Crystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to glycoside hydrolase family 63

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 

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Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.

Kurakata, Y.Uechi, A.Yoshida, H.Kamitori, S.Sakano, Y.Nishikawa, A.Tonozuka, T.

(2008) J Mol Biol 381: 116-128

  • DOI: https://doi.org/10.1016/j.jmb.2008.05.061
  • Primary Citation of Related Structures:  
    3D3I, 3W7S, 3W7T, 3W7U

  • PubMed Abstract: 

    Proteins belonging to the glycoside hydrolase family 63 (GH63) are found in bacteria, archaea, and eukaryotes. Eukaryotic GH63 proteins are processing *-glucosidase I enzymes that hydrolyze an oligosaccharide precursor of eukaryotic N-linked glycoproteins. In contrast, the functions of the bacterial and archaeal GH63 proteins are unclear. Here we determined the crystal structure of a bacterial GH63 enzyme, Escherichia coli K12 YgjK, at 1.78 A resolution and investigated some properties of the enzyme. YgjK consists of the N-domain and the A-domain, joined by a linker region. The N-domain is composed of 18 antiparallel beta-strands and is classified as a super-beta-sandwich. The A-domain contains 16 *-helices, 12 of which form an (*/*)(6)-barrel; the remaining 4 *-helices are found in an extra structural unit that we designated as the A'-region. YgjK, a member of the glycoside hydrolase clan GH-G, shares structural similarity with glucoamylase (GH15) and chitobiose phosphorylase (GH94) [corrected] both of which belong to clan GH-L or GH-L-like [corrected] In crystal structures of YgjK in complex with glucose, mannose, and galactose, all of the glucose, mannose, and galactose units were located in the catalytic cleft. YgjK showed the highest activity for the *-1,3-glucosidic linkage of nigerose, but also hydrolyzed trehalose, kojibiose, and maltooligosaccharides from maltose to maltoheptaose, although the activities were low. These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars.

  • Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein ygjK
A, B
761Escherichia coli K-12Mutation(s): 0 
Gene Names: ygjKb3080JW3051
Find proteins for P42592 (Escherichia coli (strain K12))
Explore P42592 
Go to UniProtKB:  P42592
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42592
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.687α = 90
b = 138.549β = 96.6
c = 87.543γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
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: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance