title: Crystal structure of the catalytic domain of a GH16 β-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94.
abstract: A deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94, has a β-agarase (MtAgaA) belonging to the glycoside hydrolase family (GH) 16. The optimal temperature of this bacterium for growth is 43-49 °C, and MtAgaA is stable at 60 °C, which is one of the most thermostable enzymes among GH16 β-agarases. Here, we determined the catalytic domain structure of MtAgaA. MtAgaA consists of a β-jelly roll fold, as observed in other GH16 enzymes. The structure of MtAgaA was most similar to two β-agarases from Zobellia galactanivorans, ZgAgaA, and ZgAgaB. Although the catalytic cleft structure of MtAgaA was similar to ZgAgaA and ZgAgaB, residues at subsite -4 of MtAgaA were not conserved between them. Also, an α-helix, designated as α4', was uniquely located near the catalytic cleft of MtAgaA. A comparison of the structures of the three enzymes suggested that multiple factors, including increased numbers of arginine and proline residues, could contribute to the thermostability of MtAgaA.
authors.affiliation: a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan.
authors.forename: Emiko
authors.initials: E
authors.lastname: Takagi
authors.forename: Yuji
authors.initials: Y
authors.lastname: Hatada
authors.forename: Masatake
authors.initials: M
authors.lastname: Akita
authors.forename: Yukari
authors.initials: Y
authors.lastname: Ohta
authors.forename: Gaku
authors.initials: G
authors.lastname: Yokoi
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Miyazaki
authors.forename: Atsushi
authors.initials: A
authors.lastname: Nishikawa
authors.forename: Takashi
authors.initials: T
authors.lastname: Tonozuka
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry*; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004795:Enzyme Stability; D041965:Flavobacteriaceae / Q000737:chemistry / Q000201:enzymology; D020563:Gammaproteobacteria / Q000737:chemistry* / Q000201:enzymology; D015870:Gene Expression; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006358:Hot Temperature; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011392:Proline / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D011994:Recombinant Proteins; D001120:Arginine; D011392:Proline; D006026:Glycoside Hydrolases; C019624:agarase
keywords: Microbulbifer thermotolerans; crystal structure; glycoside hydrolase family 16(GH16); thermostability; β-agarase