Hackwon Do

Class III aminotransferases represent a structurally and functionally unique subgroup. However, the contribution of specific loop elements to their active-site architecture and cofactor-dependent structural transitions remain underexplored. We elucidated the structural framework underlying the catalytic function of class III fold Pyridoxal 5′-phosphate-dependent aminotransferase from the Antarctic bacterium Hymenobacter sp. PAMC 26554 (HyAT), and report its crystal structure at 2.31 Å resolution. The structure revealed a canonical class III fold organized as a functional homotetramer. Structural analysis identified a proline-containing motif (P-x-P) within the α10-α11 loop, which induces intrinsic disorder at the active-site entrance in the apo-form and revealed that a cooperative disorder-to-order transition is requisite for active-site assembly upon cofactor binding. We propose that this flexible loop region may be involved in modulating substrate access. Notably, this proline motif was conserved in homologs from Hyperthermophiles, despite the cold-adapted nature of HyAT. This convergence implies a common evolutionary strategy where the geometric constraints of proline are exploited to decouple local active-site dynamics from global scaffold stability, thereby addressing the stability–activity trade-off across diverse thermal environments. Our findings provide new molecular insights into the structural dynamics of class III aminotransferases and highlight evolutionary strategies for tuning enzyme flexibility in extreme environments.

Antarctic microorganisms experience persistent subzero temperatures and repeated freeze–thaw cycles that require specialized mechanisms for survival. Although transcriptomic studies have identified numerous cold-responsive genes, many remain annotated as hypothetical proteins with unknown functions. In this study, we investigated PL002-1792, a strongly upregulated hypothetical protein from Antarctic Flavobacterium sp. PL002 identified under severe cold stress (−20 °C versus −6 °C; log₂ fold change = 5.61, adjusted p = 1.89 × 10⁻¹³⁸). Sequence analysis revealed a 402-amino-acid protein containing a predicted Sec/SPII lipoprotein signal peptide. AlphaFold3 prediction generated a high-confidence structural model (pTM = 0.96) with an elongated β-sheet-rich architecture resembling bacterial ice-binding proteins. Comparative analysis with the ice-binding protein from Flavobacterium frigoris (FfIBP) identified conserved glycine-rich and TXT-like motifs associated with putative ice-binding surfaces. Recombinant PL002-1792 was expressed in Escherichia coli, recovered from inclusion bodies, and successfully refolded into a predominantly β-sheet-rich conformation as confirmed by circular dichroism spectroscopy. Functional assays demonstrated moderate ice recrystallisation inhibition activity, reducing relative ice crystal mean grain size to approximately 90% of the control, and significantly enhanced freeze–thaw survival, with recombinant cells retaining 67% viability after three freeze–thaw cycles compared with 27% for the empty-vector control. These findings identify PL002-1792 as a novel antifreeze-like protein and highlight the utility of structure-guided approaches for uncovering previously uncharacterized cold-adaptation mechanisms in polar microorganisms.

Antarctic microorganisms experience persistent subzero temperatures and repeated freeze–thaw cycles that require specialized mechanisms for survival. Although transcriptomic studies have identified numerous cold-responsive genes, many remain annotated as hypothetical proteins with unknown functions. In this study, we investigated PL002-1792, a strongly upregulated hypothetical protein from Antarctic Flavobacterium sp. PL002 identified under severe cold stress (−20 °C versus −6 °C; log₂ fold change = 5.61, adjusted p = 1.89 × 10⁻¹³⁸). Sequence analysis revealed a 402-amino-acid protein containing a predicted Sec/SPII lipoprotein signal peptide. AlphaFold3 prediction generated a high-confidence structural model (pTM = 0.96) with an elongated β-sheet-rich architecture resembling bacterial ice-binding proteins. Comparative analysis with the ice-binding protein from Flavobacterium frigoris (FfIBP) identified conserved glycine-rich and TXT-like motifs associated with putative ice-binding surfaces. Recombinant PL002-1792 was expressed in Escherichia coli, recovered from inclusion bodies, and successfully refolded into a predominantly β-sheet-rich conformation as confirmed by circular dichroism spectroscopy. Functional assays demonstrated moderate ice recrystallisation inhibition activity, reducing relative ice crystal mean grain size to approximately 90% of the control, and significantly enhanced freeze–thaw survival, with recombinant cells retaining 67% viability after three freeze–thaw cycles compared with 27% for the empty-vector control. These findings identify PL002-1792 as a novel antifreeze-like protein and highlight the utility of structure-guided approaches for uncovering previously uncharacterized cold-adaptation mechanisms in polar microorganisms.

