ABSTRACT
Amino acid racemases are pivotal for
d
-amino acid (DAA) biosynthesis with wide-ranging biotechnological applications, yet their industrial deployment is hindered by narrow substrate specificity and instability. Here, we report the discovery of
Halocola ammonii
gen. nov., sp. nov. DA487
T
, a novel taxon within the proposed family
Halocolacceae
fam. nov. (order
Flavobacteriales
), isolated from hypersaline sediments. Genomic analysis revealed a robust DAA metabolic network, including a putative broad-specificity racemase RacX. Biochemical characterization demonstrated RacX’s exceptional catalytic efficiency (
k
cat
/K
m
= 151.2 s
−1
mM
−1
for
l
-Lys,
k
cat
/K
m
= 17.8 s
−1
mM
−1
for
d
-Lys) and broad substrate spectrum (15/17 tested
l
-amino acids). Homology modeling and mutagenesis identified Ala79 and Cys193 as putative catalytic residues, based on structural conservation with EcL-DER. Remarkably, the A79C variant enhanced the reverse reaction efficiency (
d
-Lys →
l
-Lys) by 44%, effectively shifting the enzyme’s catalytic bias and the resulting steady-state ratio of enzyme-bound species. Computational docking suggested that Asn80, Thr81, Asn121, and Thr124 may modulate substrate binding, though experimental structural validation is required. The thermostability-lability tradeoff (
T
1/2
55°C
=
70 min
) highlights targets for protein engineering. Our findings not only expand the phylogenetic diversity of microbial racemases but also identify a promising biocatalyst candidate for industrial DAA production.
IMPORTANCE
Microbial adaptations to extreme environments serve as a valuable source of novel biocatalysts with potential for sustainable industrial applications. In this study, we characterized
Halocola ammonii
DA487ᵀ, a halophilic bacterium representing the novel family
Halocolaceae
within the order
Flavobacteriales
, and identified a broad-specificity amino acid racemase, RacX. RacX demonstrates exceptional catalytic efficiency (
k
cat
/K
m
up to 151.2 s⁻¹ mM⁻¹ for
l
-Lys) across multiple amino acids and exhibits remarkable stability under neutral and alkaline conditions (pH 7.0–9.0)—properties intrinsically linked to its high-salt ecological niche. Unlike most known racemases from neutrophilic organisms, RacX originates from an understudied phylogenetic lineage and displays unique mechanistic features, including a strong innate bias toward
d
-amino acid (DAA) production that can be rationally reprogrammed via single-residue substitution (e.g., A79C). These functional and evolutionary insights, combined with its halotolerance and broad substrate scope, position RacX as a promising and engineerable biocatalyst for industrial processes requiring operation under high-salt or alkaline conditions, such as the synthesis of DAA precursors for antibiotics.