7CTM

Crystal structure of Thermotoga maritima alpha-glucuronidase (TM0752) in complex with NADH and D-glucuronic acid

Summary for 7CTM

• Entry DOI: 10.2210/pdb7ctm/pdb
• Descriptor: Alpha-glucosidase, putative, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, beta-D-glucopyranuronic acid, ... (5 entities in total)
• Functional Keywords: glycosyl hydrolase family 4, nad(p)-binding rossmann-fold domain, ldh c-terminal domain-like, hydrolase activity, alpha-glucuronidase, hydrolase
• Biological source: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
• Total number of polymer chains: 1
• Total formula weight: 57847.53

Authors

Manoj, N.,Mohapatra, B.S. (deposition date: 2020-08-19, release date: 2021-09-01, Last modification date: 2024-10-16)

Primary citation

Mohapatra, S.B.,Manoj, N.
Structural basis of catalysis and substrate recognition by the NAD(H)-dependent alpha-d-glucuronidase from the glycoside hydrolase family 4.
Biochem.J., 478:943-959, 2021

PubMed Abstract: Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure-function relationships within the unique GH4 family.

PubMed: 33565573
DOI: 10.1042/BCJ20200824

Experimental method

X-RAY DIFFRACTION (1.85 Å)