1
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Mydy LS, Hoppe RW, Hagemann TM, Schwabacher AW, Silvaggi NR. Mechanistic Studies of the Streptomyces bingchenggensis Aldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry 2019; 58:4136-4147. [PMID: 31524380 DOI: 10.1021/acs.biochem.9b00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The acetoacetate decarboxylase-like superfamily (ADCSF) is a little-explored group of enzymes that may contain new biocatalysts. The low level of sequence identity (∼20%) between many ADCSF enzymes and the confirmed acetoacetate decarboxylases led us to investigate the degree of diversity in the reaction and substrate specificity of ADCSF enzymes. We have previously reported on Sbi00515, which belongs to Family V of the ADCSF and functions as an aldolase-dehydratase. Here, we more thoroughly characterize the substrate specificity of Sbi00515 and find that aromatic, unsaturated aldehydes yield lower KM and higher kcat values compared to those of other small electrophilic substrates in the condensation reaction. The roles of several active site residues were explored by site-directed mutagenesis and steady state kinetics. The lysine-glutamate catalytic dyad, conserved throughout the ADCSF, is required for catalysis. Tyrosine 252, which is unique to Sbi00515, is hypothesized to orient the incoming aldehyde in the condensation reaction. Transient state kinetics and an intermediate-bound crystal structure aid in completing a proposed mechanism for Sbi00515.
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Affiliation(s)
- Lisa S Mydy
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Robert W Hoppe
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Trevor M Hagemann
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Alan W Schwabacher
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
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2
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Nigro MJ, Palazzolo MA, Colasurdo D, Iribarren AM, Lewkowicz ES. N-Acetylneuraminic acid aldolase-catalyzed synthesis of acyclic nucleoside analogues carrying a 4-hydroxy-2-oxoacid moiety. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2018.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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3
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Desbois S, John UP, Perugini MA. Dihydrodipicolinate synthase is absent in fungi. Biochimie 2018; 152:73-84. [PMID: 29959064 DOI: 10.1016/j.biochi.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
The class I aldolase dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step of the diaminopimelate (DAP) lysine biosynthesis pathway in bacteria, archaea and plants. Despite the existence, in databases, of numerous fungal sequences annotated as DHDPS, its presence in fungi has been the subject of contradictory claims. We report the characterization of DHDPS candidates from fungi. Firstly, the putative DHDPS from Coccidioides immitis (PDB ID: 3QFE) was shown to have negligible enzyme activity. Sequence analysis of 3QFE showed that three out of the seven amino acid residues critical for DHDPS activity are absent; however, exact matches to catalytic residues from two other class I aldolases, 2-keto-3-deoxygluconate aldolase (KDGA), and 4-hydroxy-2-oxoglutarate aldolase (HOGA), were identified. The presence of both KDGA and HOGA activity in 3QFE was confirmed in vitro using enzyme assays, the first report of such dual activity. Subsequent analyses of all publically available fungal sequences revealed that no entry contains all seven residues important for DHDPS function. The candidate with the highest number of identities (6 of 7), KIW77228 from Fonsecaea pedrosoi, was shown to have trace DHDPS activity in vitro, partially restored by substitution of the seventh critical residue, and to be incapable of complementing DHDPS-deficient E. coli cells. Combined with the presence of all seven sequences for the alternative α-aminoadipate (AAA) lysine biosynthesis pathway in C. immitis and F. pedrosoi, we believe that DHDPS and the DAP pathway are absent in fungi, and further, that robust informed methods for annotating genes need to be implemented.
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Affiliation(s)
- Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia
| | - Ulrik P John
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia; Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe University, VIC, 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia.
