7EC9

Structure of the Thermotoga maritima Family 5 endo-glucanase in complex with 1-deoxynojiromycin

Summary for 7EC9

• Entry DOI: 10.2210/pdb7ec9/pdb
• Descriptor: Endoglucanase, 1-DEOXYNOJIRIMYCIN, ISOPROPYL ALCOHOL, ... (4 entities in total)
• Functional Keywords: family 5 glycosyl hydrolase, inhibitor complex, tim-barrel fold, beta-glycosidase, hydrolase
• Biological source: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
• Total number of polymer chains: 2
• Total formula weight: 82077.51

Authors

Manoj, N.,Garg, P. (deposition date: 2021-03-11, release date: 2022-03-16, Last modification date: 2023-11-29)

Primary citation

Garg, P.,Manoj, N.
Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site.
Biochimie, 204:69-77, 2023

PubMed Abstract: TmCel5B is a lichenase belonging to glycoside hydrolase family 5 subfamily 36 (GH5_36). To gain insights into the active site of this subfamily which contains multifunctional endoglycanases, we determined the crystal structure of TmCel5B in complex with an iminosugar, 1-deoxynojiromycin (DNJ). DNJ is bound to the -1 subsite, making a network of non-covalent interactions with the acid/base residue Glu139, the nucleophile Glu259, and with other residues that are conserved across the GH5 family. The catalytic site displayed a Glu-Arg-Glu triad of the catalytic glutamates that is unique to the GH5_36 subfamily. Structural comparison of active sites of GH5_36 homologs revealed divergent residues and loop regions that are likely molecular determinants of homolog-specific properties. Furthermore, a comparative analysis of the binding modes of iminocyclitol complexes of GH5 homologs revealed the structural basis of their binding to GH5 glycosidases, in which the subsite binding location, the interactions of the ligand with specific conserved residues, and the electrostatic interactions of the catalytic glutamates with the ring nitrogen, are crucial.

PubMed: 36084911
DOI: 10.1016/j.biochi.2022.09.001

Experimental method

X-RAY DIFFRACTION (1.8 Å)