Alanine Ligase Research Articles

Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA

Vancomycin resistance in Enterococcus faecium BM4147 is mediated by vancomycin resistance proteins VanA and VanH. VanA is a D-alanine:D-alanine ligase of altered substrate specificity [Bugg, T. D. H., Dutka-Malen, S., Arthur, M., Courvalin, P., & Walsh, C. T. (1991) Biochemistry 30, 2017-2021], while the sequence of VanH is related to those of alpha-keto acid dehydrogenases [Arthur, M., Molinas, C., Dutka-Malen, S., & Courvalin, P. (1991) Gene (submitted)]. We report purification of VanH to homogeneity, characterization as a D-specific alpha-keto acid dehydrogenase, and comparison with D-lactate dehydrogenases from Leuconostoc mesenteroides and Lactobacillus leichmanii. VanA was found to catalyze ester bond formation between D-alanine and the D-hydroxy acid products of VanH, the best substrate being D-2-hydroxybutyrate (Km = 0.60 mM). The VanA product D-alanyl-D-2-hydroxybutyrate could then be incorporated into the UDPMurNAc-pentapeptide peptidoglycan precursor by D-Ala-D-Ala adding enzyme from Escherichia coli or by crude extract from E. faecium BM4147. The vancomycin binding constant of a synthetic modified peptidoglycan analogue N-acetyl-D-alanyl-D-2-hydroxybutyrate (Kd greater than 73 mM) was greater than 1000-fold higher than the binding constant for N-acetyl-D-alanyl-D-alanine (Kd = 54 microM), partly due to the disruption of a hydrogen bond in the vancomycin-target complex, thus providing a molecular rationale for high-level vancomycin resistance.

Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes

Two distinct genes encoding D-alanine:D-alanine (D-Ala-D-Ala) ligase (ADP forming) activity in Escherichia coli have been cloned by complementation of E. coli strain ST640(lambda 112) deficient in D-Ala-D-Ala ligase activity with a lambda library of E. coli DNA. One of the two genes, designated as ddlB, is identical with the ddl gene already sequenced [Robinson, A.C., Kenan, D.L., Sweeney, J., & Donachie, W.D. (1986) J. Bacteriol. 167, 809-817]. We describe the subcloning and DNA sequencing of the other gene, designated as ddlA on the basis of similarities with the Salmonella typhimurium ddlA gene [Daub, E., Zawadzke, L.E., Botstein, D., & Walsh, C.T. (1988) Biochemistry 27, 3701-3708]. The predicted amino acid sequence of the E. coli DdlA enzyme shows 90% homology with the S. typhimurium DdlA sequence. The ddlB gene was subcloned by use of the polymerase chain reaction into an expression vector containing an optimized ribosome binding site, which expressed the DdlB enzyme to greater than 50% soluble cell protein. Both DdlA and DdlB enzymes were purified to greater than 90% homogeneity and characterized kinetically.

Identification of vancomycin resistance protein VanA as a D-alanine:D-alanine ligase of altered substrate specificity

High-level glycopeptide resistance in Enterococcus faecium BM4147 is mediated by a 38-kDa protein VanA, whose amino acid sequence is related to Gram-negative D-alanine:D-alanine (D-Ala-D-Ala) ligases [Dutka-Malen, S., Molinas, C., Arthur, M., & Courvalin, P. (1990) Mol. Gen. Genet. 224, 364-372]. We report purification of VanA and demonstrate that it has D-Ala-D-Ala ligase activity but has substantially modified substrate specificity, compared with Gram-negative D-Ala-D-Ala ligases. VanA preferentially condenses D-Ala with D-Met or D-Phe, raising the possibility that its cellular role is to synthesize a modified cell-wall component, which is subsequently not recognized by vancomycin.

Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli

The Escherichia coli D-alanyl-D-alanine-adding enzyme, which catalyzes the final cytoplasmic step in the biosynthesis of the bacterial peptidoglycan precursor UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala-D- Ala, has been purified to homogeneity from an E. coli strain that harbors a recombinant plasmid bearing the structural gene for this enzyme, murF. The enzyme is a monomer of molecular weight 49,000, and it has a turnover number of 784 min-1 for ATP-driven amide bond formation. Experiments monitoring the fate of radiolabeled UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-2,6-diaminopimelate and D-trifluoroalanine proved that the preceding enzyme in the D-alanine branch pathway, D-alanine:D-alanine ligase (ADP), is capable of synthesizing fluorinated dipeptides, which the D-Ala-D-Ala-adding enzyme can then incorporate to form UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-2,6-diaminopimelyl-D-++ +trifluoroAla-D- trifluoroAla.

(3-Amino-2-oxoalkyl)phosphonic acids and their analogs as novel inhibitors of D-alanine:D-alanine ligase

The dipeptide D-alanyl-D-alanine is an essential precursor of bacterial peptidoglycan; thus, blocking its formation is a possible target for the design of novel antibacterial agents. The synthesis of this dipeptide by bacterial D-alanine:D-alanine ligase requires ATP. In analogy with glutamine synthetase, we hypothesized a mechanism for this enzyme involving the intermediacy of D-alanyl phosphate. Several (3-amino-2-oxoalkyl)phosphonic acids and their analogues have been synthesized as possible inhibitory mimics of this proposed intermediate. The most active of them, (3(R)-amino-2-oxobutyl)phosphonic acid (8a) and the corresponding aza analogue (22), were effective ligase inhibitors although they had no significant antibacterial activity. The ligase inhibition of these compounds is consistent with an acyl phosphate displacement step in the mechanism of DAla-DAla ligase.

ChemInform Abstract: Synthesis of an Analogue of Tabtoxinine as a Potential Inhibitor of D‐Alanine:D‐Alanine Ligase (ADP Forming).

AbstractStarting with the N‐protected D‐alaninal (I), the synthesis of the (R)‐and (S)‐β‐lactams (II) related to tabtoxinine (III), is described.

(1-Aminoethyl)boronic acid: a novel inhibitor for Bacillus stearothermophilus alanine racemase and Salmonella typhimurium D-alanine:D-alanine ligase (ADP-forming).

(1-Aminoethyl)boronic acid (Ala-B), an analogue of alanine in which a boronic acid group replaces the carboxyl group, has been synthesized and found to inhibit the first two enzymes, alanine racemase (from Bacillus stearothermophilus, EC 5.1.1.1) and D-alanine:D-alanine ligase (ADP-forming) (from Salmonella typhimurium, EC 6.3.2.4), of the D-alanine branch of bacterial peptidoglycan biosynthesis. In both cases, time-dependent, slow binding inhibition is observed due to the generation of long-lived, slowly dissociating complexes. Ala-B inhibits alanine racemase with a Ki of 20 mM and a kappa inact of 0.15-0.35 min-1. Time-dependent loss of activity is paralleled by conversion of the 420-nm chromophore of initial bound PLP aldimine to a 324-nm absorbing species. On dilution of Ala-B, racemase activity is regained with a t1/2 of ca. 1 h. The D-Ala-D-Ala ligase also shows progressive inhibition by Ala-B provided ATP (but not AMP-PNP or AMP-PCP) is present. The presence of D-alanine along with ATP also leads to Ala-B-induced inactivation. Kinetic analysis suggests Ala-B can compete with D-alanine at either of the two D-alanine binding sites, and on inactivation with Ala-B, labeled D-alanine, and labeled ATP, the inactive enzyme has stoichiometric amounts of D-alanine, ADP, Pi, and Ala-B bound. The half-life of inactive enzyme complexes varied from approximately 2 h (without D-alanine) to 4.5 days (with D-alanine). No D-Ala-D-Ala-B dipeptide was detected.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthesis of an analog of tabtoxinine as a potential inhibitor of D-alanine:D-alanine ligase (ADP forming)

The design and synthesis of a potential inhibitor of D-alanine:D-alanine ligase (ADP forming) (EC 6.3.2.4) are described. This enzyme, which catalyzes the second step in the biosynthesis of bacterial peptidoglycan, is believed to generate D-alanyl phosphate as an enzyme-bound intermediate. With tabtoxinine, a potent inhibitor of glutamine synthetase, as a model, beta-lactams 9R and 9S were synthesized as potential precursors of a D-alanyl phosphate mimic.

Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming).

A gene coding for D-alanine:D-alanine (D-Ala-D-Ala) ligase (ADP forming) (EC 6.3.2.4) activity has been isolated from a lambda library of Salmonella typhimurium DNA. Insertion mutations in the gene indicate that the gene is not essential for growth of the bacterium. The encoded enzyme was purified from an overproducing strain of S. typhimurium. D-Ala-D-Ala ligase is a protein of 39,271 molecular weight and has a kcat of 644 min-1 at pH 7.2. A 2.4-kilobase SalI-SphI fragment containing the gene was sequenced, and the ddlA gene consists of 1092 nucleotides. The gene sequence was compared to the sequence of the ddl gene of Escherichia coli [Robinson, A. C., Kenan, D. J., Sweeney, J., & Donachie, W. D. (1986) J. Bacteriol. 167, 809-817]. Because of differences between the S. typhimurium gene and the E. coli ddl gene, the S. typhimurium gene has been named ddlA.