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4
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Mydy LS, Hoppe RW, Ochsenwald JM, Berndt RT, Severin GB, Schwabacher AW, Silvaggi NR. Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold. Biochemistry 2015; 54:3978-88. [PMID: 26039798 DOI: 10.1021/acs.biochem.5b00483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The acetoacetate decarboxylase-like superfamily (ADCSF) is a group of ~4000 enzymes that, until recently, was thought to be homogeneous in terms of the reaction catalyzed. Bioinformatic analysis shows that the ADCSF consists of up to seven families that differ primarily in their active site architectures. The soil-dwelling bacterium Streptomyces bingchenggensis BCW-1 produces an ADCSF enzyme of unknown function that shares a low level of sequence identity (~20%) with known acetoacetate decarboxylases (ADCs). This enzyme, Sbi00515, belongs to the MppR-like family of the ADCSF because of its similarity to the mannopeptimycin biosynthetic protein MppR from Streptomyces hygroscopicus. Herein, we present steady state kinetic data that show Sbi00515 does not catalyze the decarboxylation of any α- or β-keto acid tested. Rather, we show that Sbi00515 catalyzes the condensation of pyruvate with a number of aldehydes, followed by dehydration of the presumed aldol intermediate. Thus, Sbi00515 is a pyruvate aldolase-dehydratase and not an acetoacetate decarboxylase. We have also determined the X-ray crystal structures of Sbi00515 in complexes with formate and pyruvate. The structures show that the overall fold of Sbi00515 is nearly identical to those of both ADC and MppR. The pyruvate complex is trapped as the Schiff base, providing evidence that the Schiff base chemistry that drives the acetoacetate decarboxylases has been co-opted to perform a new function, and that this core chemistry may be conserved across the superfamily. The structures also suggest possible catalytic roles for several active site residues.
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Affiliation(s)
- Lisa S Mydy
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Robert W Hoppe
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Jenna M Ochsenwald
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Robert T Berndt
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Geoffrey B Severin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Alan W Schwabacher
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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5
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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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6
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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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7
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Raimondi W, Bonne D, Rodriguez J. Asymmetric transformations involving 1,2-dicarbonyl compounds as pronucleophiles. Chem Commun (Camb) 2012; 48:6763-75. [PMID: 22655291 DOI: 10.1039/c2cc30691c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article concentrates on the versatile nucleophilic reactivity of 1,2-dicarbonyl compounds in various asymmetric transformations. Although underexploited in comparison to their 1,3-dicarbonyl homologues, the presence of adjacent multiple reactive centres allows the selection of specific activation modes for enhancing the reactivity of these important ambident pronucleophiles. They can be involved in selective formation of C-C, C-O or C-N bonds leading to various optically active targets in the acyclic and cyclic series including three- to seven-membered ring systems. Recent contributions in the field of biochemical, organometallic and organic catalytic transformations as well as some relevant stoichiometric approaches are discussed from synthetic and mechanistic point of views highlighting some important stereochemical issues.
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Affiliation(s)
- Wilfried Raimondi
- Aix-Marseille Université, UMR CNRS 7313 iSm2, Centre Saint Jérôme, service 531, 13397 Marseille, France
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8
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Baker P, Carere J, Seah SYK. Probing the Molecular Basis of Substrate Specificity, Stereospecificity, and Catalysis in the Class II Pyruvate Aldolase, BphI. Biochemistry 2011; 50:3559-69. [DOI: 10.1021/bi101947g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jason Carere
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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9
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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10
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Chou CY, Ko TP, Wu KJ, Huang KF, Lin CH, Wong CH, Wang AHJ. Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val-251. J Biol Chem 2011; 286:14057-64. [PMID: 21270125 DOI: 10.1074/jbc.m110.179465] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In a recent directed-evolution study, Escherichia coli D-sialic acid aldolase was converted by introducing eight point mutations into a new enzyme with relaxed specificity, denoted RS-aldolase (also known formerly as L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase), which showed a preferred selectivity toward L-KDO. To investigate the underlying molecular basis, we determined the crystal structures of D-sialic acid aldolase and RS-aldolase. All mutations are away from the catalytic center, except for V251I, which is near the opening of the (α/β)(8)-barrel and proximal to the Schiff base-forming Lys-165. The change of specificity from D-sialic acid to RS-aldolase can be attributed mainly to the V251I substitution, which creates a narrower sugar-binding pocket, but without altering the chirality in the reaction center. The crystal structures of D-sialic acid aldolase·l-arabinose and RS-aldolase·hydroxypyruvate complexes and five mutants (V251I, V251L, V251R, V251W, and V251I/V265I) of the D-sialic acid aldolase were also determined, revealing the location of substrate molecules and how the contour of the active site pocket was shaped. Interestingly, by mutating Val251 alone, the enzyme can accept substrates of varying size in the aldolase reactions and still retain stereoselectivity. The engineered D-sialic acid aldolase may find applications in synthesizing unnatural sugars of C(6) to C(10) for the design of antagonists and inhibitors of glycoenzymes.
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Affiliation(s)
- Chien-Yu Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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11
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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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12
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Pauluhn A, Ahmed H, Lorentzen E, Buchinger S, Schomburg D, Siebers B, Pohl E. Crystal structure and stereochemical studies of KD(P)G aldolase fromThermoproteus tenax. Proteins 2008; 72:35-43. [DOI: 10.1002/prot.21890] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Mechanism of the Class I KDPG aldolase. Bioorg Med Chem 2006; 14:3002-10. [PMID: 16403639 PMCID: PMC3315828 DOI: 10.1016/j.bmc.2005.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 12/04/2005] [Accepted: 12/09/2005] [Indexed: 11/17/2022]
Abstract
In vivo, 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible, stereospecific retro-aldol cleavage of KDPG to pyruvate and D-glyceraldehyde-3-phosphate. The enzyme is a lysine-dependent (Class I) aldolase that functions through the intermediacy of a Schiff base. Here, we propose a mechanism for this enzyme based on crystallographic studies of wild-type and mutant aldolases. The three dimensional structure of KDPG aldolase from the thermophile Thermotoga maritima was determined to 1.9A. The structure is the standard alpha/beta barrel observed for all Class I aldolases. At the active site Lys we observe clear density for a pyruvate Schiff base. Density for a sulfate ion bound in a conserved cluster of residues close to the Schiff base is also observed. We have also determined the structure of a mutant of Escherichia coli KDPG aldolase in which the proposed general acid/base catalyst has been removed (E45N). One subunit of the trimer contains density suggesting a trapped pyruvate carbinolamine intermediate. All three subunits contain a phosphate ion bound in a location effectively identical to that of the sulfate ion bound in the T. maritima enzyme. The sulfate and phosphate ions experimentally locate the putative phosphate binding site of the aldolase and, together with the position of the bound pyruvate, facilitate construction of a model for the full-length KDPG substrate complex. The model requires only minimal positional adjustments of the experimentally determined covalent intermediate and bound anion to accommodate full-length substrate. The model identifies the key catalytic residues of the protein and suggests important roles for two observable water molecules. The first water molecule remains bound to the enzyme during the entire catalytic cycle, shuttling protons between the catalytic glutamate and the substrate. The second water molecule arises from dehydration of the carbinolamine and serves as the nucleophilic water during hydrolysis of the enzyme-product Schiff base. The second water molecule may also mediate the base-catalyzed enolization required to form the carbon nucleophile, again bridging to the catalytic glutamate. Many aspects of this mechanism are observed in other Class I aldolases and suggest a mechanistically and, perhaps, evolutionarily related family of aldolases distinct from the N-acetylneuraminate lyase (NAL) family.
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Affiliation(s)
- Matthew J. Walters
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Andrew R. McEwan
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA
| | - Eric J. Toone
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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14
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Williams GJ, Woodhall T, Nelson A, Berry A. Structure-guided saturation mutagenesis of N-acetylneuraminic acid lyase for the synthesis of sialic acid mimetics. Protein Eng Des Sel 2005; 18:239-46. [PMID: 15897188 DOI: 10.1093/protein/gzi027] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analogues of N-acetylneuraminic acid (sialic acid, NANA, Neu5Ac), including 6-dipropylcarboxamides, have been found to be selective and potent inhibitors of influenza sialidases. Sialic acid analogues are, however, difficult to synthesize by traditional chemical methods and the enzyme N-acetylneuraminic acid lyase (NAL) has previously been used for the synthesis of a number of analogues. The activity of this enzyme towards 6-dipropylcarboxamides is, however, low. Here, we used structure-guided saturation mutagenesis to produce variants of NAL with improved activity and specificity towards 6-dipropylcarboxamides. Three residues were targeted for mutagenesis, Asp191, Glu192 and Ser208. Only substitution at position 192 produced significant improvements in activity towards the dipropylamide. One variant, E192N, showed a 49-fold improvement in catalytic efficiency towards the target analogue and a 690-fold shift in specificity from sialic acid towards the analogue. These engineering efforts provide a scaffold for the further tailoring of NAL for the synthesis of sialic acid mimetics.
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Affiliation(s)
- G J Williams
- Astbury Centre for Structural Biology, School of Biochemistry, University of Leeds, Leeds LS2 9JT, UK
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15
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Theodossis A, Walden H, Westwick EJ, Connaris H, Lamble HJ, Hough DW, Danson MJ, Taylor GL. The Structural Basis for Substrate Promiscuity in 2-Keto-3-deoxygluconate Aldolase from the Entner-Doudoroff Pathway in Sulfolobus solfataricus. J Biol Chem 2004; 279:43886-92. [PMID: 15265860 DOI: 10.1074/jbc.m407702200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic Archaea Sulfolobus solfataricus grows optimally above 80 degrees C and metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to D-2-keto-3-deoxygluconate (KDG). KDG aldolase (KDGA) then catalyzes the cleavage of KDG to D-glyceraldehyde and pyruvate. It has recently been shown that all the enzymes of this pathway exhibit a catalytic promiscuity that also enables them to be used for the metabolism of galactose. This phenomenon, known as metabolic pathway promiscuity, depends crucially on the ability of KDGA to cleave KDG and D-2-keto-3-deoxygalactonate (KDGal), in both cases producing pyruvate and D-glyceraldehyde. In turn, the aldolase exhibits a remarkable lack of stereoselectivity in the condensation reaction of pyruvate and D-glyceraldehyde, forming a mixture of KDG and KDGal. We now report the structure of KDGA, determined by multiwavelength anomalous diffraction phasing, and confirm that it is a member of the tetrameric N-acetylneuraminate lyase superfamily of Schiff base-forming aldolases. Furthermore, by soaking crystals of the aldolase at more than 80 degrees C below its temperature activity optimum, we have been able to trap Schiff base complexes of the natural substrates pyruvate, KDG, KDGal, and pyruvate plus D-glyceraldehyde, which have allowed rationalization of the structural basis of promiscuous substrate recognition and catalysis. It is proposed that the active site of the enzyme is rigid to keep its thermostability but incorporates extra functionality to be promiscuous.
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Affiliation(s)
- Alex Theodossis
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, Fife KY16 9ST, Scotland
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16
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Iwersen M, Dora H, Kohla G, Gasa S, Schauer R. Solubilisation and properties of the sialate-4-O-acetyltransferase from guinea pig liver. Biol Chem 2003; 384:1035-47. [PMID: 12956420 DOI: 10.1515/bc.2003.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The O-acetylation of sialic acids turns out to be one of the most important modifications that influence the diverse biological and pathophysiological properties of glycoconjugates in animals and microorganisms. To understand the functions of this esterification, knowledge of the properties, structures and regulation of expression of the enzymes involved is essential. Attempts to solubilise, purify or clone the gene of one of the sialate-O-acetyltransferases have failed so far. Here we report on the solubilisation of the sialate-4-O-acetyltransferase from guinea pig liver, the first and essential step in the purification and molecular characterisation of this enzyme, by the zwitterionic detergent CHAPS. This enzyme O-acetylates sialic acids at C-4 both free and bound to oligosaccharides, glycoproteins and glycolipids with varying activity, however, gangliosides proved to be the best substrates. Correspondingly, a rapid enzyme test was elaborated using the ganglioside GD3. The soluble O-acetyltransferase maximally operated at 30 degrees C, pH 5.6, and 50-70 mM KCl and K2HPO4 concentrations. The Km values were 3.6 microM for AcCoA and 1.2 microM for GD3. CoA inhibits the enzyme with a Ki value of 14.8 microM. A most important discovery enabling further enzyme purification is its need for an unknown low molecular mass and heat-stable cofactor that can be separated from the crude enzyme preparation by 30 kDa ultrafiltration.
