Muconate Lactonizing Enzyme Research Articles

A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.

The genome of Labrenzia aggregata IAM 12614 encodes an uncharacterized member of the muconate lactonizing enzyme (MLE) subgroup of the enolase superfamily (UniProt ID A0NXQ8 ). The gene encoding A0NXQ8 is located between genes that encode members of the proline racemase superfamily, 4R-hydroxyproline 2-epimerase (UniProt ID A0NXQ7 ; 4HypE) and trans-3-hydroxy-l-proline dehydratase (UniProt ID A0NXQ9 ; t3LHypD). A0NXQ8 was screened with a library of proline analogues; two reactions were observed with cis-3-hydroxy-l-proline (c3LHyp), competing 2-epimerization to trans-3-hydroxy-d-proline (1,1-proton transfer) and dehydration to Δ(1)-pyrroline-2-carboxylate (β-elimination; c3LHyp dehydratase), with eventual total dehydration. The genome context encoding A0NXQ8 both (1) confirms its novel c3LHyp dehydratase function and (2) provides evidence for metabolic pathways that allow L. aggregata to utilize several isomeric 3- and 4-hydroxyprolines as sole carbon sources.

SABER: A computational method for identifying active sites for new reactions

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified.

Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.

The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the alpha-proton of a carboxylate substrate that is coordinated to an essential Mg(2+). The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the beta-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologous MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, gi 70731221 ; anti, Mycobacterium smegmatis, gi 118470554 ) document that the conserved Lys at the end of the second beta-strand in the (beta/alpha)(7)beta-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of "pseudoconvergent" evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction.

Evolution of Enzymatic Activities in the Enolase Superfamily: N-Succinylamino Acid Racemase and a New Pathway for the Irreversible Conversion of d- to l-Amino Acids

Members of the mechanistically diverse enolase superfamily catalyze reactions that are initiated by abstraction of the alpha-proton of a carboxylate anion to generate an enolate anion intermediate that is stabilized by coordination to a Mg2+ ion. The catalytic groups, ligands for an essential Mg2+ and acid/base catalysts, are located in the (beta/alpha)8-barrel domain of the bidomain proteins. The assigned physiological functions in the muconate lactonizing enzyme (MLE) subgroup (Lys acid/base catalysts at the ends of the second and sixth beta-strands in the barrel domain) are cycloisomerization (MLE), dehydration (o-succinylbenzoate synthase; OSBS), and epimerization (L-Ala-D/L-Glu epimerase). We previously studied a putatively promiscuous member of the MLE subgroup with uncertain physiological function from Amycolatopsis that was discovered based on its ability to catalyze the racemization of N-acylamino acids (N-acylamino acid racemase; NAAAR) but also catalyzes the OSBS reaction [OSBS/NAAAR; Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. In this manuscript, we report functional characterization of a homologue of this protein encoded by the genome of Geobacillus kaustophilus as well as two other proteins that are encoded by the same operon, a divergent member of the Gcn5-related N-acetyltransferase (GNAT) superfamily of enzymes whose members catalyze the transfer an acyl group from an acyl-CoA donor to an amine acceptor, and a member of the M20 peptidase/carboxypeptidase G2 family. We determined that the member of the GNAT superfamily is succinyl-CoA:D-amino acid N-succinyltransferase, the member of the enolase superfamily is N-succinylamino acid racemase (NSAR), and the member of the M20 peptidase/carboxypeptidase G2 family is N-succinyl-L-amino acid hydrolase. We conclude that (1) these enzymes constitute a novel, irreversible pathway for the conversion of D- to L-amino acids and (2) the NSAR reaction is a new physiological function in the MLE subgroup. The NSAR is also functionally promiscuous and catalyzes an efficient OSBS reaction; intriguingly, the operon for menaquinone biosynthesis in G. kaustophilus does not encode an OSBS, raising the possibility that the NSAR is a bifunctional enzyme rather than an accidentally promiscuous enzyme.

