PDBsum entry 2py2

Antifreeze protein

PDB id

2py2

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Contents

			Protein chains

					(+ 0 more) 127 a.a. *

			Metals

					_CA ×6

			Waters ×581

* Residue conservation analysis

PDB id:

2py2

Links

Name:

Antifreeze protein

Title:

Structure of herring type ii antifreeze protein

Structure:

Antifreeze protein type ii. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Clupea harengus. Atlantic herring. Organism_taxid: 7950. Gene: hafp. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.70Å

R-factor:

0.209

R-free:

0.240

Authors:

Y.Liu,Z.Li,Q.Lin,J.Seetharaman,J.Sivaraman,C.-L.Hew

Key ref:

Y.Liu et al. (2007). Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. Plos One, 2, e548. PubMed id: 17579720

Date:

15-May-07

Release date:

26-Jun-07

PROCHECK

	Headers

	References

Protein chains

Q91992 (Q91992_CLUHA) - Antifreeze protein from Clupea harengus

Seq: Struc:					147 a.a. 127 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	Plos One 2:e548 (2007)
PubMed id: 17579720

Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.
Y.Liu, Z.Li, Q.Lin, J.Kosinski, J.Seetharaman, J.M.Bujnicki, J.Sivaraman, C.L.Hew.

ABSTRACT

In order to survive under extremely cold environments, many organisms produce antifreeze proteins (AFPs). AFPs inhibit the growth of ice crystals and protect organisms from freezing damage. Fish AFPs can be classified into five distinct types based on their structures. Here we report the structure of herring AFP (hAFP), a Ca(2+)-dependent fish type II AFP. It exhibits a fold similar to the C-type (Ca(2+)-dependent) lectins with unique ice-binding features. The 1.7 A crystal structure of hAFP with bound Ca(2+) and site-directed mutagenesis reveal an ice-binding site consisting of Thr96, Thr98 and Ca(2+)-coordinating residues Asp94 and Glu99, which initiate hAFP adsorption onto the [10-10] prism plane of the ice lattice. The hAFP-ice interaction is further strengthened by the bound Ca(2+) through the coordination with a water molecule of the ice lattice. This Ca(2+)-coordinated ice-binding mechanism is distinct from previously proposed mechanisms for other AFPs. However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21396978

M.Lopes-Ferreira, G.S.Magalhães, J.H.Fernandez, I.d.e. .L.Junqueira-de-Azevedo, P.Le Ho, C.Lima, R.H.Valente, and A.M.Moura-da-Silva (2011).
Structural and biological characterization of Nattectin, a new C-type lectin from the venomous fish Thalassophryne nattereri.

Biochimie, 93, 971-980.

20030710

N.Xiao, K.Suzuki, Y.Nishimiya, H.Kondo, A.Miura, S.Tsuda, and T.Hoshino (2010).
Comparison of functional properties of two fungal antifreeze proteins from Antarctomyces psychrotrophicus and Typhula ishikariensis.

FEBS J, 277, 394-403.

18612417

L.A.Graham, S.C.Lougheed, K.V.Ewart, and P.L.Davies (2008).
Lateral transfer of a lectin-like antifreeze protein gene in fishes.

PLoS ONE, 3, e2616.

18753634

Z.Chen, C.H.Cheng, J.Zhang, L.Cao, L.Chen, L.Zhou, Y.Jin, H.Ye, C.Deng, Z.Dai, Q.Xu, P.Hu, S.Sun, Y.Shen, and L.Chen (2008).
Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish.

Proc Natl Acad Sci U S A, 105, 12944-12949.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.