 |
|
|
 |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
457 a.a.
_CL
_CA
Key reference
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.
Literature references that cite this PDB file's key reference
PubMed id Reference
17220218 J.C.Fong, and F.H.Yildiz (2007).
The rbmBCDEF gene cluster modulates development of rugose colony morphology and biofilm formation in Vibrio cholerae.J Bacteriol, 189, 2319-2330.
17192265 W.S.Jung, C.K.Hong, S.Lee, C.S.Kim, S.J.Kim, S.I.Kim, and S.Rhee (2007).
Structural and functional insights into intramolecular fructosyl transfer by inulin fructotransferase.J Biol Chem, 282, 8414-8423.
PDB codes: 2inu 2inv
16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.Appl Microbiol Biotechnol, 71, 23-33.
15155751 G.Michel, K.Pojasek, Y.Li, T.Sulea, R.J.Linhardt, R.Raman, V.Prabhakar, R.Sasisekharan, and M.Cygler (2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.J Biol Chem, 279, 32882-32896.
PDB codes: 1ofl 1ofm 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. Where a reference describes a PDB structure, the PDB codes are shown on the right.
 |