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Dhanabalan K, Cheng Y, Thach T, Subramanian R. Many locks to one key: N-acetylneuraminic acid binding to proteins. IUCRJ 2024; 11:664-674. [PMID: 38965900 PMCID: PMC11364026 DOI: 10.1107/s2052252524005360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell-cell interactions, development, immune response, oncogenesis and host-pathogen interactions. This review focuses on the β-anomeric form of N-acetylneuraminic acid (Neu5Ac), particularly its binding affinity towards various proteins, as elucidated by solved protein structures. Specifically, we delve into the binding mechanisms of Neu5Ac to proteins involved in sequestering and transporting Neu5Ac in Gram-negative bacteria, with implications for drug design targeting these proteins as antimicrobial agents. Unlike the initial assumptions, structural analyses revealed significant variability in the Neu5Ac binding pockets among proteins, indicating diverse evolutionary origins and binding modes. By comparing these findings with existing structures from other systems, we can effectively highlight the intricate relationship between protein structure and Neu5Ac recognition, emphasizing the need for tailored drug design strategies to inhibit Neu5Ac-binding proteins across bacterial species.
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Affiliation(s)
| | - YiYang Cheng
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Trung Thach
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Ramaswamy Subramanian
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
- Weldon School of Biomedical EngineeringPurdue UniversityWest LafayetteIN47907USA
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2
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Kumar JP, Rao H, Nayak V, Ramaswamy S. Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum. Acta Crystallogr F Struct Biol Commun 2018; 74:725-732. [PMID: 30387778 PMCID: PMC6213981 DOI: 10.1107/s2053230x18012992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/13/2018] [Indexed: 12/18/2022] Open
Abstract
N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatum is a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterial N-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure-function relationship, the steady-state kinetic parameters of the enzyme are also reported.
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Affiliation(s)
- Jay Prakash Kumar
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
- School of Life Science, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, Karnataka 560 065, India
| | - Harshvardhan Rao
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Vinod Nayak
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - S. Ramaswamy
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
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3
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Campeotto I, Lebedev A, Schreurs AMM, Kroon-Batenburg LMJ, Lowe E, Phillips SEV, Murshudov GN, Pearson AR. Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools. Sci Rep 2018; 8:14876. [PMID: 30291262 PMCID: PMC6173773 DOI: 10.1038/s41598-018-32962-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Twinning is a crystal growth anomaly, which has posed a challenge in macromolecular crystallography (MX) since the earliest days. Many approaches have been used to treat twinned data in order to extract structural information. However, in most cases it is usually simpler to rescreen for new crystallization conditions that yield an untwinned crystal form or, if possible, collect data from non-twinned parts of the crystal. Here, we report 11 structures of engineered variants of the E. coli enzyme N-acetyl-neuraminic lyase which, despite twinning and incommensurate modulation, have been successfully indexed, solved and deposited. These structures span a resolution range of 1.45-2.30 Å, which is unusually high for datasets presenting such lattice disorders in MX and therefore these data provide an excellent test set for improving and challenging MX data processing programs.
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Affiliation(s)
- Ivan Campeotto
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK. .,Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK.
| | - Andrey Lebedev
- Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK
| | - Antoine M M Schreurs
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Loes M J Kroon-Batenburg
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Edward Lowe
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK
| | - Simon E V Phillips
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK
| | - Garib N Murshudov
- Structural Studies Division, MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Hamburg Centre for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
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4
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Daniels AD, Campeotto I, van der Kamp MW, Bolt AH, Trinh CH, Phillips SEV, Pearson A, Nelson A, Mulholland AJ, Berry A. Reaction mechanism of N-acetylneuraminic acid lyase revealed by a combination of crystallography, QM/MM simulation, and mutagenesis. ACS Chem Biol 2014; 9:1025-32. [PMID: 24521460 PMCID: PMC4004234 DOI: 10.1021/cb500067z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N-Acetylneuraminic acid lyase (NAL) is a Class I aldolase that catalyzes the reversible condensation of pyruvate with N-acetyl-d-mannosamine (ManNAc) to yield the sialic acid N-acetylneuraminic acid (Neu5Ac). Aldolases are finding increasing use as biocatalysts for the stereospecific synthesis of complex molecules. Incomplete understanding of the mechanism of catalysis in aldolases, however, can hamper development of new enzyme activities and specificities, including control over newly generated stereocenters. In the case of NAL, it is clear that the enzyme catalyzes a Bi-Uni ordered condensation reaction in which pyruvate binds first to the enzyme to form a catalytically important Schiff base. The identity of the residues required for catalysis of the condensation step and the nature of the transition state for this reaction, however, have been a matter of conjecture. In order to address, this we crystallized a Y137A variant of the E. coli NAL in the presence of Neu5Ac. The three-dimensional structure shows a full length sialic acid bound in the active site of subunits A, B, and D, while in subunit C, discontinuous electron density reveals the positions of enzyme-bound pyruvate and ManNAc. These 'snapshot' structures, representative of intermediates in the enzyme catalytic cycle, provided an ideal starting point for QM/MM modeling of the enzymic reaction of carbon-carbon bond formation. This revealed that Tyr137 acts as the proton donor to the aldehyde oxygen of ManNAc during the reaction, the activation barrier is dominated by carbon-carbon bond formation, and proton transfer from Tyr137 is required to obtain a stable Neu5Ac-Lys165 Schiff base complex. The results also suggested that a triad of residues, Tyr137, Ser47, and Tyr110 from a neighboring subunit, are required to correctly position Tyr137 for its function, and this was confirmed by site-directed mutagenesis. This understanding of the mechanism and geometry of the transition states along the C-C bond-forming pathway will allow further development of these enzymes for stereospecific synthesis of new enzyme products.