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Affiliation(s)
- Matthias Iwersen
- Biochemisches Institut, Christian-Albrechts-Universität, Olshausenstr. 40, D-24098 Kiel, Germany
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17
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Joerger AC, Mayer S, Fersht AR. Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity. Proc Natl Acad Sci U S A 2003; 100:5694-9. [PMID: 12711733 PMCID: PMC156263 DOI: 10.1073/pnas.0531477100] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2003] [Indexed: 11/18/2022] Open
Abstract
N-acetylneuraminate lyase (NAL) and dihydrodipicolinate synthase (DHDPS) belong to the NAL subfamily of (betaalpha)(8)-barrels. They share a common catalytic step but catalyze reactions in different biological pathways. By rational design, we have introduced various mutations into the NAL scaffold from Escherichia coli to switch the activity toward DHDPS. These mutants were tested with respect to their catalytic properties in vivo and in vitro as well as their stability. One point mutation (L142R) was sufficient to create an enzyme that could complement a bacterial auxotroph lacking the gene for DHDPS as efficiently as DHDPS itself. In vitro, this mutant had an increased DHDPS activity of up to 19-fold as defined by the specificity constant k(cat)K(M) for the new substrate l-aspartate-beta-semialdehyde when compared with the residual activity of NAL wild-type, mainly because of an increased turnover rate. At the same time, mutant L142R maintained much of its original NAL activity. We have solved the crystal structure of mutant L142R at 1.8 A resolution in complex with the inhibitor beta-hydroxypyruvate. This structure reveals that the conformations of neighboring active site residues are left virtually unchanged by the mutation. The high flexibility of R142 may favor its role in assisting in catalysis. Perhaps, nature has exploited the catalytic promiscuity of many enzymes to evolve novel enzymes or biological pathways during the course of evolution.
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Affiliation(s)
- Andreas C Joerger
- Cambridge University Chemical Laboratory and Cambridge Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom
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18
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Krüger D, Schauer R, Traving C. Characterization and mutagenesis of the recombinant N-acetylneuraminate lyase from Clostridium perfringens: insights into the reaction mechanism. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:3831-9. [PMID: 11432751 DOI: 10.1046/j.1432-1327.2001.02297.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The N-acetylneuraminate lyase from Clostridium perfringens was expressed in Escherichia coli as a fusion protein with a His-tag and purified to homogeneity using metal chelate affinity and anion exchange chromatography. The purified enzyme has a pH optimum of 7.6 and a temperature optimum of 65-70 degrees C. In kinetic studies the lyase exhibits a Km of 3.2 mM for Neu5Ac and a Vmax of 27.5 U x mg(-1). To clarify the functional role of some putative active site residues, site-directed mutagenesis was performed. Lysine 161 was identified as the residue forming the Schiff base intermediate with the substrate. Tyrosine 133 was shown to be also a catalytically important residue; it seems to function as an acceptor for the proton of the C4 hydroxyl group, as already suggested by other groups. Furthermore, it is involved in stabilizing the Schiff base intermediate. Mutations of aspartate 187 and glutamate 188 indicate that both residues are involved in substrate binding. In this respect the carboxy group of aspartate 187 seems to be particularly important. Based on the results of these studies, a model of the reaction mechanism is discussed.
