligands in the cyanobacterial CO 2 uptake complex NDH-1 4: The essentiality of arginine in zinc coordination and catalysis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149149. [PMID: 38906312 DOI: 10.1016/j.bbabio.2024.149149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Inorganic carbon uptake in cyanobacteria is facilitated by an energetically intensive CO2-concentrating mechanism (CCM). Specialized Type-1 NDH complexes function as a part of this mechanism to couple photosynthetic energy generated by redox reactions of the electron transport chain (ETC) to CO2 hydration. This active site of CO2 hydration incorporates an arginine side chain as a Zn ligand, diverging from the typical histidine and/or cysteine residues found in standard CAs. In this study, we focused on mutating three amino acids in the active site of the constitutively expressed NDH-14 CO2 hydration complex in Synechococcus sp. PCC7942: CupB-R91, which acts as a zinc ligand, and CupB-E95 and CupB-H89, both of which closely interact with the arginine ligand. These mutations aimed to explore how they affect the unusual metal ligation by CupB-R91 and potentially influence the unusual catalytic process. The most severe defects in activity among the targeted residues are due to a substitution of CupB-R91 and the ionically interacting E95 since both proved essential for the structural stability of the CupB protein. On the other hand, CupB-H89 mutations show a range of catalytic phenotypes indicating a role of this residue in the catalytic mechanism of CO2-hydration, but no evidence was obtained for aberrant carbonic anhydrase activity that would have indicated uncoupling of the CO2-hydration activity from proton pumping. The results are discussed in terms of possible alternative CO2 hydration mechanisms.
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Affiliation(s)
- Ross M Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Minquan Zhang
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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2
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Angeli A. Bacterial γ-carbonic anhydrases. Enzymes 2024; 55:93-120. [PMID: 39223000 DOI: 10.1016/bs.enz.2024.05.002] [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: 09/04/2024]
Abstract
Carbonic anhydrases (CAs) are a ubiquitous family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate and protons, playing pivotal roles in a variety of biological processes including respiration, calcification, acid-base balance, and CO2 fixation. Recent studies have expanded the understanding of CAs, particularly the γ-class from diverse biological sources such as pathogenic bacteria, extremophiles, and halophiles, revealing their unique structural adaptations and functional mechanisms that enable operation under extreme environmental conditions. This chapter discusses the comprehensive catalytic mechanism and structural insights from X-ray crystallography studies, highlighting the molecular adaptations that confer stability and activity to these enzymes in harsh environments. It also explores the modulation mechanism of these enzymes, detailing how different modulators interact with the active site of γ-CAs. Comparative analyzes with other CA classes elucidate the evolutionary trajectories and functional diversifications of these enzymes. The synthesis of this knowledge not only sheds light on the fundamental aspects of CA biology but also opens new avenues for therapeutic and industrial applications, particularly in designing targeted inhibitors for pathogenic bacteria and developing biocatalysts for industrial processes under extreme conditions. The continuous advancement in structural biology promises further insights into this enzyme family, potentially leading to novel applications in medical and environmental biotechnology.
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Affiliation(s)
- Andrea Angeli
- Neurofarba Department, University of Florence, Sesto Fiorentino, Florence, Italy.
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3
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Neelam, Singh H. 1H, 15N and 13C resonance assignments of S2A mutant of human carbonic anhydrase II. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:45-49. [PMID: 38520652 DOI: 10.1007/s12104-024-10166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/22/2024] [Indexed: 03/25/2024]
Abstract
In preparation for a detailed exploration of the structural and functional aspects of the Ser2Ala mutant of human carbonic anhydrase II, we present here almost complete sequence-specific resonance assignments for 1H, 15N, and 13C. The mutation of serine to alanine at position 2, located in the N-terminal region of the enzyme, significantly alters the hydrophilic nature of the site, rendering it hydrophobic. Consequently, there is an underlying assumption that this mutation would repel water from the site. However, intriguingly, comparative analysis of the mutant structure with the wild type reveals minimal discernible differences. These assignments serve as the basis for in-depth studies on histidine dynamics, protonation states, and its intricate role in protein-water interactions and catalysis.
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Affiliation(s)
- Neelam
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India
| | - Himanshu Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India.
