PDBsum entry 1ktw

Hydrolase

PDB id: 1ktw

Contents

Protein chains

457 a.a. *

Ligands

G4S-DGS

G4S-DGS-G4S-DGS

Metals

_CL ×2

_CA ×10

_NA ×4

Waters ×522

* Residue conservation analysis

PDB id:

1ktw

Name:

Hydrolase

Title:

Iota-carrageenase complexed to iota-carrageenan fragments

Structure:

Iota-carrageenase. Chain: a, b. Fragment: catalytic domain, residues 28-491. Engineered: yes

Source:

Alteromonas sp. Atcc 43554. Organism_taxid: 116059. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.203 R-free: 0.238

Authors:

G.Michel,R.Kahn,O.Dideberg

Key ref:

G.Michel et al. (2003). The structural bases of the processive degradation of iota-carrageenan, a main cell wall polysaccharide of red algae. J Mol Biol, 334, 421-433. PubMed id: 14623184 DOI: 10.1016/j.jmb.2003.09.056

Date:

18-Jan-02 Release date: 10-Jun-03

Protein chains

Q9F5I8  (CGIA_ALTMA) -  Iota-carrageenase from Alteromonas macleodii

Seq: 491 a.a.

Struc: 457 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.157 - iota-carrageenase.

DOI no: 10.1016/j.jmb.2003.09.056

J Mol Biol 334:421-433 (2003)

PubMed id: 14623184

The structural bases of the processive degradation of iota-carrageenan, a main cell wall polysaccharide of red algae.

G.Michel, W.Helbert, R.Kahn, O.Dideberg, B.Kloareg.

ABSTRACT

iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers.

Selected figure(s)

Figure 3.
Figure 3. Movement of domain A results in the formation of a tunnel-shaped active site. A, Stereo view of the superposition of molecule 1 complexed to i-carrageenan oligosaccharides with molecule 2. Molecules 1 and 2 are shown as blue and brown coils, respectively. Molecular surface of A. fortis i-carrageenase in the open conformation (B) and in the substrate-induced tunnel conformation (C). The surface is colored according to electrostatic potential, ranging from + (deep blue) to - (red). The i-carrageenan oligosaccharides are shown as balls and sticks. Oxygen and sulfur atoms are shown in red and green, respectively. Carbon atoms are shown in yellow (A) or in white (C). Figure 3 and Figure 6 were prepared using GRASP. [65.]

Figure 6.
Figure 6. Model of the enzymatic dissociation of i-carrageenan fibers. A, Molecular surface of A. fortis i-carrageenase seen from the direction opposite to the active site groove. The surface is colored according to electrostatic potential, ranging from + (deep blue) to - (red). The trace of a i-carrageenan chain engaged in hydrolysis is shown as a black line, from the reducing (R) to the non-reducing (NR) ends. B, Model of the enzymatic dissociation of i-carrageenan double-helix aggregates. Positive signs represent basic residues at the outer surface of i-carrageenase. The calcium ions coordinating the i-carrageenan double helices are shown as red dots. We postulate that the polycationic character of the outer, non-catalytic face of i-carrageenase is invoved with the displacement of these calcium ions, resulting in the peeling of the i-carrageenan fibers.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 421-433) copyright 2003.

Figures were selected by an automated process.