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Affiliation(s)
- D Krüger
- Biochemisches Institut, Christian-Albrechts-Universität, Kiel, Germany
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19
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Barbosa JA, Smith BJ, DeGori R, Ooi HC, Marcuccio SM, Campi EM, Jackson WR, Brossmer R, Sommer M, Lawrence MC. Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme. J Mol Biol 2000; 303:405-21. [PMID: 11031117 DOI: 10.1006/jmbi.2000.4138] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The N-acetylneuraminate lyase (NAL) sub-family of (beta/alpha)(8) enzymes share a common catalytic step but catalyse reactions in different biological pathways. Known examples include NAL, dihydrodipicolinate synthetase (DHDPS), d-5-keto-4-deoxyglucarate dehydratase, 2-keto-3-deoxygluconate aldolase, trans-o-hydroxybenzylidenepyruvate hydrolase-aldolase and trans-2'-carboxybenzalpyruvate hydratase-aldolase. Little is known about the way in which the three-dimensional structure of the respective active sites are modulated across the sub-family to achieve cognate substrate recognition. We present here the structure of Haemophilus influenzae NAL determined by X-ray crystallography to a maximum resolution of 1.60 A, in native form and in complex with three substrate analogues (sialic acid alditol, 4-deoxy-sialic acid and 4-oxo-sialic acid). These structures reveal for the first time the mode of binding of the complete substrate in the NAL active site. On the basis of the above structures, that of substrate-complexed DHDPS and sequence comparison across the sub-family we are able to propose a unified model for active site modulation. The model is one of economy, allowing wherever appropriate the retention or relocation of residues associated with binding common substrate substituent groups. Our structures also suggest a role for the strictly conserved tyrosine residue found in all active sites of the sub-family, namely that it mediates proton abstraction by the alpha-keto acid carboxylate in a substrate-assisted catalytic reaction pathway.
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Affiliation(s)
- J A Barbosa
- Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria, Australia
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20
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Kiefelt MJ, Wilson JC, Bennett S, Gredley M, von Itzstein M. Synthesis and evaluation of C-9 modified N-acetylneuraminic acid derivatives as substrates for N-acetylneuraminic acid aldolase. Bioorg Med Chem 2000; 8:657-64. [PMID: 10732983 DOI: 10.1016/s0968-0896(99)00325-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Several C-9 modified N-acetylneuraminic acid derivatives have been synthesised and evaluated as substrates of N-acetylneuraminic acid aldolase. Simple C-9 acyl or ether modified derivatives of N-acetylneuraminic acid were found to be accepted as substrates by the enzyme, albeit being transformed more slowly than Neu5Ac itself. 1H NMR spectroscopy was used to evaluate the extent of the enzyme catalysed transformation of these compounds. Interestingly, the chain-extended Neu5Ac derivative 16 is not a substrate for N-acetylneuraminate lyase and behaves as an inhibitor of the enzyme.
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Affiliation(s)
- M J Kiefelt
- Department of Medicinal Chemistry, Monash University, Parkville, Victoria, Australia
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21
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Sommer U, Traving C, Schauer R. The sialate pyruvate-lyase from pig kidney: purification, properties and genetic relationship. Glycoconj J 1999; 16:425-35. [PMID: 10737328 DOI: 10.1023/a:1007030627948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
For further insight into the structural relationship between mammalian and microbial sialate pyruvate-lyases, the enzyme from pig kidney was purified to homogeneity from the tissue homogenate by a heat precipitation step followed by anion exchange and Hydrophobic Interaction Chromatography or native gel electrophoresis, respectively. The pure enzyme preparation exhibited an about 1000-fold increase of specific activity compared to the supernatant after the first centrifugation and revealed a single band at 34-37 kDa after SDS-PAGE, which represents the monomeric form of the protein. While the native enzyme seems to be a trimer according to the molecular weight obtained by gel filtration (108 kDa), crosslinking with dimethylpimelimidate suggests it to be a tetramer. The lyase is optimally active at about 75 degrees C and in the pH range of 7.6 to 8.0 and belongs to the class I-aldolases, due to its non-requirement of metal ions and the presence of lysine as the main functional residue in its catalytic centre. These data are similar to those obtained with bacterial lyases. However, peptide fragments of this enzyme show less similarity to primary lyase structures of microbia than to those derived from expressed sequence tags of mammals.
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Affiliation(s)
- U Sommer
- Biochemisches Institut der Christian-Albrechts-Universität, Kiel, Germany
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