Escherichia coli K12 YgjK complexed with glucose

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.146 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YgjK
A, B
760Escherichia coli K-12Mutation(s): 0 
Gene Names: b3080JW3051ygjK
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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
C6 H12 O6
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.64α = 90
b = 138.68β = 96.82
c = 87.06γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary