3K1D

Crystal structure of glycogen branching enzyme synonym: 1,4-alpha-D-glucan:1,4-alpha-D-GLUCAN 6-glucosyl-transferase from mycobacterium tuberculosis H37RV

Summary for 3K1D

• Entry DOI: 10.2210/pdb3k1d/pdb
• Descriptor: 1,4-alpha-glucan-branching enzyme (2 entities in total)
• Functional Keywords: mycobacterium tuberculosis h37rv, mesophilic human pathogen, glgb rv1326c gene, glycosyl transferase, n-terminal sandwic, glycogen biosynthesis, glycosyltransferase, transferase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 80828.07

Authors

Pal, K.,Kumar, S.,Swaminathan, K. (deposition date: 2009-09-27, release date: 2010-05-05, Last modification date: 2023-11-01)

Primary citation

Pal, K.,Kumar, S.,Sharma, S.,Garg, S.K.,Alam, M.S.,Xu, H.E.,Agrawal, P.,Swaminathan, K.
Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity
J.Biol.Chem., 285:20897-20903, 2010

PubMed Abstract: The open reading frame Rv1326c of Mycobacterium tuberculosis (Mtb) H37Rv encodes for an alpha-1,4-glucan branching enzyme (MtbGlgB, EC 2.4.1.18, Uniprot entry Q10625). This enzyme belongs to glycoside hydrolase (GH) family 13 and catalyzes the branching of a linear glucose chain during glycogenesis by cleaving a 1-->4 bond and making a new 1-->6 bond. Here, we show the crystal structure of full-length MtbGlgB (MtbGlgBWT) at 2.33-A resolution. MtbGlgBWT contains four domains: N1 beta-sandwich, N2 beta-sandwich, a central (beta/alpha)(8) domain that houses the catalytic site, and a C-terminal beta-sandwich. We have assayed the amylase activity with amylose and starch as substrates and the glycogen branching activity using amylose as a substrate for MtbGlgBWT and the N1 domain-deleted (the first 108 residues deleted) MtbDelta108GlgB protein. The N1 beta-sandwich, which is formed by the first 105 amino acids and superimposes well with the N2 beta-sandwich, is shown to have an influence in substrate binding in the amylase assay. Also, we have checked and shown that several GH13 family inhibitors are ineffective against MtbGlgBWT and MtbDelta108GlgB. We propose a two-step reaction mechanism, for the amylase activity (1-->4 bond breakage) and isomerization (1-->6 bond formation), which occurs in the same catalytic pocket. The structural and functional properties of MtbGlgB and MtbDelta108GlgB are compared with those of the N-terminal 112-amino acid-deleted Escherichia coli GlgB (ECDelta112GlgB).

PubMed: 20444687
DOI: 10.1074/jbc.M110.121707

Experimental method

X-RAY DIFFRACTION (2.33 Å)