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This is a 1-chain structure with sequence from Staphylococcus aureus subsp. aureus NCTC 8325 ^{[1] [2]} to the rescue.

Function of your protein

The function of this protein is to catalyze the formation of dipeptide products in gram-positive bacteria. The positioning of the carboxylate substrate next to ATP is dependent on the formation of a salt-bridge interaction, which is facilitated by Arg305. Hence, Arg305 is essential in the recognition of the carboxylate substrate.

One group of enzymes, called L-amino acid ligases (LALs), which catalyze the formation of dipeptide products in Gram-positive bacteria, have not been investigated in S. aureus until now. The ATP-grasp enzyme SAOUHSC_02373 from S. aureus NCTC 8325 was found to be a novel LAL with high selectivity for L-aspartate and L-methionine substrates, forming an L-aspartyl–L-methionine dipeptide. It was named L-aspartate–L-methionine ligase (LdmS). The mechanism of LdmS was investigated using X-ray crystallography, molecular modeling, and site-directed mutagenesis.

LdmS was found to share a similar mechanism to other ATP-grasp enzymes but possesses a unique active site architecture that confers selectivity for L-Asp and L-Met substrates. Phylogenetic analysis showed that LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with the control of Met and Cys metabolism, supporting a role for LdmS in Staphylococcal sulfur amino acid metabolism.

Biological relevance and broader implications

Enzymes involved in the amino acid metabolism of Staphylococcus aureus are being studied as potential targets for new antibiotics. Staphylococci are a type of Gram-positive bacteria that can act as commensals or serious human pathogens. Staphylococcus aureus is a significant threat in both hospital and community settings as it can cause infections of varying degrees of severity, from minor to life-threatening. The number of severe cases is estimated to be in the hundreds of thousands to millions annually across the world.

The development of antibiotic resistance in S. aureus is a significant cause for concern. Traditional antibiotics have targeted essential bacterial processes, but the increasing resistance of pathogenic bacteria to current antibiotics has necessitated the exploration of new targets to combat infections. One such avenue involves the study of nonessential metabolic pathways to identify their roles in virulence and persistence. In the case of S. aureus, there is mounting evidence that nonessential aspects of amino acid metabolism, specifically those associated with Met and Cys metabolism, become conditionally essential in a host environment. Therefore, they present promising new targets for the development of antibiotics and antibiotic adjuvants (3-7). However, to take full advantage of such targets, a thorough understanding of these metabolic pathways is crucial.

Important Amino Acids

ADP's adenine group is located within a hydrophobic pocket that is surrounded by Val171, Val186, Ile188, Leu290, Ile300, and Lys217. This positioning is strengthened by hydrogen bonds formed by Lys173 and Glu215 sidechains and the mainchain backbone of Gln216 and Ile218. A cavity with polar characteristics is shaped by the sidechains of Gln244, Tyr252, Asn255, Asn307, and Ser309, in conjunction with the backbone of Gly308 and Ser309. In addition, the closure of the P-loop and N-loop creates a hydrophobic cavity that consists of Pro26, Leu34, Pro36, Leu44, Tyr111, Ala181, and Tyr184, with the guanidinium sidechain of Arg47 situated just below the opening of the cavity. Because of their properties and relative locations, these sites were considered as potential locations for accommodating the sidechains of L-Asp and L-Met.

In LdmS, the catalytic triad comprising of N255, D288, and S309 is responsible for the formation of the ʟ-aspartate-ʟ-methionine bond. N255 and D288 work together to coordinate the divalent metal ion, whereas S309 activates the nucleophile. The catalytic triad is essential for the biochemical reaction to occur.

Structural highlights

of 50/50 beta sheets to alpha helixes. You can see the round globular shape with a clear central opening.

Using X-ray crystallography, the conformational states of LdmS were unveiled, indicating the occurrence of structural changes during catalysis. By employing a combination of site-directed mutagenesis and molecular docking techniques, the factors responsible for selectivity towards the L-Asp and L-Met substrates were identified. The analysis revealed the presence of separate polar and hydrophobic cavities that were capable of accommodating the respective substrates.

The important ligands are citric acid (CIT), Chloride ion (CL), Magnesium ion (MG), and Sodium ion (NA). You can see them clearly .

Another important ligand in this protein is ADP which you can see as the grey bars .