The Refined X-ray Structure of Muconate Lactonizing Enzyme from Pseudomonas putidaPRS2000 at 1.85 Å Resolution

We report here the refined X-ray crystal structure of muconate lactoniz- ing enzyme (MLE) from Pseudomonas putidaPRS2000 at a resolution of 1.85 Å with an R-factor of 16.8%. An enzyme from the β-ketoadipate path- way, MLE catalyses the conversion of cis,cis-muconate to muconolactone. It is a homo-octamer, one monomer consisting of 373 amino acid residues. MLE has two large domains and a C-terminal subdomain: an α + β domain, an αβ-barrel domain and a C-terminal meandering subdomain. The αβ-barrel domain is highly irregular. Its structure is (β/α) 7β, with the structural role of the last α-helix being replaced by both the C-terminal subdomain and part of the N-terminal domain. The fifth, seventh and eighth barrel strands are unusual because they have left-handed twist about their axes. The strand crossing angles also vary enormously, from +9° to −69°; the first and last strands, which close the barrel, cross at an angle of −69°, making extensive strand – strand hydrogen bonding impossible. The first barrel strand is also unusual because it starts in the N-terminal domain and forms hydrogen bonds to the C-terminal subdomain β-sheet as well as to its neighbouring strands in the barrel. It thus cements the whole protein together. As in other αβ-barrel proteins, the active site of MLE, present in each subunit is at the C-terminal ends of the barrel β-strands. The active site cleft contains an essential manganese ion, is lined with charged and other polar residues, and contains many of the crystallographic water molecules. The manganese ion is octahedrally co-ordinated to three side-chain carboxylate groups and three water molecules, and is at the centre of a radiating web of ionic and hydrogen-bonding interactions. Additionally, two water molecules are buried in the centre of the barrel and two hydrophilic side-chains (Lys167 and Arg196) make both hydrophobic and hydrophilic packing interactions with much of the barrel interior. The barrel interior is thus also unusual because it is so hydrophilic; the dominating force appears to be the need to solvate the metal ion effectively. This might account for the irregularity of the barrel. The catalytic mechanism has been investigated by docking both substrate and product in the active site with the C-COO −of muconolactone superimposed on the corresponding atoms of cis,cis-muconate. In agreement with earlier kinetic and spectroscopic results, the manganese ion does not interact directly with substrate or product. Our model thus confirms that Glu327 is the general acid, that Lys169 is the general base, and that the manganese ion and Lys167 provide electrophilic stabilisation of the enol/enolate intermediate that forms during the course of the reaction.

Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution.

The structure of the Mg2+ complex of yeast enolase has been determined from crystals grown in solutions of poly(ethylene glycol) at pH 8.1. Crystals belong to the space group P2(1) and have unit cell dimensions a = 72.5 A, b = 73.2 A, c = 89.1 A, and beta = 104.4 degrees. There is one dimer in the asymmetric unit. The current crystallographic R-factor is 19.0% for all recorded data to 1.9 A resolution. The electron density indicates a hexacoordinate Mg2+ at the high-affinity cation binding site. The octahedral coordination sphere consists of a meridional arrangement of three carboxylate oxygens from the side chains of Asp 246, Asp 320, and Glu 295, and three well-ordered water molecules. Octahedral coordination is the preferred geometry for alkaline earth metal ions in complexes with oxygen donor groups. In previous crystallographic studies of enolase, Zn2+ and Mg2+ complexes at the high-affinity site were reported to exist in trigonal bipyramidal coordination. This geometry was suggested to enhance the electrophilicity of the metal ion and promote rapid ligand exchange [Lebioda, L., & Stec, B. (1989) J. Am. Chem. Soc. 111, 8511-8513]. The octahedral arrangement of carboxylate and water ligands in the MgII-enolase complex determined here is most consistent with reports of the Mn2+ and Mg2+ coordination complexes of mandelate racemase and muconate lactonizing enzyme. These latter enzymes have alpha/beta-barrel folds comparable to enolase.(ABSTRACT TRUNCATED AT 250 WORDS)

A Functionally Diverse Enzyme Superfamily that Abstracts the α Protons of Carboxylic Acids

Mandelate racemase and muconate lactonizing enzyme are structurally homologous but catalyze different reactions, each initiated by proton abstraction from carbon. The structural similarity to mandelate racemase of a previously unidentified gene product was used to deduce its function as a galactonate dehydratase. In this enzyme superfamily that has evolved to catalyze proton abstraction from carbon, three variations of homologous active site architectures are now represented: lysine and histidine bases in the active site of mandelate racemase, only a lysine base in the active site of muconate lactonizing enzyme, and only a histidine base in the active site of galactonate dehydratase. This discovery supports the hypothesis that new enzymatic activities evolve by recruitment of a protein catalyzing the same type of chemical reaction.

