Structure Prediction of a Novel Exo-β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12

Abstract

We report a detailed structural analysis of the psychrophilic exo-β-1,3-glucanase (GaExg55) from Glaciozyma antarctica PI12. This study elucidates the structural basis of exo-1,3-β-1,3-glucanase from this psychrophilic yeast. The structural prediction of GaExg55 remains a challenge because of its low sequence identity (37 %). A 3D model was constructed for GaExg55. Threading approach was employed to determine a suitable template and generate optimal target-template alignment for establishing the model using MODELLER9v15. The primary sequence analysis of GaExg55 with other mesophilic exo-1,3-β-glucanases indicated that an increased flexibility conferred to the enzyme by a set of amino acids substitutions in the surface and loop regions of GaExg55, thereby facilitating its structure to cold adaptation. A comparison of GaExg55 with other mesophilic exo-β-1,3-glucanases proposed that the catalytic activity and structural flexibility at cold environment were attained through a reduced amount of hydrogen bonds and salt bridges, as well as an increased exposure of the hydrophobic side chains to the solvent. A molecular dynamics simulation was also performed using GROMACS software to evaluate the stability of the GaExg55 structure at varying low temperatures. The simulation result confirmed the above findings for cold adaptation of the psychrophilic GaExg55. Furthermore, the structural analysis of GaExg55 with large catalytic cleft and wide active site pocket confirmed the high activity of GaExg55 to hydrolyze polysaccharide substrates.

Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12

“…These findings are linked to the increment of structure flexibility under cold conditions [40]. The increment of structural flexibility in cold adaptation is also supported by other findings such as G. antarctica esterase [41], exo-b-1,3-glucanase [42], laminarinase [43], β-mannanase [44], α-amylase [45] and lipase (HSL)-like esterase [46]. Structural elucidation of G. antarctica fuculose aldolase using X-ray crystallography data shows that the enzyme retains a highly conserved catalytic histidine triad, an increase in its non-polar residues on the protein surface and a lower number of arginine residues, features that serve for adaptation in the cold [47].…”

A Novel Cold-Adapted Leucine Dehydrogenase from Antarctic Sea-Ice Bacterium Pseudoalteromonas sp. ANT178

“…PsLeuDH also had less hydrophobic interactions compared to BsLeuDH, it might make PsLeuDH less rigid and contributed to decrease in structural stability [ 18 ]. Secondly, PsLeuDH revealed higher glycine residues and fewer proline and arginine residues that could affect the cold-adapted proteins properties which might offer higher flexibility to proteins [ 19 ]. Several amino acid residues in BsLeuDH were replaced by glycine residues in PsLeuDH.…”

“…Some arginine residues in PsLeuDH were replaced by other residues at the same position in BsLeuDH. One of the stability factors in protein structure referred to salt bridges formed by arginine residues [ 19 ], arginine might make protein molecules more stable through ionic interaction. Compared with mesophilic enzyme BsLeuDH, PsLeuDH had higher flexibility and lower thermal stability, resulting in higher catalytic efficiency at low temperature [ 21 ].…”

Biotechnological Aspects of Salt-Tolerant Xylanases: A Review

“…The molecular characteristics involved in the high structural flexibility of salt-tolerant enzymes include the following: (I) At the level of the primary structure, a high proportion of small amino acids is observed for salt-tolerant xylanases . Small amino acids have small side chain groups, which can reduce the interactions among the residues, subsequently leading to a total increase of structural flexibility. , (II) At the secondary structure level, a high percentage of random coil structures at the expense of α-helices is observed in salt-tolerant xylanases. , Random coil structures possess a higher structural flexibility than α-helices and, thus, enhance the overall flexibility. , (III) At the tertiary structure level, salt-tolerant xylanases have fewer salt bridges and hydrogen bonds than their counterparts . The decreased non-covalent bonds in the protein structure are considered beneficial for the conversion to different enzyme conformations, thus leading to increased structural flexibility. , …”