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223 a.a.
Key reference
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.
Literature references that cite this PDB file's key reference
PubMed id Reference
18553118 D.E.Kim, E.Y.Lee, and H.S.Kim (2009).
Cloning and Characterization of Alginate Lyase from a Marine Bacterium Streptomyces sp. ALG-5.Mar Biotechnol (NY), 11, 10-16.
19002649 T.Kobayashi, K.Uchimura, M.Miyazaki, Y.Nogi, and K.Horikoshi (2009).
A new high-alkaline alginate lyase from a deep-sea bacterium Agarivorans sp.Extremophiles, 13, 121-129.
18566914 B.Nocek, L.Bigelow, J.Abdullah, and A.Joachimiak (2008).
Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.J Struct Funct Genomics, 9, 1-6.
PDB code: 2a5z
18574239 H.J.Rozeboom, T.M.Bjerkan, K.H.Kalk, H.Ertesvåg, S.Holtan, F.L.Aachmann, S.Valla, and B.W.Dijkstra (2008).
Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.J Biol Chem, 283, 23819-23828.
PDB codes: 2pyg 2pyh
17947240 A.Ochiai, T.Itoh, Y.Maruyama, A.Kawamata, B.Mikami, W.Hashimoto, and K.Murata (2007).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
16612536 L.Marsh (2006).
Evolution of structural shape in bacterial globin-related proteins.J Mol Evol, 62, 575-587. 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 code is shown on the right.
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