3-Carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida is homologous to the class II fumarase family: a new reaction in the evolution of a mechanistic motif.

The gene (pcaB) for 3-carboxymuconate lactonizing enzyme (CMLE; 3-carboxymuconate cycloisomerase; EC 5.5.1.2) from Pseudomonas putida has been cloned into pMG27NS, a temperature-sensitive expression vector, and expressed in Escherichia coli N4830. The specific activity and kinetic parameters of the recombinant CMLE were comparable to those previously reported. A comparison of the deduced amino acid sequence of CMLE with sequences available in the PIR and Genbank databases revealed that CMLE has highly significant sequence homology to the class II fumarase family, particularly to adenylosuccinate lyase from Bacillus subtilis. CMLE has no significant homology to muconate lactonizing enzyme (MLE) from P. putida, its sister enzyme in the beta-ketoadipate pathway. These findings fully corroborate a prediction made by us on the basis of mechanistic and stereochemical analyses of CMLE and MLE [Chari, R. V. J., Whitman, C. P., Kozarich, J. W., Ngai, K.-L., & Ornston, L. N. (1987) J. Am. Chem. Soc. 109, 5514-5519] and suggest that CMLE and MLE were recruited into this specialized pathway from two different enzyme families.

Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-.ANG. resolution: identification of the active site and possible catalytic residues

The crystal structure of mandelate racemase (MR) has been solved at 3.0-A resolution by multiple isomorphous replacement and subsequently refined against X-ray diffraction data to 2.5-A resolution by use of both molecular dynamics refinement (XPLOR) and restrained least-squares refinement (PROLSQ). The current crystallographic R-factor for this structure is 18.3%. MR is composed of two major structural domains and a third, smaller, C-terminal domain. The N-terminal domain has an alpha + beta topology consisting of a three-stranded antiparallel beta-sheet followed by an antiparallel four alpha-helix bundle. The central domain is a singly wound parallel alpha/beta-barrel composed of eight central strands of beta-sheet and seven alpha-helices. The C-terminal domain consists of an irregular L-shaped loop with several short sections of antiparallel beta-sheet and two short alpha-helices. This C-terminal domain partially covers the junction between the major domains and occupies a region of the central domain that is filled by an eight alpha-helix in all other known parallel alpha/beta-barrels except for the barrel domain in muconate lactonizing enzyme (MLE) [Goldman, A., Ollis, D. L., & Steitz, T. A. (1987) J. Mol. Biol. 194, 143] whose overall polypeptide fold and amino acid sequence are strikingly similar to those of MR [Neidhart, D. J., Kenyon, G. L., Gerlt, J. A., & Petsko, G. A. (1990) Nature 347, 692]. In addition, the crystal structure reveals that, like MLE, MR is tightly packed as an octamer of identical subunits. The active site of MR is located between the two major domains, at the C-terminal ends of the beta-strands in the alpha/beta-barrel domain. The catalytically essential divalent metal ion is ligated by three side-chain carboxyl groups contributed by residues of the central beta-sheet. A model of a productive substrate complex of MR has been constructed on the basis of difference Fourier analysis at 3.5-A resolution of a complex between MR and (R,S)-p-iodomandelate, permitting identification of residues that may participate in substrate binding and catalysis. The ionizable groups of both Lys 166 and His 297 are positioned to interact with the chiral center of substrate, suggesting that both of these residues may function as acid/base catalysts.(ABSTRACT TRUNCATED AT 400 WORDS)

Related enzymes catalyze different reactions

Two enzymes-mandelate racemase (MR) and muconate lactonizing enzyme (MLE)-that catalyze mechanistically distinct reactions have been shown to be structurally homologous, and thus very likely evolutionary related [ Nature , 347, 692 (1990)]. This is the first clear example of two enzymes that appear to have evolved from a common ancestor's catalyzing different chemical reactions, according to the chemists who carried out the research. MR and MLE are both part of a biochemical pathway that allows Pseudomonas putida to metabolize aromatic carboxylic acids. MR catalyzes the interconversion of two enantiomers. MLE catalyzes the cycloisomerization of cis,cis -muconic acid to muconolactone by syn addition to a double bond. The research was carried out by Gregory A. Petsko and David J. Neidhart of Massachusetts Institute of Technology, Cambridge; George L. Kenyon of the University of California, San Francisco; and John A. Gerlt of the University of Maryland, College Park. (Petsko has since moved to Brandeis Unive...

