Theo Sonke

Cloning, Sequence Analysis, and Expression in Escherichia coli of the Gene Encoding an α-Amino Acid Ester Hydrolase from Acetobacter turbidans

ABSTRACT The α-amino acid ester hydrolase from Acetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing β-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified α-amino acid ester hydrolase allowed cloning and genetic characterization of the corresponding gene from an A. turbidans genomic library. The gene, designated aehA, encodes a polypeptide with a molecular weight of 72,000. Comparison of the determined N-terminal sequence and the deduced amino acid sequence indicated the presence of an N-terminal leader sequence of 40 amino acids. The aehA gene was subcloned in the pET9 expression plasmid and expressed in Escherichia coli. The recombinant protein was purified and found to be dimeric with subunits of 70 kDa. A sequence similarity search revealed 26% identity with a glutaryl 7-ACA acylase precursor from Bacillus laterosporus, but no homology was found with other known penicillin or cephalosporin acylases. There was some similarity to serine proteases, including the conservation of the active site motif, GXSYXG. Together with database searches, this suggested that the α-amino acid ester hydrolase is a β-lactam antibiotic acylase that belongs to a class of hydrolases that is different from the Ntn hydrolase superfamily to which the well-characterized penicillin acylase from E. coli belongs. The α-amino acid ester hydrolase of A. turbidans represents a subclass of this new class of β-lactam antibiotic acylases.

N,N-Acetals as N-acyliminium ion precursors: Synthesis and absolute stereochemistry of epiquinamide

A stereoselective synthesis of (+)-epiquinamide is presented in combination with determination of the absolute configuration of the natural product. Key steps in the sequence involved chemoenzymatic formation of an enantiomerically pure cyanohydrin, reductive cyclization to the corresponding cyclic N,N-acetal, and subsequent conversion into a suitable N-acyliminium ion precursor to enable construction of the second ring.

l-Selective Amidase with Extremely Broad Substrate Specificity from Ochrobactrum anthropi NCIMB 40321

ABSTRACT An industrially attractive l-specific amidase was purified to homogeneity from Ochrobactrum anthropi NCIMB 40321 wild-type cells. The purified amidase displayed maximum initial activity between pH 6 and 8.5 and was fully stable for at least 1 h up to 60°C. The purified enzyme was strongly inhibited by the metal-chelating compounds EDTA and 1,10-phenanthroline. The activity of the EDTA-treated enzyme could be restored by the addition of Zn2+ (to 80%), Mn2+ (to 400%), and Mg2+ (to 560%). Serine and cysteine protease inhibitors did not influence the purified amidase. This enzyme displayed activity toward a broad range of substrates consisting of α-hydrogen- and (bulky) α,α-disubstituted α-amino acid amides, α-hydroxy acid amides, and α-N-hydroxyamino acid amides. In all cases, only the l-enantiomer was hydrolyzed, resulting in E values of more than 150. Simple aliphatic amides, β-amino and β-hydroxy acid amides, and dipeptides were not converted. The gene encoding this l-amidase was cloned via reverse genetics. It encodes a polypeptide of 314 amino acids with a calculated molecular weight of 33,870. Since the native enzyme has a molecular mass of about 66 kDa, it most likely has a homodimeric structure. The deduced amino acid sequence showed homology to a few other stereoselective amidases and the acetamidase/formamidase family of proteins (Pfam FmdA_AmdA). Subcloning of the gene in expression vector pTrc99A enabled efficient heterologous expression in Escherichia coli. Altogether, this amidase has a unique set of properties for application in the fine-chemicals industry.

Crystal Structure of the Leucine Aminopeptidase from Pseudomonas putida Reveals the Molecular Basis for its Enantioselectivity and Broad Substrate Specificity

The zinc-dependent leucine aminopeptidase from Pseudomonas putida (ppLAP) is an important enzyme for the industrial production of enantiomerically pure amino acids. To provide a better understanding of its structure-function relationships, the enzyme was studied by X-ray crystallography. Crystal structures of native ppLAP at pH 9.5 and pH 5.2, and in complex with the inhibitor bestatin, show that the overall folding and hexameric organization of ppLAP are very similar to those of the closely related di-zinc leucine aminopeptidases (LAPs) from bovine lens and Escherichia coli. At pH 9.5, the active site contains two metal ions, one identified as Mn(2+) or Zn(2+) (site 1), and the other as Zn(2+) (site 2). By using a metal-dependent activity assay it was shown that site 1 in heterologously expressed ppLAP is occupied mainly by Mn(2+). Moreover, it was shown that Mn(2+) has a significant activation effect when bound to site 1 of ppLAP. At pH 5.2, the active site of ppLAP is highly disordered and the two metal ions are absent, most probably due to full protonation of one of the metal-interacting residues, Lys267, explaining why ppLAP is inactive at low pH. A structural comparison of the ppLAP-bestatin complex with inhibitor-bound complexes of bovine lens LAP, along with substrate modelling, gave clear and new insights into its substrate specificity and high level of enantioselectivity.