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4
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Paul TK, Taraphder S. Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction. J Phys Chem B 2022; 126:1413-1425. [PMID: 35138854 DOI: 10.1021/acs.jpcb.1c08760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an in-depth study on the theoretical calculation of an optimum reaction coordinate as a linear or nonlinear combination of important collective variables (CVs) sampled from an ensemble of reactive transition paths for an intramolecular proton transfer reaction catalyzed by the enzyme human carbonic anhydrase (HCA) II. The linear models are optimized by likelihood maximization for a given number of CVs. The nonlinear models are based on an artificial neural network with the same number of CVs and optimized by minimizing the root-mean-square error in comparison to a training set of committor estimators generated for the given transition. The nonlinear reaction coordinate thus obtained yields the free energy of activation and rate constant as 9.46 kcal mol-1 and 1.25 × 106 s-1, respectively. These estimates are found to be in quantitative agreement with the known experimental results. We have also used an extended autoencoder model to show that a similar analysis can be carried out using a single CV only. The resultant free energies and kinetics of the reaction slightly overestimate the experimental data. The implications of these results are discussed using a detailed microkinetic scheme of the proton transfer reaction catalyzed by HCA II.
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Affiliation(s)
- Tanmoy Kumar Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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5
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Paul TK, Taraphder S. Molecular modelling of two coordination states of Zn(II) ion at the active site of human carbonic anhydrase II. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Zanetti-Polzi L, Aschi M, Daidone I. Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study. Phys Chem Chem Phys 2021; 22:19975-19981. [PMID: 32857091 DOI: 10.1039/d0cp03652h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the energy variation upon PT, and from that we also calculate the PT reaction free energy, making use of a hybrid quantum mechanics/molecular dynamics approach. In agreement with the experimental data, we obtain that the reaction free energy is basically the same in the two systems. Yet, we show that the instantaneous PT energy is on average lower in the mutant possibly contributing to the faster PT rate. Analysis of the contribution to the PT energetics of the solvent and of each protein residue, also not in the vicinity of the active site, provides evidence for electrostatic tuning of the PT energy arising from the combined effect of the solvent and the protein environment. These findings open up a way to the more general task of the rational design of mutants with either enhanced or reduced PT rate.
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Affiliation(s)
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
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7
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Paul S, Paul TK, Taraphder S. Orthogonal order parameters to model the reaction coordinate of an enzyme catalyzed reaction. J Mol Graph Model 2019; 90:18-32. [PMID: 30959266 DOI: 10.1016/j.jmgm.2019.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/01/2019] [Accepted: 03/26/2019] [Indexed: 01/03/2023]
Abstract
The choice of suitable collective variables in formulating an optimal reaction coordinate is a challenging task for activated transitions between a pair of stable states especially when dealing with biochemical changes such as enzyme catalyzed reactions. A detailed benchmarking study is carried out on the choice of collective variables that can distinguish between the stable states unambiguously. We specifically address the issue if these variables may be directly used to model the optimal reaction coordinate, or if it would be better to use their orthogonalized counterparts. The proposed computational scheme is applied to the rate determining intramolecular proton transfer step in the enzyme human carbonic anhydrase II. The optimum reaction coordinate is determined with and without orthogonalization of the collective variables pertinent to a key conformational fluctuation and the actual proton transfer step at the active site of the enzyme. Suitability of the predicted reaction coordinates in different processes is examined in terms of the free energy profile projected along the reaction coordinate, the rate constant of transition and the underlying molecular mechanism of barrier crossing. Our results indicate that a better agreement with earlier simulation and experimental data is obtained when the orthogonalized collective variables are used to model the reaction coordinate.
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Affiliation(s)
- Sanjib Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India
| | - Tanmoy Kumar Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India.