Crystal structure of muconate lactonizing enzyme at 6.5 Å resolution

We have obtained crystals of Pseudomonas putida muconate lactonizing enzyme. They diffract to better than 2.4 Å resolution and have two monomers in the asymmetric unit, related by a non-crystallographic 2-fold axis. The cell dimensions are 139.3 Å × 139.3 Å × 84.1 Å, and the space group is I4. The electron density map at 6.5 Å resolution shows that the enzyme is an octamer with D 4 symmetry.

Metabolism of phenol and resorcinol in Trichosporon cutaneum.

Trichosporon cutaneum was grown with phenol or resorcinol as the carbon source. The formation of beta-ketoadipate from phenol, catechol, and resorcinol was shown by a manometric method using antipyrine and also by its isolation and crystallization. Metabolism of phenol begins with o-hydroxylation. This is followed by ortho-ring fission, lactonization to muconolactone, and delactonization to beta-ketoadipate. No meta-ring fission could be demonstrated. Metabolism of resorcinol begins with o-hydroxylation to 1,2,4-benzenetriol, which undergoes ortho-ring fission yielding maleylacetate. Isolating this product leads to its decarboxylation and isomerization to trans-acetylacrylic acid. Maleylacetate is reduced by crude extracts to beta-ketoadipate with either reduced nicotinamide adenine dinucleotide or reduced nicotinamide adenine dinucleotide phosphate as a cosubstrate. The enzyme catalyzing this reaction was separated from catechol 1,2-oxygenase, phenol hydroxylase, and muconate lactonizing enzyme on a diethyl-aminoethyl-Sephadex A50 column. As a result it was purified some 50-fold, as was the muconate-lactonizing enzyme. Methyl-, fluoro-, and chlorophenols are converted to a varying extent by crude extracts and by purified enzymes. None of these derivatives is converted to maleylacetate, beta-ketoadipate, or their derivatives. Cells grown on resorcinol contain enzymes that participate in the degradation of phenol and vice versa.

Genetic control of enzyme induction in the -ketoadipate pathway of Pseudomonas putida: two-point crosses with a regulatory mutant strain.

Several mutant strains of Pseudomonas putida, selected on the basis of their inability to grow at the expense of benzoate, have been shown to be unable to form inducibly both muconate lactonizing enzyme and muconolactone isomerase. A secondary mutant strain derived from one of these pleiotropically negative strains forms these two enzymes and, in addition, catechol oxygenase in the absence of inducer. This constitutive mutant strain was used as a donor in transductionally mediated two-point crosses to determine the order of point mutations within the structural genes for muconate lactonizing enzyme and muconolactone isomerase (the catB and catC genes, respectively). The gene order conformed precisely with the one that has been established by deletion mapping.

Regulation of the enzymes of the beta-ketoadipate pathway in Moraxella calcoacetica. 4. Constitutive synthesis of beta-ketoadipate succinyl-CoA transferases II and 3.

Mutants of Moraxella calcoacetica which synthesize constitutively β‐ketoadipate succinyl‐CoA transferase, but in which all other enzymes of the β‐ketoadipate pathway are still normally inducible, have been isolated by selection for the ability to grow with β‐ketoadipate. The constitutively synthesized transferase was identified as transferase III. This enzyme is induced in the wild type by adipate and its physiological function is probably adipate activation. The properties of these constitutive mutants confirm that the synthesis of transferase III is regulated independently of the synthesis of enzymes that mediate reactions of the β‐ketoadipate pathway.Two phenotypically different classes of mutants which synthesize transferase II constitutively have also been isolated by the same selective procedure. Both classes of mutants synthesize constitutively the five enzymes that convert catechol to β‐ketoadipyl‐CoA. Strict coordinacy between four of these enzymes (muconate lactonizing enzyme, muconolactone isomerase, β‐ketoadipate enol‐lactone hydrolase II and β‐ketoadipate succinyl‐CoA transferase II) is maintained in one class of mutants. However in the other class this coordinacy is destroyed and muconate lactonizing enzyme is synthesized in succinate‐grown cells at a relative level much lower than those of the other three enzymes. These findings are discussed and evaluated in terms of earlier evidence concerning the regulation of the synthesis of enzymes of the catechol branch by M. calcoacetica.