ATP-dependent inactivation and slow binding inhibition of Salmonella typhimurium D-alanine:D-alanine ligase (ADP) by (aminoalkyl)phosphinate and aminophosphonate analogues of D-alanine.

In Salmonella typhimurium, D-alanine:D-alanine ligase (ADP) (EC 6.3.2.4) is the second enzyme in the three enzyme D-alanine branch pathway of peptidoglycan biosynthesis. The interaction of this enzyme with a possible transition-state analogue, the (aminoalkyl)phosphinate D-3-[(1-aminoethyl)phosphinyl]-2-heptylpropionic acid [Parsons et al. (1987) Abstracts of Papers, 193rd National Meeting of the American Chemical Society, Denver, CO, MEDI 63, American Chemical Society, Washington, DC], has been studied. This compound is a potent active site directed inhibitor and is competitive with D-alanine (Ki = 1.2 microM); it exhibits time-dependent inhibition in the presence of ATP. Kinetic analysis revealed a rapid onset of steady-state inhibition (kon = 1.35 X 10(4) M-1 s-1) followed by slow dissociation of inhibitory complex(es) with a half-life of 8.2 h. The inhibitory complex was shown to consist of E...I...ATP in equilibrium with E...I, Pi, and ADP. Similar time-dependent inhibition was also observed with D-(1-aminoethyl)phosphonic acid (D-Ala-P) (Ki = 0.5 mM; kon = 27 M-1 s-1; t1/2 for regain = 1.73 min) but not with D-(1-aminoethyl)phosphinic acid, which behaved as a simple competitive inhibitor (Ki = 0.4 mM). The mechanism of inhibition is discussed in the light of the precedents of glutamine synthase inhibition by methionine sulfoximine and phosphinothricin.

Towards new inhibitors of D-alanine:D-alanine ligase: The synthesis of 3-amino butenylphosphonic and aminophosphonamidic acids.

The condensation of sodium salt of tetraethyl methylenediphosphonate with N-Cbz alaninal followed by the standard acidolytic removal of protecting groups provides an efficient method for the synthesis of 3-aminobutenylphosphonic acid E 3 ; N-Cbz-aminophosphonamidic acid 4 was prepared from diphenyl 1-amino ethylphosphonic acid through methyl phosphochloridate alanine methyl ester condensation in the presence of triethylamine and alkaline partial deprotection.

ChemInform Abstract: (β‐Chloro‐α‐aminoethyl)phosphonic Acids as Inhibitors of Alanine Racemase and D‐ Alanine:D‐Alanine Ligase.

AbstractAusgehend vom Phosphonsäureester (I) werden die Phosphonsäuren (III), (IV) und (VI) dargestellt, deren inhibierende Wirkung auf Alanin‐ Racemasen und D‐Alanin:D‐Alanin‐Ligasen aus Pseudomonas aeruginosa und Streptocoecus faecalis untersucht wird.

Growth Inhibition of Escherichia coli W by d -Norvalyl- d -Alanine: an Analogue of d -Alanine in Position 4 of the Peptide Subunit of Peptidoglycan

Position 4 analogues of d-alanine in the peptide subunit of uridine 5'-diphosphate-N-acetylmuramyl-Ala(1)-dGlu(2)- Lys(3)-dAla(4)-dAla(5) have a significant inhibitory effect on penicillin-sensitive peptidoglycan synthesis in Gaffkya homari (C. V. Carpenter, S. Goyer, and F. C. Neuhaus, 1976). The specificity profile of this in vitro system has been used as a basis for designing analogues with potential antibacterial activity. To circumvent the specificity determinants exerted by d-alanine:d-alanine ligase (adenosine 5'-diphosphate), attention was directed to dd-dipeptides of the type d-alanyl-analogue-d-alanine as a method for incorporating analogues into position 4 of the peptide subunit in vivo. Of the three dipeptides, dAbu-dAla, dNva-dAla, and dVal-dAla, only dNva-dAla (5 x 10(-4) M) inhibited the growth of Escherichia coli W in the presence of 5 x 10(-6) M d-cycloserine. This concentration of d-cycloserine did not inhibit growth, but it potentiated the bactericidal activity of the dipeptide. The lack of antibacterial activity observed with dAbu-dAla and dVal-dAla was correlated with the poor ability of these dipeptides to be taken up via the dipeptide transport system of this organism. Prevention of lysis induced by dNva-dAla plus d-cycloserine by certain dipeptides and not by others supported this correlation. It is proposed that the d-norvalyl residue of the dipeptide is incorporated in vivo into position 4 of the peptide subunit of peptidoglycan, and that this subunit is not an effective substrate in the reaction(s) catalyzed by the penicillin-susceptible enzyme(s) of cross-linked peptidoglycan synthesis.

Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase.

The temperature-sensitive Escherichia coli mutant strain ST-640 lyses at the restrictive temperature except when an osmotic stabilizer or a high concentration of d-alanine is present. The presence of dl-alanyl-dl-alanine does not prevent lysis. The rate of murein synthesis, followed in a wall medium, is decreased at both 30 and 42 C. d-Alanyl-d-alanine and uridine diphosphate-N-acetyl-muramyl (UDP-MurNAc)-pentapeptide are synthesized in decreased amounts, accompanied by accumulation of UDP-MurNAc-tripeptide at 42 C but not at 30 C. Uridine nucleotide precursors leak into the medium, especially out of the mutant cells. This leakage is prevented when NaCl is present. The d-alanine: d-alanine ligase (ADP) (EC 6.3.2.4) of the mutant strain, assayed in crude extracts, is temperature sensitive. The impaired ligase is relatively resistant to d-cycloserine and other inhibitors of the enzyme. Combined genetic and enzymatic results show that the low ligase activity is due to a mutation in the ddl gene, the structural gene for d-alanine: d-alanine ligase.

Studies on Escherichia coli enzymes involved in the synthesis of uridine diphosphate-N-acetyl-muramyl-pentapeptide.

The specific activities of l-alanine:d-alanine racemase, d-alanine:d-alanine ligase, and the l-alanine, d-glutamic acid, meso-diaminopimelic acid, and d-alanyl-d-alanine adding enzymes were followed during growth of Escherichia coli. The specific activities were nearly independent of the growth phase. d-Alanine:d-alanine ligase was inhibited by d-alanyl-d-alanine, d-cycloserine, glycine, and glycyl-glycine. l-Alanine:d-alanine racemase was found to be sensitive to d-cycloserine, glycine, and glycyl-glycine. The l-alanine adding enzyme was inhibited by glycine and glycyl-glycine.

On the mechanism of action of the antibiotic O-carbamyld-serine in Streptococcus faecalis.

Lynch, Judith L. (Northwestern University, Evanston, Ill.), and Francis C. Neuhaus. On the mechanism of action of the antibiotic O-carbamyl-d-serine in Streptococcus faecalis. J. Bacteriol. 91:449-460. 1966.-The antibiotic O-carbamyl-d-serine, an analogue of d-alanine, is an inhibitor of bacterial cell-wall biosynthesis. Growth of Streptococcus faecalis R in the presence of O-carbamyl-d-serine resulted in the accumulation of the cell-wall precursor uridine diphosphate-NAc-muramyl-l-alanyl-d-glutamyl-l- lysine (UDP-NAc-muramyl-l-ala-d-glu-l-lys). The incorporation of d-alanine from l-alanine into peptidoglycan is catalyzed by the sequential action of the following enzymes: (i) alanine racemase; (ii) d-alanine: d-alanine ligase [adenosine diphosphate (ADP)]; (iii) UDP-NAc-muramyl-l-ala-d-glu-l-lys: d-ala-d-ala ligase (ADP); (iv) phospho-NAc-muramyl-pentapeptide translocase [uridine monophosphate (UMP)]. O-carbamyl-d-serine is an effective inhibitor of the alanine recemase (K(i)= 4.8 x 10(-4)m, K(m) of l-alanine = 6.8 x 10(-3)m). In addition, d-ala-O-carbamyl-d-ser was formed when d-alanine and O-carbamyl-d-serine were incubated with d-alanine: d-alanine ligase (ADP). This dipeptide was utilized by the UDP-NAc-muramyl-l-ala-d-glu-l-lys: d-ala-d-ala ligase (ADP) with the formation of UDP-NAc-muramyl-l-ala-d-glu-l-lys-d-ala- O-carbamyl-d-ser. From a consideration of the following results, i.e., (i) accumulation of UDP-NAc-muramyl-l-ala-d-glu-l-lys; (ii) absence of d-ala-O-carbamyl-d-ser accumulation in bacterial cultures grown in the presence of O-carbamyl-d-serine; and (iii) effective inhibition of the racemase, it was concluded that the first enzyme, the racemase, is the primary site of antibiotic action.