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Affiliation(s)
- Adam D. Daniels
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Ivan Campeotto
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Amanda H. Bolt
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Chi H. Trinh
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Simon E. V. Phillips
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Arwen
R. Pearson
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Adam Nelson
- Astbury Centre for Structural Molecular
Biology and School of Chemistry, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.,E-mail:
| | - Alan Berry
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.,E-mail:
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5
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Huynh N, Aye A, Li Y, Yu H, Cao H, Tiwari VK, Shin DW, Chen X, Fisher AJ. Structural basis for substrate specificity and mechanism of N-acetyl-D-neuraminic acid lyase from Pasteurella multocida. Biochemistry 2013; 52:8570-9. [PMID: 24152047 DOI: 10.1021/bi4011754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac, the most common form of sialic acid) to form pyruvate and N-acetyl-d-mannosamine. Although equilibrium favors sialic acid cleavage, these enzymes can be used for high-yield chemoenzymatic synthesis of structurally diverse sialic acids in the presence of excess pyruvate. Engineering these enzymes to synthesize structurally modified natural sialic acids and their non-natural derivatives holds promise in creating novel therapeutic agents. Atomic-resolution structures of these enzymes will greatly assist in guiding mutagenic and modeling studies to engineer enzymes with altered substrate specificity. We report here the crystal structures of wild-type Pasteurella multocida N-acetylneuraminate lyase and its K164A mutant. Like other bacterial lyases, it assembles into a homotetramer with each monomer folding into a classic (β/α)₈ TIM barrel. Two wild-type structures were determined, in the absence of substrates, and trapped in a Schiff base intermediate between Lys164 and pyruvate, respectively. Three structures of the K164A variant were determined: one in the absence of substrates and two binary complexes with N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Both sialic acids bind to the active site in the open-chain ketone form of the monosaccharide. The structures reveal that every hydroxyl group of the linear sugars makes hydrogen bond interactions with the enzyme, and the residues that determine specificity were identified. Additionally, the structures provide some clues for explaining the natural discrimination of sialic acid substrates between the P. multocida and Escherichia coli NALs.
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Affiliation(s)
- Nhung Huynh
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Cell Biology Graduate Program, University of California , One Shields Avenue, Davis, California 95616, United States
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6
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Timms N, Windle CL, Polyakova A, Ault JR, Trinh CH, Pearson AR, Nelson A, Berry A. Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy. Chembiochem 2013; 14:474-81. [PMID: 23418011 PMCID: PMC3792637 DOI: 10.1002/cbic.201200714] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/29/2022]
Abstract
Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E. coli. The protein, purified in high yield, has all the properties expected of a class I NAL. The S. aureus NAL which contains no natural cysteine residues was subjected to site-directed mutagenesis to introduce a cysteine in place of Lys165 in the enzyme active site. Subsequently chemical mutagenesis completely converted the cysteine into γ-thialysine through dehydroalanine (Dha) as demonstrated by ESI-MS. Initial kinetic characterisation showed that the protein containing γ-thialysine regained 17 % of the wild-type activity. To understand the reason for this lower activity, we solved X-ray crystal structures of the wild-type S. aureus NAL, both in the absence of, and in complex with, pyruvate. We also report the structures of the K165C variant, and the K165-γ-thialysine enzyme in the presence, or absence, of pyruvate. These structures reveal that γ-thialysine in NAL is an excellent structural mimic of lysine. Measurement of the pH-activity profile of the thialysine modified enzyme revealed that its pH optimum is shifted from 7.4 to 6.8. At its optimum pH, the thialysine-containing enzyme showed almost 30 % of the activity of the wild-type enzyme at its pH optimum. The lowered activity and altered pH profile of the unnatural amino acid-containing enzyme can be rationalised by imbalances of the ionisation states of residues within the active site when the pK(a) of the residue at position 165 is perturbed by replacement with γ-thialysine. The results reveal the utility of chemical mutagenesis for the modification of enzyme active sites and the exquisite sensitivity of catalysis to the local structural and electrostatic environment in NAL.
