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

The open reading frame Rv1326c of Mycobacterium tuberculosis (Mtb) H37Rv encodes for an alpha-1,4-glucan branching enzyme (MtbGlgB, EC, 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).
PDB ID: 3K1DDownload
MMDB ID: 81848
PDB Deposition Date: 2009/9/27
Updated in MMDB: 2011/05
Experimental Method:
x-ray diffraction
Resolution: 2.33  Å
Source Organism:
Similar Structures:
Biological Unit for 3K1D: monomeric; determined by author and by software (PISA)
Molecular Components in 3K1D
Label Count Molecule
Protein (1 molecule)
1,4-alpha-glucan-branching Enzyme
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB