Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus

Holton, Simon J.; Anandhakrishnan, M.; Geerlof, Arie; Wilmanns, Matthias

doi:10.1016/j.jsb.2012.10.009

Cited by 15 publications

(18 citation statements)

References 22 publications

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“…The d -LDH encoding gene in some strains (2-6, XZL9, and XZL4) is interrupted by a premature stop codon. We compared the remaining d -LDHs with those from L. bulgaricus 2122. Some residues of d -specific lactate dehydrogenase that are essential for substrate specificity and catalysis have changed (Tyr52Leu, Asn77Thr, Val78Ala and Trp135Val)23 (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

2014

Sci Rep

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Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.

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Section: Resultsmentioning

confidence: 99%

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

2014

Sci Rep

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“…Comparative sequence analysis indicates that the three residues essential for lactate dehydrogenase catalysis are conserved in VanH and correspond to residues Arg‐231, Glu‐260, and His‐292 in VanH A . Structure‐based analysis of lactate dehydrogenase also suggests that a cluster of hydrophobic residues in the active site is responsible for the preferential binding of the hydrophobic sidechain of d ‐isomers of the substrate . Whether this model can be directly applied to VanH enzymes necessitates further structural and functional studies.…”

Section: Vancomycin Resistance Mechanisms: Two Main Routes For Modifimentioning

confidence: 99%

“…Structure-based analysis of lactate dehydrogenase also suggests that a cluster of hydrophobic residues in the active site is responsible for the preferential binding of the hydrophobic sidechain of D-isomers of the substrate. 26,[28][29][30] Whether this model can be directly applied to VanH enzymes necessitates further structural and functional studies. ATP is utilized as a co-substrate by the D-Ala-D-Ala and D-Ala-D-lac ligases in a two-step reaction whereby the γ-phosphate of ATP is transferred to the carboxyl group of D-Ala, followed by the second step of condensation of the amino group of D-Ala or the hydroxyl group of D-lac with the acyl group of the activated D-Ala, liberating free phosphate and the product D-Ala-D-Ala or D-Ala-D-lac.…”

Section: Vanh Dehydrogenasementioning

confidence: 99%

Molecular mechanisms of vancomycin resistance

2020

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Vancomycin and related glycopeptides are drugs of last resort for the treatment of severe infections caused by Gram‐positive bacteria such as Enterococcus species, Staphylococcus aureus, and Clostridium difficile. Vancomycin was long considered immune to resistance due to its bactericidal activity based on binding to the bacterial cell envelope rather than to a protein target as is the case for most antibiotics. However, two types of complex resistance mechanisms, each comprised of a multi‐enzyme pathway, emerged and are now widely disseminated in pathogenic species, thus threatening the clinical efficiency of vancomycin. Vancomycin forms an intricate network of hydrogen bonds with the d‐Ala‐d‐Ala region of Lipid II, interfering with the peptidoglycan layer maturation process. Resistance to vancomycin involves degradation of this natural precursor and its replacement with d‐Ala‐d‐lac or d‐Ala‐d‐Ser alternatives to which vancomycin has low affinity. Through extensive research over 30 years after the initial discovery of vancomycin resistance, remarkable progress has been made in molecular understanding of the enzymatic cascades responsible. Progress has been driven by structural studies of the key components of the resistance mechanisms which provided important molecular understanding such as, for example, the ability of this cascade to discriminate between vancomycin sensitive and resistant peptidoglycan precursors. Important structural insights have been also made into the molecular evolution of vancomycin resistance enzymes. Altogether this molecular data can accelerate inhibitor discovery and optimization efforts to reverse vancomycin resistance. Here, we overview our current understanding of this complex resistance mechanism with a focus on the structural and molecular aspects.

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“…Hydroxy acid dehydrogenases are responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids, having wide biotechnological applications, like synthesis of antibiotics, flavor development in dairy products, and production of valuable synthons (10). Due to their highly specific activity in the reduction of pyruvate and the high stability of the enzyme and substrate, LDHs serve as an efficient system for cofactor regeneration (11).…”

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confidence: 99%

NADP ⁺ -Preferring d -Lactate Dehydrogenase from Sporolactobacillus inulinus

Zhu

Wang

et al. 2015

Appl Environ Microbiol

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e Hydroxy acid dehydrogenases, including L-and D-lactate dehydrogenases (L-LDH and D-LDH), are responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids and extensively used in a wide range of biotechnological applications. A common feature of LDHs is their high specificity for NAD ؉ as a cofactor. An LDH that could effectively use NADPH as a coenzyme could be an alternative enzymatic system for regeneration of the oxidized, phosphorylated cofactor. In this study, a D-lactate dehydrogenase from a Sporolactobacillus inulinus strain was found to use both NADH and NADPH with high efficiencies and with a preference for NADPH as its coenzyme, which is different from the coenzyme utilization of all previously reported LDHs. The biochemical properties of the D-LDH enzyme were determined by X-ray crystal structural characterization and in vivo and in vitro enzymatic activity analyses. The residue Asn 174 was demonstrated to be critical for NADPH utilization. Characterization of the biochemical properties of this enzyme will contribute to understanding of the catalytic mechanism and provide referential information for shifting the coenzyme utilization specificity of 2-hydroxyacid dehydrogenases.L actic acid, existing as D-and L-isomers, is an important organic acid that can be widely used in food, cosmetic, chemical, and many other industries (1, 2). The most important application of lactic acid is the production of biodegradable polymer poly(lactic acid) (3). Since the thermoresistance of pure poly(L-lactic acid) is rather low, development of a stereocomplex of poly(L-lactic acid) and poly(D-lactic acid) with a melting point as high as that of petroleum-based polymers is considered an advance in poly(lactic acid) modification (4, 5).L-Lactate dehydrogenase (L-LDH) and D-lactate dehydrogenase (D-LDH) are responsible for the synthesis of L-and D-lactic acids, respectively (2, 6). Given the potential use of chiral hydroxyl acids as valuable synthons and precursors for chiral products in the biotechnological industry (7), it is of significant interest to gain in-depth insights into the substrate specificities, catalytic kinetics, and molecular mechanisms of 2-hydroxyacid dehydrogenase enzymes. The L-isomer-specific 2-hydroxyacid dehydrogenase is a cytoplasmic enzyme present in essentially all major organ systems. This enzyme has been extensively characterized and used as an indicator of pathological conditions (8). However, the D-isomer-specific 2-hydroxyacid dehydrogenase has gained much less attention. Sequence alignments have shown that D-LDH and L-LDH display significant differences in their amino acid sequences and belong to two distinct families: the D-and L-2-hydroxyacid dehydrogenases, respectively (9).Hydroxy acid dehydrogenases are responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids, having wide biotechnological applications, like synthesis of antibiotics, flavor development in dairy products, and production of valuable synthons (10). Due to their highly specific a...

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Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus

Cited by 15 publications

References 22 publications

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

Molecular mechanisms of vancomycin resistance

NADP ⁺ -Preferring d -Lactate Dehydrogenase from Sporolactobacillus inulinus

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Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus

Cited by 15 publications

References 22 publications

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

Molecular mechanisms of vancomycin resistance

NADP + -Preferring d -Lactate Dehydrogenase from Sporolactobacillus inulinus

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NADP ⁺ -Preferring d -Lactate Dehydrogenase from Sporolactobacillus inulinus