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

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity

Pal, K.Kumar, S.Sharma, S.Garg, S.K.Alam, M.S.Xu, H.E.Agrawal, P.Swaminathan, K.

(2010) J Biol Chem 285: 20897-20903

  • DOI: https://doi.org/10.1074/jbc.M110.121707
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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).

  • Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore 117543.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,4-alpha-glucan-branching enzyme722Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: glgBRv1326c
Find proteins for P9WN45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN45 
Go to UniProtKB:  P9WN45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN45
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.373α = 90
b = 156.861β = 90
c = 48.021γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-19
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description