PDBsum entry 5b5h

Antifreeze protein

PDB id: 5b5h

Contents

Protein chain

223 a.a.

Ligands

SO4 ×2

Metals

_NA ×2

Waters ×315

PDB id:

5b5h

Name:

Antifreeze protein

Title:

Hydrophobic ice-binding site confer hyperactivity on antifreeze protein from a snow mold fungus

Structure:

Antifreeze protein. Chain: a. Engineered: yes

Source:

Typhula ishikariensis. Organism_taxid: 69361. Gene: k1-a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.00Å R-factor: 0.121 R-free: 0.136

Authors:

J.Cheng,Y.Hanada,A.Miura,S.Tsuda,H.Kondo

Key ref:

J.Cheng et al. (2016). Hydrophobic ice-binding sites confer hyperactivity of an antifreeze protein from a snow mold fungus. Biochem J, 473, 4011-4026. PubMed id: 27613857 DOI: 10.1042/BCJ20160543

Date:

06-May-16 Release date: 28-Sep-16

Protein chain

Q76CE8  (IBPKA_TYPIS) -  Ice-binding protein K1-A from Typhula ishikariensis

Seq: 243 a.a.

Struc: 223 a.a.

DOI no: 10.1042/BCJ20160543

Biochem J 473:4011-4026 (2016)

PubMed id: 27613857

Hydrophobic ice-binding sites confer hyperactivity of an antifreeze protein from a snow mold fungus.

J.Cheng, Y.Hanada, A.Miura, S.Tsuda, H.Kondo.

ABSTRACT

Snow mold fungus, Typhula ishikariensis, secretes seven antifreeze protein isoforms (denoted TisAFPs) that assist in the survival of the mold under snow cover. Here, the X-ray crystal structure of a hyperactive isoform, TisAFP8, at 1.0 Å resolution is presented. TisAFP8 folds into a right-handed β-helix accompanied with a long α-helix insertion. TisAFP8 exhibited significantly high antifreeze activity that is comparable with other hyperactive AFPs, despite its close structural and sequence similarity with the moderately active isoform TisAFP6. A series of mutations introduced into the putative ice-binding sites (IBSs) in the β-sheet and adjacent loop region reduced antifreeze activity. A double-mutant A20T/A212S, which comprises a hydrophobic patch between the β-sheet and loop region, caused the greatest depression of antifreeze activity of 75%, when compared with that of the wild-type protein. This shows that the loop region is involved in ice binding and hydrophobic residues play crucial functional roles. Additionally, bound waters around the β-sheet and loop region IBSs were organized into an ice-like network and can be divided into two groups that appear to mediate separately TisAFP and ice. The docking model of TisAFP8 with the basal plane via its loop region IBS reveals a better shape complementarity than that of TisAFP6. In conclusion, we present new insights into the ice-binding mechanism of TisAFP8 by showing that a higher hydrophobicity and better shape complementarity of its IBSs, especially the loop region, may render TisAFP8 hyperactive to ice binding.