PDBsum entry: 1uai

Lyase

PDB id: 1uai

Contents

Protein chain

223 a.a. *

Waters ×346

* Residue conservation analysis

PDB id:

1uai

Name:

Lyase

Title:

Crystal structure of the alginate lyase from corynebacterium sp.

Structure:

Polyguluronate lyase. Chain: a. Synonym: alginate lyase. Ec: 4.2.2.11

Source:

Corynebacterium sp.. Organism_taxid: 1720

Resolution:

1.20Å R-factor: 0.170 R-free: 0.190

Authors:

Y.Kakuta

Key ref:

T.Osawa et al. (2005). Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution. J Mol Biol, 345, 1111-1118. PubMed id: 15644208 DOI: 10.1016/j.jmb.2004.10.081

Date:

11-Mar-03 Release date: 27-Jul-04

Protein chain

Q9RB42  (Q9RB42_9CORY) -  Polyguluronate lyase (Precursor)

Seq: 256 a.a.

Struc: 223 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.2.11 - Poly(alpha-L-guluronate) lyase.
• Reaction: Eliminative cleavage of polysaccharides containing a terminal alpha-L- guluronate group, to give oligosaccharides with 4-deoxy-alpha-L-erythro- hex-4-enuronosyl groups at their non-reducing ends.

 Gene Ontology (GO) functional annotation 

• Biochemical function: lyase activity (2 terms)

DOI no: 10.1016/j.jmb.2004.10.081

J Mol Biol 345:1111-1118 (2005)

PubMed id: 15644208

Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution.

T.Osawa, Y.Matsubara, T.Muramatsu, M.Kimura, Y.Kakuta.

ABSTRACT

The crystal structure of alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. (ALY-1) was determined at 1.2A resolution using the MAD method and bromide ions. The structure of ALY-1 is abundant in beta-strands and has a deep cleft, similar to the jellyroll beta-sandwich found in 1,3-1,4-beta-glucanase. The structure suggests that alginate molecules may penetrate into the cleft to interact with the catalytic site of ALY-1. The reported crystal structure of another type of alginate lyase, A1-III, differs from that of ALY-1 in that it consists almost entirely of alpha-helical structure. Nevertheless, the putative catalytic residues in both enzymes are positioned in space in nearly identical arrangements. This finding suggests that both alginate lyases may have evolved through convergent evolution.

Selected figure(s)

Figure 2.
Figure 2. Final 2F[o] -F[c] electron density map at 1.2 Å resolution, contoured at 3 s, of the putative active site. All Figures here were prepared using program Pymol (http://www.pymol.org).

Figure 5.
Figure 5. A stereo view of ALY-1 superimposed on 1,3-1,4-b-glucanase in complex with the suicide inhibitor (PDB code 1byh). ALY-1 and 1,3-1,4-b-glucanase are shown as dark gray and bright gray, respectively. The suicide inhibitor bound to 1,3-1,4-b-glucanase is shown in gray in a stick model.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 1111-1118) copyright 2005.

Figures were selected by an automated process.