3WZ1

Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94

Summary for 3WZ1

• Entry DOI: 10.2210/pdb3wz1/pdb
• Descriptor: Agarase, SODIUM ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase family 16, beta-jelly roll fold, beta-agarase, agarose, hydrolase
• Biological source: Microbulbifer thermotolerans
• Total number of polymer chains: 1
• Total formula weight: 32257.44

Authors

Takagi, E.,Hatada, Y.,Akita, M.,Ohta, Y.,Yokoi, G.,Miyazaki, T.,Nishikawa, A.,Tonozuka, T. (deposition date: 2014-09-12, release date: 2014-11-19, Last modification date: 2023-11-08)

Primary citation

Takagi, E.,Hatada, Y.,Akita, M.,Ohta, Y.,Yokoi, G.,Miyazaki, T.,Nishikawa, A.,Tonozuka, T.
Crystal structure of the catalytic domain of a GH16 beta-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94
Biosci.Biotechnol.Biochem., 79:625-632, 2015

PubMed 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.

PubMed: 25483365
DOI: 10.1080/09168451.2014.988680

Experimental method

X-RAY DIFFRACTION (1.6 Å)