Crystal Structure of Bacillus cereus d-Alanyl Carrier Protein Ligase (DltA) in Complex with ATP

Osman, Khan Towhid; Du, Liqin; He, Yong; Luo, Yu

doi:10.1016/j.jmb.2009.03.040

Cited by 50 publications

(70 citation statements)

References 47 publications

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“…3, d and e). Thus, our data is consistent with a proposed bifunctional role for Arg 326 where initial stabilization of the ATP phosphates is replaced with a stabilizing role of the adenylated intermediate (15).…”

supporting

confidence: 90%

“…In the PaaK1 ATP co-structure, the C-terminal domain is properly oriented to position the invariant Lys 422 (Fig. 2a, red) within the active site, consistent with superfamily members occupying conformation 1 (11,14,15,26,28).…”

Section: Dimerization Leads To Formation Of An Intermolecularmentioning

confidence: 59%

“…In the case of an AFE, the first two stages can be defined as the pre-and postadenylation state. It is noteworthy that capturing these different states in the context of one enzyme is rare, with DltA from Bacillus cereus serving as the only reported example (15,30). To explore the reorganization of key structural features in PaaK1 as the enzyme progresses through the adenylation reaction, we report the high resolution structures of PaaK1 in complex with ATP (Fig.…”

Section: Pre-and Postadenylation Complexes Of Paak1 Reveal Dynamic Enmentioning

confidence: 99%

“…The general mechanism of the AFE superfamily indicates that catalysis relies on a large conformational change (9,14), yet it is rare that a single enzyme is captured in multiple conformations. Furthermore, there are very few ATP-bound structures (15) mak-ing it difficult to refine the general catalytic mechanism of these metabolically important enzymes.…”

mentioning

confidence: 99%

“…3c), where it is proposed to shield point charges and facilitate nucleophillic attack at the ␣-phosphate (15). Despite the flexibility of the lysine residue, only the ⑀-amino of Lys 422 is reoriented in the PaaK1-phenylacetyl adenylate co-structure such that it forms two hydrogen bonds with the ␣ phosphate (Fig.…”

mentioning

confidence: 99%

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Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315

Law¹,

Boulanger

2011

Journal of Biological Chemistry

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The phenylacetic acid (PAA) degradation pathway is the sole aerobic route for phenylacetic acid metabolism in bacteria and facilitates degradation of environmental pollutants such as styrene and ethylbenzene. The PAA pathway also is implicated in promoting Burkholderia cenocepacia infections in cystic fibrosis patients. Intriguingly, the first enzyme in the PAA pathway is present in two copies (paaK1 and paaK2), yet each subsequent enzyme is present in only a single copy.

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supporting

confidence: 90%

Section: Dimerization Leads To Formation Of An Intermolecularmentioning

confidence: 59%

Section: Pre-and Postadenylation Complexes Of Paak1 Reveal Dynamic Enmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315

Law¹,

Boulanger

2011

Journal of Biological Chemistry

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Rational hinge engineering of carboxylic acid reductase from Mycobacterium smegmatis enhances its catalytic efficiency in biocatalysis

Wang

Sun

Diao

et al. 2021

Biotechnology Journal

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Background: Carboxylic acid reductases (CARs) represent useful tools for the production of aldehydes from ubiquitous organic carboxylic acids. However, the low catalytic efficiency of these enzymes hampers their application.Methods: Herein, a CAR originating from Mycobacterium smegmatis was redesigned through rational hinge engineering to enhance the catalytic efficiency.Results: Based on the unique domain architecture of CARs and their superfamily, a mutagenesis library of the hinge region was designed. The best mutant R505I/N506K showed a 6.57-fold improved catalytic efficiency. Molecular dynamics simulations showed the increased catalytic efficiency was due to the strong binding of the acyl-AMP complex with it. Meanwhile, the ε-nitrogen atom of Lys610 frequently interacted with the ribose-ring oxygen atom of the complex, the distance (d1) between them represents a great indicator for that. The d1 value was used as a nimble indicator to evaluate unexplored mutants of that region for enhanced activity by in silico mutational experiments. Overall, eight mutants were identified to show higher enhanced activity compared with wild-type enzyme and R505F/N506G showed the highest catalytic efficiency.Conclusion: Altogether, the two-step strategy used here provided useful references for the engineering of CARs and other similar multiple-domain enzymes.

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Origin, Microbiology, Nutrition, and Pharmacology of D‐Amino Acids

Friedman

2010

Chemistry & Biodiversity

162

108

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Exposure of food proteins to certain processing conditions induces two major chemical changes: racemization of all L-amino acids (LAAs) to D-amino acids (DAAs) and concurrent formation of cross-linked amino acids such as lysinoalanine (LAL). The diet contains both processing-induced and naturally-formed DAA. The latter include those found in microorganisms, plants, and marine invertebrates. Racemization impairs digestibility and nutritional quality. Racemization of LAA residues to their D-isomers in food and other proteins is pH-, time-, and temperature-dependent. Although racemization rates of LAA residues in a protein vary, relative rates in different proteins are similar. The nutritional utilization of different DAAs varies widely in animals and humans. Some DAAs may exert both adverse and beneficial biological effects. Thus, although D-Phe is utilized as a nutritional source of L-Phe, high concentrations of D-Tyr in such diets inhibit the growth of mice. Both D-Ser and LAL induce histological changes in the rat kidney. The wide variation in the utilization of DAAs is illustrated by the fact that, whereas D-Meth is largely utilized as a nutritional source of the L-isomer, D-Lys is not. Similarly, although L-CysSH has a sparing effect on L-Meth when fed to mice, D-CysSH does not. Since DAAs are consumed as part of their normal diet, a need exists to develop a better understanding of their roles in foods, microbiology, nutrition, and medicine. To contribute to this effort, this overview surveys our present knowledge of the chemistry, nutrition, safety, microbiology, and pharmacology of DAAs. Also covered are the origin and distribution of DAAs in food and possible roles of DAAs in human physiology, aging, and the etiology and therapy of human diseases.

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Crystal Structure of Bacillus cereus d-Alanyl Carrier Protein Ligase (DltA) in Complex with ATP

Cited by 50 publications

References 47 publications

Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315

Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315

Rational hinge engineering of carboxylic acid reductase from Mycobacterium smegmatis enhances its catalytic efficiency in biocatalysis

Origin, Microbiology, Nutrition, and Pharmacology of D‐Amino Acids

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