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Affiliation(s)
- Nicole Timms
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Anna Polyakova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Chemistry, University of LeedsLeeds, LS2 9JT (UK)
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
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Owen RL, Yorke BA, Pearson AR. X-ray-excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:505-10. [PMID: 22525748 PMCID: PMC3370260 DOI: 10.1107/s0907444912002946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/23/2012] [Indexed: 11/10/2022]
Abstract
During X-ray irradiation protein crystals radiate energy in the form of small amounts of visible light. This is known as X-ray-excited optical luminescence (XEOL). The XEOL of several proteins and their constituent amino acids has been characterized using the microspectrophotometers at the Swiss Light Source and Diamond Light Source. XEOL arises primarily from aromatic amino acids, but the effects of local environment and quenching within a crystal mean that the XEOL spectrum of a crystal is not the simple sum of the spectra of its constituent parts. Upon repeated exposure to X-rays XEOL spectra decay non-uniformly, suggesting that XEOL is sensitive to site-specific radiation damage. However, rates of XEOL decay were found not to correlate to decays in diffracting power, making XEOL of limited use as a metric for radiation damage to protein crystals.
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Affiliation(s)
- Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Briony A. Yorke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Arwen R. Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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Molecular characterization of a novel N-acetylneuraminate lyase from Lactobacillus plantarum WCFS1. Appl Environ Microbiol 2011; 77:2471-8. [PMID: 21317263 DOI: 10.1128/aem.02927-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac) to form pyruvate and N-acetyl-d-mannosamine (ManNAc). In nature, N-acetylneuraminate lyase occurs mainly in pathogens. However, this paper describes how an N-acetylneuraminate lyase was cloned from the human gut commensal Lactobacillus plantarum WCFS1 (LpNAL), overexpressed, purified, and characterized for the first time. This novel enzyme, which reaches a high expression level (215 mg liter(-1) culture), shows similar catalytic efficiency to the best NALs previously described. This homotetrameric enzyme (132 kDa) also shows high stability and activity at alkaline pH (pH > 9) and good temperature stability (60 to 70°C), this last feature being further improved by the presence of stabilizing additives. These characteristics make LpNAL a promising biocatalyst. When its sequence was compared with that of other, related (real and putative) NALs described in the databases, it was seen that NAL enzymes could be divided into four structural groups and three subgroups. The relation of these subgroups with human and other mammalian NALs is also discussed.
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Campeotto I, Bolt AH, Harman TA, Dennis C, Trinh CH, Phillips SEV, Nelson A, Pearson AR, Berry A. Structural insights into substrate specificity in variants of N-acetylneuraminic Acid lyase produced by directed evolution. J Mol Biol 2010; 404:56-69. [PMID: 20826162 PMCID: PMC3014015 DOI: 10.1016/j.jmb.2010.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 11/18/2022]
Abstract
The substrate specificity of Escherichia coli N-acetylneuraminic acid lyase was previously switched from the natural condensation of pyruvate with N-acetylmannosamine, yielding N-acetylneuraminic acid, to the aldol condensation generating N-alkylcarboxamide analogues of N-acetylneuraminic acid. This was achieved by a single mutation of Glu192 to Asn. In order to analyze the structural changes involved and to more fully understand the basis of this switch in specificity, we have isolated all 20 variants of the enzyme at position 192 and determined the activities with a range of substrates. We have also determined five high-resolution crystal structures: the structures of wild-type E. coli N-acetylneuraminic acid lyase in the presence and in the absence of pyruvate, the structures of the E192N variant in the presence and in the absence of pyruvate, and the structure of the E192N variant in the presence of pyruvate and a competitive inhibitor (2R,3R)-2,3,4-trihydroxy-N,N-dipropylbutanamide. All structures were solved in space group P21 at resolutions ranging from 1.65 Å to 2.2 Å. A comparison of these structures, in combination with the specificity profiles of the variants, reveals subtle differences that explain the details of the specificity changes. This work demonstrates the subtleties of enzyme–substrate interactions and the importance of determining the structures of enzymes produced by directed evolution, where the specificity determinants may change from one substrate to another.
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Affiliation(s)
- Ivan Campeotto
- Astbury Center for Structural Molecular Biology, Garstang Building, University of Leeds, Leeds LS2 9JT, UK
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