PDBsum entry 1kde

Antifreeze protein

PDB id: 1kde

Contents

Protein chain

65 a.a. *

* Residue conservation analysis

PDB id:

1kde

Name:

Antifreeze protein

Title:

North-atlantic ocean pout antifreeze protein type iii isoform hplc12 mutant, nmr, 22 structures

Structure:

Antifreeze protein type iii isoform hplc12 mutant. Chain: a. Synonym: kdel. Engineered: yes. Mutation: yes. Other_details: qae-component

Source:

Macrozoarces americanus. Ocean pout. Organism_taxid: 8199. Variant: hplc-12. Tissue: blood. Gene: k38. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

22 models

Authors:

F.D.Sonnichsen,C.I.Deluca,P.L.Davies,B.D.Sykes

Key ref:

F.D.Sönnichsen et al. (1996). Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction. Structure, 4, 1325-1337. PubMed id: 8939756 DOI: 10.1016/S0969-2126(96)00140-2

Date:

08-Jul-96 Release date: 21-Apr-97

Protein chain

P19614  (ANP12_ZOAAM) -  Type-3 ice-structuring protein HPLC 12 from Zoarces americanus

Seq: 66 a.a.

Struc: 65 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(96)00140-2

Structure 4:1325-1337 (1996)

PubMed id: 8939756

Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction.

F.D.Sönnichsen, C.I.DeLuca, P.L.Davies, B.D.Sykes.

ABSTRACT

BACKGROUND: Antifreeze proteins are found in certain fish inhabiting polar sea water. These proteins depress the freezing points of blood and body fluids below that of the surrounding sea water by binding to and inhibiting the growth of seed ice crystals. The proteins are believed to bind irreversibly to growing ice crystals in such a way as to change the curvature of the ice-water interface, leading to freezing point depression, but the mechanism of high-affinity ice binding is not yet fully understood. RESULTS: The solution structure of the type III antifreeze protein was determined by multidimensional NMR spectroscopy. Twenty-two structures converged and display a root mean square difference from the mean of 0.26 A for backbone atoms and 0.62 A for all non-hydrogen atoms. The protein exhibits a compact fold with a relatively large hydrophobic core, several short and irregular beta sheets and one helical turn. The ice-binding site, which encompasses parts of the C-terminal sheet and a loop, is planar and relatively nonpolar. The site is further characterized by the low solvent accessibilities and the specific spatial arrangement of the polar side-chain atoms of the putative ice-binding residues Gln9, Asn14, Thr15, Thr18 and Gln44. CONCLUSIONS: In agreement with the adsorption-inhibition mechanism of action, interatomic distances between active polar protein residues match the spacing of water molecules in the prism planes (¿10&1macr;0¿) of the hexagonal ice crystal. The particular side-chain conformations, however, limit the number and strength of possible proten-ice hydrogen bonds. This suggests that other entropic and enthalpic contributions, such as those arising from hydrophobic groups, could play a role in the high-affinity protein-ice adsorption.

Selected figure(s)

Figure 6.
Figure 6. Solvent accessible surface of type III AFP. The surface was calculated for the restrained minimized average structure. The view shows the ice-binding site with the surface colored by atom type (O=red, N=blue, C/S=white) and labeling of the polar areas with the corresponding residue or atom. Figure 6. Solvent accessible surface of type III AFP. The surface was calculated for the restrained minimized average structure. The view shows the ice-binding site with the surface colored by atom type (O=red, N=blue, C/S=white) and labeling of the polar areas with the corresponding residue or atom. (Figure generated using the program InsightII [Biosym, Palo Alto, CA].)

Figure 8.
Figure 8. Model for the type III AFP bound to the {10 Image 0} plane of ice. (a) View nearly parallel to the ice surface, with the c-axis of the hexagonal ice vertical. Ice water molecules (including protons) are in CPK presentation, and the protein backbone is shown in stick presentation. The polar contacts or hydrogen bonds between protein atoms and ice surface atoms are indicated by yellow lines. (Figure generated using the program InsightII [Biosym, Palo Alto, CA].) (b) Presentation of the excluded molecular surface. The ice surface and protein surface is shown on the left and right, respectively. The applied color gradient from white via blue to red represents distances between the protein and ice surface in the complex from 0 å (direct contact) over 1.4 å (water inaccessible) to 3 å. Figure 8. Model for the type III AFP bound to the {10 [3]Image 0} plane of ice. (a) View nearly parallel to the ice surface, with the c-axis of the hexagonal ice vertical. Ice water molecules (including protons) are in CPK presentation, and the protein backbone is shown in stick presentation. The polar contacts or hydrogen bonds between protein atoms and ice surface atoms are indicated by yellow lines. (Figure generated using the program InsightII [Biosym, Palo Alto, CA].) (b) Presentation of the excluded molecular surface. The ice surface and protein surface is shown on the left and right, respectively. The applied color gradient from white via blue to red represents distances between the protein and ice surface in the complex from 0 å (direct contact) over 1.4 å (water inaccessible) to 3 å. (Figure generated using the program GRASP [[4]55].)

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 1325-1337) copyright 1996.

Figures were selected by an automated process.