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8
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Paul S, Paul TK, Taraphder S. Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II. J Phys Chem B 2018; 122:2851-2866. [DOI: 10.1021/acs.jpcb.7b10713] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Tanmoy Kumar Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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9
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Wilson RH, Zamfir S, Sumner I. Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme. J Mol Graph Model 2017; 76:403-411. [DOI: 10.1016/j.jmgm.2017.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 11/28/2022]
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10
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Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
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Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
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11
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Ge X, Gunner MR. Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Proteins 2016; 84:639-54. [DOI: 10.1002/prot.25013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/24/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaoxia Ge
- Physics Department; City College of New York; New York NY 10031
| | - M. R. Gunner
- Physics Department; City College of New York; New York NY 10031
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12
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Paul S, Taraphder S. Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II. J Phys Chem B 2015; 119:11403-15. [DOI: 10.1021/acs.jpcb.5b03655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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13
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Velez-Vega C, McKay DJJ, Aravamuthan V, Pearlstein R, Duca JS. Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH. J Chem Inf Model 2014; 54:3344-61. [PMID: 25405925 DOI: 10.1021/ci500571h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.
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Affiliation(s)
- Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
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14
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McCullagh M, Saunders MG, Voth GA. Unraveling the mystery of ATP hydrolysis in actin filaments. J Am Chem Soc 2014; 136:13053-8. [PMID: 25181471 PMCID: PMC4183606 DOI: 10.1021/ja507169f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Actin
performs its myriad cellular functions by the growth and
disassembly of its filamentous form. The hydrolysis of ATP in the
actin filament has been shown to modulate properties of the filament,
thus making it a pivotal regulator of the actin life cycle. Actin
has evolved to selectively hydrolyze ATP in the filamentous form,
F-actin, with an experimentally observed rate increase over the monomeric
form, G-actin, of 4.3 × 104. The cause of this dramatic
increase in rate is investigated in this paper using extensive QM/MM
simulations of both G- and F-actin. To compute the free energy of
hydrolysis in both systems, metadynamics is employed along two collective
variables chosen to describe the reaction coordinates of hydrolysis.
F-actin is modeled as a monomer with restraints applied to coarse-grained
variables enforced to keep it in a filament-like conformation. The
simulations reveal a barrier height reduction for ATP hydrolysis in
F-actin as compared to G-actin of 8 ± 1 kcal/mol, in good agreement
with the experimentally measured barrier height reduction of 7 ±
1 kcal/mol. The barrier height reduction is influenced by an enhanced
rotational diffusion of water in F-actin as compared to G-actin and
shorter water wires between Asp154 and the nucleophilic water in F-actin,
leading to more rapid proton transport.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States
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15
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Boone CD, Pinard M, McKenna R, Silverman D. Catalytic mechanism of α-class carbonic anhydrases: CO2 hydration and proton transfer. Subcell Biochem 2014; 75:31-52. [PMID: 24146373 DOI: 10.1007/978-94-007-7359-2_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The carbonic anhydrases (CAs; EC 4.2.1.1) are a family of metalloenzymes that catalyze the reversible hydration of carbon dioxide (CO2) and dehydration of bicarbonate (HCO3 (-)) in a two-step ping-pong mechanism: [Formula: see text] CAs are ubiquitous enzymes and are categorized into five distinct classes (α, β, γ, δ and ζ). The α-class is found primarily in vertebrates (and the only class of CA in mammals), β is observed in higher plants and some prokaryotes, γ is present only in archaebacteria whereas the δ and ζ classes have only been observed in diatoms.The focus of this chapter is on α-CAs as the structure-function relationship is best understood for this class, in particular for humans. The reader is referred to other reviews for an overview of the structure and catalytic mechanism of the other CA classes. The overall catalytic site structure and geometry of α-CAs are described in the first section of this chapter followed by the kinetic studies, binding of CO2, and the proton shuttle network.
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Affiliation(s)
- Christopher D Boone
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA,
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16
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Appraisal of sildenafil binding on the structure and promiscuous esterase activity of native and histidine-modified forms of carbonic anhydrase II. Biophys Chem 2013; 175-176:1-16. [DOI: 10.1016/j.bpc.2013.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 11/17/2022]
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17
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Mikulski R, West D, Sippel KH, Avvaru BS, Aggarwal M, Tu C, McKenna R, Silverman DN. Water networks in fast proton transfer during catalysis by human carbonic anhydrase II. Biochemistry 2012; 52:125-31. [PMID: 23215152 DOI: 10.1021/bi301099k] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Variants of human carbonic anhydrase II (HCA II) with amino acid replacements at residues in contact with water molecules in the active-site cavity have provided insights into the proton transfer rates in this protein environment. X-ray crystallography and (18)O exchange measured by membrane inlet mass spectrometry have been used to investigate structural and catalytic properties of variants of HCA II containing replacements of Tyr7 with Phe (Y7F) and Asn67 with Gln (N67Q). The rate constants for transfer of a proton from His64 to the zinc-bound hydroxide during catalysis were 4 and 9 μs(-1) for Y7F and Y7F/N67Q, respectively, compared with a value of 0.8 μs(-1) for wild-type HCA II. These higher values observed for Y7F and Y7F/N67Q HCA II could not be explained by differences in the values of the pK(a) of the proton donor (His64) and acceptor (zinc-bound hydroxide) or by the orientation of the side chain of the proton shuttle residue His64. They appeared to be associated with a reduced level of branching in the networks of hydrogen-bonded water molecules between proton shuttle residue His64 and the zinc-bound solvent molecule as observed in crystal structures at 1.5-1.6 Å resolution. Moreover, Y7F/N67Q HCA II is unique among the variants studied in having a direct, hydrogen-bonded chain of water molecules between the zinc-bound solvent and N(ε) of His64. This study provides the clearest example to date of the relevance of ordered water structure to rate constants for proton transfer in catalysis by carbonic anhydrase.
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Affiliation(s)
- Rose Mikulski
- Department of Pharmacology, University of Florida, Gainesville, FL 32610, USA
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18
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Bernadat G, Supuran CT, Iorga BI. Carbonic anhydrase binding site parameterization in OPLS-AA force field. Bioorg Med Chem 2012. [PMID: 23182217 DOI: 10.1016/j.bmc.2012.10.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH(-) forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes.
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Affiliation(s)
- Guillaume Bernadat
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Labex LERMIT, Centre de Recherche de Gif, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
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19
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Zimmerman S, Domsic JF, Tu C, Robbins AH, McKenna R, Silverman DN, Ferry JG. Role of Trp19 and Tyr200 in catalysis by the γ-class carbonic anhydrase from Methanosarcina thermophila. Arch Biochem Biophys 2012; 529:11-7. [PMID: 23111186 DOI: 10.1016/j.abb.2012.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 10/27/2022]
Abstract
Although widely distributed in Nature, only two γ class carbonic anhydrases are reported besides the founding member (Cam). Although roles for active-site residues important for catalysis have been identified in Cam, second shell residues have not been investigated. Two residues (Trp19 and Tyr200), positioned distant from the catalytic metal, were investigated by structural and kinetic analyses of replacement variants. Steady-state k(cat)/K(m) and k(cat) values decreased 3- to 10-fold for the Trp19 variants whereas the Y200 variants showed up to a 5-fold increase in k(cat). Rate constants for proton transfer decreased up to 10-fold for the Trp19 variants, and an increase of ~2-fold for Y200F. The pK(a) values for the proton donor decreased 1-2 pH units for Trp19 and Y200 variants. The variant structures revealed a loop composed of residues 62-64 that occupies a different conformation than previously reported. The results show that, although Trp19 and Y200 are non-essential, they contribute to an extended active-site structure distant from the catalytic metal that fine tunes catalysis. Trp19 is important for both CO(2)/bicarbonate interconversion, and the proton transfer step of catalysis.
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Affiliation(s)
- Sabrina Zimmerman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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20
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Schueler C, Becker HM, McKenna R, Deitmer JW. Transport activity of the sodium bicarbonate cotransporter NBCe1 is enhanced by different isoforms of carbonic anhydrase. PLoS One 2011; 6:e27167. [PMID: 22076132 PMCID: PMC3208603 DOI: 10.1371/journal.pone.0027167] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 10/11/2011] [Indexed: 12/31/2022] Open
Abstract
Transport metabolons have been discussed between carbonic anhydrase II (CAII) and several membrane transporters. We have now studied different CA isoforms, expressed in Xenopus oocytes alone and together with the electrogenic sodium bicarbonate cotransporter 1 (NBCe1), to determine their catalytic activity and their ability to enhance NBCe1 transport activity. pH measurements in intact oocytes indicated similar activity of CAI, CAII and CAIII, while in vitro CAIII had no measurable activity and CAI only 30% of the activity of CAII. All three CA isoforms increased transport activity of NBCe1, as measured by the transport current and the rate of intracellular sodium rise in oocytes. Two CAII mutants, altered in their intramolecular proton pathway, CAII-H64A and CAII-Y7F, showed significant catalytic activity and also enhanced NBCe1 transport activity. The effect of CAI, CAII, and CAII mutants on NBCe1 activity could be reversed by blocking CA activity with ethoxyzolamide (EZA, 10 µM), while the effect of the less EZA-sensitive CAIII was not reversed. Our results indicate that different CA isoforms and mutants, even if they show little enzymatic activity in vitro, may display significant catalytic activity in intact cells, and that the ability of CA to enhance NBCe1 transport appears to depend primarily on its catalytic activity.