Identification of the catalytic residues of alpha-amino acid ester hydrolase from Acetobacter turbidans by labeling and site-directed mutagenesis

The α-amino acid ester hydrolase fromAcetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing the side chain peptide bond in β-lactam antibiotics. Data base searches revealed that the enzyme contains an active site serine consensus sequence Gly-X-Ser-Tyr-X-Gly that is also found in X-prolyl dipeptidyl aminopeptidase. The serine hydrolase inhibitorp-nitrophenyl-p′-guanidino-benzoate appeared to be an active site titrant and was used to label the α-amino acid ester hydrolase. Electrospray mass spectrometry and tandem mass spectrometry analysis of peptides from a CNBr digest of the labeled protein showed that Ser205, situated in the consensus sequence, becomes covalently modified by reaction with the inhibitor. Extended sequence analysis showed alignment of this Ser205with the catalytic nucleophile of some α/β-hydrolase fold enzymes, which posses a catalytic triad composed of a nucleophile, an acid, and a base. Based on the alignments, 10 amino acids were selected for site-directed mutagenesis (Arg85, Asp86, Tyr143, Ser156, Ser205, Tyr206, Asp338, His370, Asp509, and His610). Mutation of Ser205, Asp338, or His370 to an alanine almost fully inactivated the enzyme, whereas mutation of the other residues did not seriously affect the enzyme activity. Circular dichroism measurements showed that the inactivation was not caused by drastic changes in the tertiary structure. Therefore, we conclude that the catalytic domain of the α-amino acid ester hydrolase has an α/β-hydrolase fold structure with a catalytic triad of Ser205, Asp338, and His370. This distinguishes the α-amino acid ester hydrolase from the Ntn-hydrolase family of β-lactam antibiotic acylases.

New developments in the synthesis of natural and unnatural amino acids

Amino acids play an important role in biochemistry and chemistry. They are the building blocks of proteins and play an essential role in the regulation of the metabolism of living organisms.

Enzymatic and chiral HPLC resolution of α-azido acids and amides

Abstract For the first time, enzymatic resolution of α-azido acid amides has been successfully demonstrated with high yields and enantiomeric excess. In one case dynamic kinetic resolution was achieved leading to more than 50% yield of the enantiomerically pure azido acid. Chiral HPLC was also used to separate racemic α-azido acids and the separation process was automated. Two routes to enantiopure α-azido acid building blocks for solid-phase peptide synthesis have, therefore, been established.

Substrate Specificity and Stereoselectivity of Two Sulfolobus 2‐Keto‐3‐deoxygluconate Aldolases towards Azido‐Substituted Aldehydes

The 2‐keto‐3‐deoxygluconate aldolases (KDGAs) isolated from Sulfolobus species convert pyruvate and glyceraldehyde reversibly into 2‐keto‐3‐deoxygluconate and ‐galactonate. As a result of their high thermostability and activity on nonphosphorylated substrates, KDGA enzymes have potential as biocatalysts for the production of building blocks for fine chemical and pharmaceutical applications. Up to now, wild‐type enzymes have only shown moderate stereocontrol for their natural reaction. However, if a set of azido‐functionalized aldehydes were applied as alternative acceptors in the reaction with pyruvate, the stereoselectivity was strongly increased to give enantiomeric or diastereomeric excess values up to 97 %. The Sulfolobus acidocaldarius KDGA displayed a higher stereoselectivity than Sulfolobus solfataricus KDGA for all tested reactions. The azido‐containing products are useful chiral intermediates in the synthesis of nitrogen heterocycles.

Flow injection analysis electrospray ionization mass spectrometry for high-throughput screening of a gene library for amidase activity

In high-throughput screening of gene and mutant libraries, high analysis speeds and short method development times are important factors. Mass spectrometry (MS) is considered to be a generic analytical technique with a relatively short development time. Furthermore, when applying flow injection analysis (FIA) for sample introduction, the requirements for high throughput are met. In this work, the use of a single quadrupole electrospray MS instrument for assaying amidase activity in a gene library is demonstrated. The desired selectivity for measuring the amino acid, the reaction product of the amidase reaction, in the presence of high concentrations of the corresponding amino acid amide substrate was obtained by selective ionization of the amino acid in negative ion mode electrospray. The only sample preparation required was a 200-fold dilution of the reaction mixture. For obtaining quantitative results, a complementary calibration procedure was set up to correct for the change in ionization suppression as a function of conversion. This approach was used to screen a Mycobacterium neoaurum gene library consisting of 11,520 clones with alpha-methylleucine amide as substrate within 24h. Conversion was measured on the [M-H]- species of the corresponding alpha-methylleucine (m/z 144). Five positive clones were detected with a conversion ranging from 0.2% to 3.4%.

Purification and use of E. coli peptide deformylase for peptide deprotection in chemoenzymatic peptide synthesis

Peptide deformylases (PDFs) catalyze the removal of the formyl group from the N-terminal methionine residue in nascent polypeptide chains in prokaryotes. Its deformylation activity makes PDF an attractive candidate for the biocatalytic deprotection of formylated peptides that are used in chemoenzymatic peptide synthesis. For this application it is essential to use PDF preparations that are free of contamination by peptidases that can cleave internal peptide bonds. Therefore, different purification methods were attempted and an industrially applicable purification procedure was developed based on a single anion-exchange chromatography step of an engineered PDF variant that was equipped with an anionic octaglutamate tag. The deformylation activity and stability of the engineered enzyme were similar to those of the wild-type PDF. This purification method furnished a PDF preparation with a 1500-fold decreased level of contamination by amidases and peptidases as compared to cell-free extract. It was shown that the enzyme could be used for deprotection of a formylated dipeptide that was prepared by thermolysin-mediated coupling.