Phosphopantetheine adenylyltransferase (PPAT), a key enzyme in the universal Coenzyme A biosynthetic pathway, is essential for cellular metabolism. However, the adaptive mechanisms of PPAT in psychrophilic (cold-adapted) organisms remain poorly understood. Here, we characterize PPAT from the psychrophilic methanotroph Methylocapsa palsarum ( Mpa PPAT). Sequence analysis identified a unique five-amino-acid insertion (SCRLS) within a surface-exposed loop, a feature conserved among psychrophilic homologues. To investigate its function, we determined the crystal structures of wild-type (WT) Mpa PPAT and a loop-deletion mutant ( Mpa PPAT(Δ67–71)) and performed comparative biochemical analyses. Structurally, Mpa PPAT forms a dimer-of-trimers hexamer. Biochemically, WT Mpa PPAT maintains high catalytic activity at low temperatures (10–20 °C), whereas the Mpa PPAT(Δ67–71) mutant exhibits impaired cold activity. The mutant structure reveals that the deletion of the distant surface loop induces a long-range allosteric change, resulting in a dual impairment: 1) a stabilization and rigidification (“clamping”) of the central α-helix 4 (H4) at the hexameric core interface, and 2) a dramatic shift in the central pore’s electrostatic potential from positive (WT) to negative (mutant). Our findings reveal that the SCRLS insertion is a critical allosteric modulator that provides a sophisticated dual mechanism for enzymatic cold adaptation. It maintains the conformational flexibility of the hexameric core, preventing the “clamping” effect, and simultaneously ensures a positively charged central channel to electrostatically steer negatively charged substrates (ATP and phosphopantetheine) into the active site, thereby overcoming the kinetic challenges of a low-temperature environment.

Background: Adenine phosphoribosyltransferase (APRT) is an enzyme that facilitates adenosine monophosphate (AMP) biosynthesis by transferring a phosphoribosyl group to adenine using phosphoribosyl pyrophosphate as a donor. While the human enzyme is well characterized, structural insights into bacterial APRTs remain limited. Fusobacterium nucleatum is associated with periodontal disease, yet its APRT enzyme (FnAPRT) has not been structurally investigated. Objective: This study aimed to examine the crystal structure of FnAPRT and ligand-induced conformational changes to understand its enzymatic and substrate recognition mechanisms. Methods: The FnAPRT protein was heterologously expressed in Escherichia coli, followed by initial purification using nickel-charged affinity resin chromatography and further purification through size-exclusion chromatography. The FnAPRT structure was resolved using X-ray crystallography and compared with that of E. coli APRT (EcAPRT), exhibiting the highest amino acid sequence similarity among bacterial APRT structures. Results: AMP and phosphate (PO₄) were observed in the active site of FnAPRT. Significant differences in ligand positioning were observed between the AMP-PO₄-bound structures of FnAPRT and EcAPRT. Structural shifts induced by AMP-PO₄ binding were detected. The Arg78 and Lys82 residues from the alternate subunit occupied the PO₄ site in the absence of ligands, but they interacted with PO₄ upon AMP-PO₄ binding. Structural comparison of the AMP-PO₄-bound FnAPRT with that of the adenine-bound EcAPRT highlighted variations in the adenine-binding site and associated structural changes. Discussion: Structural comparison of the AMP-PO₄-bound FnAPRT with that of the adeninebound EcAPRT highlighted variations in the adenine-binding site and the associated structural changes. Conclusion: The AMP-PO₄-bound FnAPRT exhibited distinct ligand-binding modes despite sharing a high sequence similarity with EcAPRT. The structures demonstrated ligand movement during bacterial APRT reactions.

Cold-active lipolytic enzymes enable low-temperature biocatalysis, but remain underexplored in Antarctic actinomycetes. Here, we report the discovery and first-step characterization of a CALB-like cold-active lipolytic enzyme (PanLip) from Pseudonocardia antarctica. Sequence and structure analyses revealed a canonical α/β-hydrolase fold with a conserved Ser–Asp–His triad and short helical elements around the pocket reminiscent of CALB’s α5/α10 lid. Mature PanLip was expressed primarily as inclusion bodies in E. coli; an N-terminally truncation (PanLipΔN) improved solubility and PanLipΔN was purified by Ni–NTA. Far-UV CD confirmed a folded α/β architecture. PanLipΔN favored short-chain substrates (p-NPA, k_cat/K_M = 2.4 × 10⁵ M⁻¹·s⁻¹) but also showed measurable hydrolytic activity toward natural triglycerides, consistently with a lipase-family esterase. The enzyme showed an activity optimum near 25 °C and pH 8.0. The enzyme tolerated low salt (maximal at 0.1 M NaCl), mild glycerol, and selected organic solvents (notably n-hexane), but was inhibited by high salt, Triton X-100, and SDS. AlphaFold predicted high local confidence for the catalytic core; DALI placed PanLip closest to fungal lipases (AFLB/CALB). Temperature-series MD and CABS-flex indicated enhanced surface breathing and flexible segments adjacent to the active site—including a region topologically matching CALB α10—supporting a flexibility-assisted access mechanism at low temperature. Structure-based MSAs did not support a cold adaptation role for the reported VDLPGRS motif. Taken together, these findings position PanLip as a promising cold-active catalyst with CALB-like access control and potential for low-temperature biocatalysis.

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.

Sulfurtransferases transfer of sulfur atoms from thiols to acceptors like cyanide. They are categorized as thiosulfate sulfurtransferases (TSTs) and 3-mercaptopyruvate sulfurtransferases (MSTs). TSTs transfer sulfur from thiosulfate to cyanide, producing thiocyanate. MSTs transfer sulfur from 3-mercaptopyruvate to cyanide, yielding pyruvate and thiocyanate. The present study aimed to isolate and characterize the sulfurtransferase FrST from Frondihabitans sp. PAMC28461 using biochemical and structural analyses. FrST exists as a dimer and can be classified as a TST rather than an MST according to sequence-based clustering and enzyme activity. Furthermore, the discovery of activity over a wide temperature range and the broad substrate specificity exhibited by FrST suggest promising prospects for its utilization in industrial applications, such as the detoxification of cyanide.