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Affiliation(s)
- Christina Schueler
- Abteilung für Allgemeine Zoologie, FB Biologie, TU Kaiserslautern, Kaiserslautern, Germany.
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21
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Mikulski R, Domsic JF, Ling G, Tu C, Robbins AH, Silverman DN, McKenna R. Structure and catalysis by carbonic anhydrase II: role of active-site tryptophan 5. Arch Biochem Biophys 2011; 516:97-102. [PMID: 22001224 DOI: 10.1016/j.abb.2011.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/27/2011] [Accepted: 09/28/2011] [Indexed: 11/25/2022]
Abstract
The tryptophan residue Trp5, highly conserved in the α class of carbonic anhydrases including human carbonic anhydrase II (HCA II), is positioned at the entrance of the active site cavity and forms a π-stacking interaction with the imidazole ring of the proton shuttle His64 in its outward orientation. We have observed that replacement of Trp5 in HCA II caused significant structural changes, as determined by X-ray diffraction, in the conformation of 11 residues at the N-terminus and in the orientation of the proton shuttle residue His64. Most significantly, two variants W5H and W5E HCA II had His64 predominantly outward in orientation, while W5F and wild type showed the superposition of both outward and inward orientations in crystal structures. Although Trp5 influences the orientation of the proton shuttle His64, this orientation had no significant effect on the rate constant for proton transfer near 1μs(-1), determined by exchange of (18)O between CO(2) and water measured by mass spectrometry. The apparent values of the pK(a) of the zinc-bound water and the proton shuttle residue suggest that different active-site conformations influence the two stages of catalysis, the proton transfer stage and the interconversion of CO(2) and bicarbonate.
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Affiliation(s)
- Rose Mikulski
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, United States
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22
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Maupin CM, Castillo N, Taraphder S, Tu C, McKenna R, Silverman DN, Voth GA. Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II. J Am Chem Soc 2011; 133:6223-34. [PMID: 21452838 PMCID: PMC4120857 DOI: 10.1021/ja1097594] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.
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Affiliation(s)
- C. Mark Maupin
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Norberto Castillo
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Srabani Taraphder
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Chemistry, James Frank Institute, and Computation Institute, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637
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23
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Li H, Chen H, Steinbronn C, Wu B, Beitz E, Zeuthen T, Voth GA. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J Mol Biol 2011; 407:607-20. [DOI: 10.1016/j.jmb.2011.01.036] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 01/14/2011] [Accepted: 01/15/2011] [Indexed: 11/30/2022]
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24
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Kinetic and crystallographic studies of the role of tyrosine 7 in the active site of human carbonic anhydrase II. Arch Biochem Biophys 2010; 506:181-7. [PMID: 21145876 DOI: 10.1016/j.abb.2010.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 11/21/2022]
Abstract
The rate limiting step in catalysis of bicarbonate dehydration by human carbonic anhydrase II (HCA II) is an intramolecular proton transfer from His64 to the zinc-bound hydroxide. We have examined the role of Tyr7 using site-specific mutagenesis and measuring catalysis by the ¹⁸O exchange method using membrane inlet mass spectrometry. The side chain of Tyr7 in HCA II extends into the active-site cavity about 7 Å from the catalytic zinc atom. Replacement of Tyr7 with eight other amino acids had no effect on the interconversion of bicarbonate and CO₂, but in some cases caused enhancements in the rate constant of proton transfer by nearly 10-fold. The variant Y7I HCA II enhanced intramolecular proton transfer approximately twofold; its structure was determined by X-ray crystallography at 1.5 Å resolution. No changes were observed in the ordered solvent structure in the active-site cavity or in the conformation of the side chain of the proton shuttle His64. However, the first 11 residues of the amino-terminal chain in Y7I HCA II assumed an alternate conformation compared with the wild type. Differential scanning calorimetry showed variants at position 7 had a melting temperature approximately 8 °C lower than that of the wild type.
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25
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Hakkim V, Subramanian V. Role of Second Coordination Sphere Amino Acid Residues on the Proton Transfer Mechanism of Human Carbonic Anhydrase II (HCA II). J Phys Chem A 2010; 114:7952-9. [DOI: 10.1021/jp101515h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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26
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Roy A, Taraphder S. Transition path sampling study of the conformational fluctuation of His-64 in human carbonic anhydrase II. J Phys Chem B 2009; 113:12555-64. [PMID: 19685901 DOI: 10.1021/jp9010982] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here a transition path sampling study of the conformational fluctuation of His-64 that is known to be important in the enzymatic catalysis of human carbonic anhydrase II. The dynamical transition between experimentally detected conformations of His-64 could not be observed using classical molecular dynamics trajectories extended to 3.5 ns, indicating the transition to be rare on the time scale of molecular dynamics. Using the transition path sampling method, an ensemble of transition paths between these two conformers has been generated and analyzed in detail to identify the mechanism of coupling of His-64 to its neighboring residues during the conformational transition. It is found that both Asn-62 and Tyr-7 may contribute toward retaining the His-64 residue in its outward conformation. Trp-5, on the other hand, shows marked motions at the transition state. The number of water molecules inside a part of the active site cavity and the corresponding cavity volume are also found to vary coupled to the His-64 conformational dynamics.
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Affiliation(s)
- Arijit Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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27
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Prakash M, Subramanian V, Gadre SR. Stepwise Hydration of Protonated Carbonic Acid: A Theoretical Study. J Phys Chem A 2009; 113:12260-75. [DOI: 10.1021/jp904576u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Prakash
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - Shridhar R. Gadre
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
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28
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Maupin CM, Zheng J, Tu C, McKenna R, Silverman DN, Voth GA. Effect of active-site mutation at Asn67 on the proton transfer mechanism of human carbonic anhydrase II. Biochemistry 2009; 48:7996-8005. [PMID: 19634894 DOI: 10.1021/bi901037u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rate-limiting proton transfer (PT) event in the site-specific mutant N67L of human carbonic anhydrase II (HCA II) has been examined by kinetic, X-ray, and simulation approaches. The X-ray crystallography studies, which were previously reported, and molecular dynamics (MD) simulations indicate that the proton shuttling residue, His64, predominantly resides in the outward orientation with a significant disruption of the ordered water in the active site for the dehydration pathway. While disorder is seen in the active-site water, water cluster analysis indicates that the N67L mutant may form water clusters similar to those seen in the wild-type (WT). For the hydration pathway of the enzyme, the active site water cluster analysis reveals an inability of the N67L mutant to stabilize water clusters when His64 is in the inward orientation, thereby favoring PT when His64 is in the outward orientation. The preference of the N67L mutant to carry out the PT when His64 is in the outward orientation for both the hydration and dehydration pathway is reasoned to be the main cause of the observed reduction in the overall rate. To probe the mechanism of PT, solvent H/D kinetic isotope effects (KIEs) were experimentally studied with catalysis measured by the exchange of (18)O between CO(2) and water. The values obtained from the KIEs were determined as a function of the deuterium content of solvent, using the proton inventory method. No differences were detected in the overarching mechanism of PT between WT and N67L HCA II, despite changes in the active-site water structure and/or the orientation of His64.
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Affiliation(s)
- C Mark Maupin
- Center for Biophysical Modeling and Simulation and the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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29
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Proton transport in carbonic anhydrase: Insights from molecular simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:332-41. [PMID: 19765680 DOI: 10.1016/j.bbapap.2009.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 09/03/2009] [Accepted: 09/05/2009] [Indexed: 12/14/2022]
Abstract
This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.
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30
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Maupin CM, McKenna R, Silverman DN, Voth GA. Elucidation of the proton transport mechanism in human carbonic anhydrase II. J Am Chem Soc 2009; 131:7598-608. [PMID: 19438233 PMCID: PMC2774804 DOI: 10.1021/ja8091938] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human carbonic anhydrase II (HCA II) is one of the fastest known enzymes, which utilizes a rate-limiting proton transport (PT) step in its enzymatic reaction. To evaluate the PT event at an atomistic level, the multistate empirical valence bond (MS-EVB) method has been utilized in this work. It is observed that the PT event in HCA II exploits a transient active site water cluster to transport the excess proton between the catalytic zinc-bound water/hydroxide and the proton shuttling residue, His64. This PT event is found to be dependent on the enzyme's ability to form and stabilize the active site water cluster in addition to its ability to orient His64 in a favorable conformation. Evaluation of the PT free energy barrier for different orientations of His64 reveals this residue's vital role as a proton transporter and elucidates its direct effect on the barrier to PT through the active site water. It is suggested that the rate-limiting step oscillates between the active site water PT event to His64 and the de/protonation of His64 depending on the exogenous buffer concentration and the orientation of His64. In the absence of a PT acceptor/donor at position 64, it is found that the excess proton will utilize one of three distinct paths to enter/leave the active site. This latter result not only allows for an increased understanding of how enzymes capitalize on the protein/solvent interface to guide excess protons to/from areas of interest, it also provides valuable insight into the chemical rescue experiments on HCA II mutants.
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Affiliation(s)
- C. Mark Maupin
- Center for Biophysical Modeling and Simulation and Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
| | - David N. Silverman
- Department of Biochemistry and Molecular Biology, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
- Department of Pharmacology and Therapeutics, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112
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31
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Chen X, Wu G, Wu B, Duncombe BJ, Stace AJ. Enhanced Acidity of Zn2+ in the Presence of Small Numbers of Water Molecules. J Phys Chem B 2008; 112:15525-8. [DOI: 10.1021/jp8086804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xiaojing Chen
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Guohua Wu
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Bohan Wu
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Bridgette J. Duncombe
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Anthony J. Stace
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
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32
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Zheng J, Avvaru BS, Tu C, McKenna R, Silverman DN. Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II. Biochemistry 2008; 47:12028-36. [PMID: 18942852 DOI: 10.1021/bi801473w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis by the zinc metalloenzyme human carbonic anhydrase II (HCA II) is limited in maximal velocity by proton transfer between His64 and the zinc-bound solvent molecule. Asn62 extends into the active site cavity of HCA II adjacent to His64 and has been shown to be one of several hydrophilic residues participating in a hydrogen-bonded solvent network within the active site. We compared several site-specific mutants of HCA II with replacements at position 62 (Ala, Val, Leu, Thr, and Asp). The efficiency of catalysis in the hydration of CO 2 for the resulting mutants has been characterized by (18)O exchange, and the structures of the mutants have been determined by X-ray crystallography to 1.5-1.7 A resolution. Each of these mutants maintained the ordered water structure observed by X-ray crystallography in the active site cavity of wild-type HCA II; hence, this water structure was not a variable in comparing with wild type the activities of mutants at residue 62. Crystal structures of wild-type and N62T HCA II showed both an inward and outward orientation of the side chain of His64; however, other mutants in this study showed predominantly inward (N62A, N62V, N62L) or predominantly outward (N62D) orientations of His64. A significant role of Asn62 in HCA II is to permit two conformations of the side chain of His64, the inward and outward, that contributes to maximal efficiency of proton transfer between the active site and solution. The site-specific mutant N62D had a mainly outward orientation of His64, yet the difference in p K a between the proton donor His64 and zinc-bound hydroxide was near zero, as in wild-type HCA II. The rate of proton transfer in catalysis by N62D HCA II was 5% that of wild type, showing that His64 mainly in the outward orientation is associated with inefficient proton transfer compared with His64 in wild type which shows both inward and outward orientations. These results emphasize the roles of the residues of the hydrophilic side of the active site cavity in maintaining efficient catalysis by carbonic anhydrase.
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Affiliation(s)
- Jiayin Zheng
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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