7XSH

Crystal structure of ClAgl29B bound with L-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 

Starting Model: experimental
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Literature

Discovery of alpha-l-Glucosidase Raises the Possibility of alpha-l-Glucosides in Nature.

Shishiuchi, R.Kang, H.Tagami, T.Ueda, Y.Lang, W.Kimura, A.Okuyama, M.

(2022) ACS Omega 7: 47411-47423

  • DOI: https://doi.org/10.1021/acsomega.2c06991
  • Primary Citation of Related Structures:  
    7XSF, 7XSG, 7XSH

  • PubMed Abstract: 

    Glucose, a common monosaccharide in nature, is dominated by the d-enantiomer. Meanwhile, the discovery of l-glucose-utilizing bacteria and the elucidation of their metabolic pathways 10 years ago suggests that l-glucose exists naturally. Most carbohydrates exist as glycosides rather than monosaccharides; therefore, we expected that nature also contains l-glucosides. Sequence analysis within glycoside hydrolase family 29 led us to identify two α-l-glucosidases, ClAgl29A and ClAgl29B, derived from Cecembia lonarensis LW9. ClAgl29A and ClAgl29B exhibited higher K m , k cat , and k cat / K m values for p -nitrophenyl α-l-glucoside than that for p -nitrophenyl α-l-fucoside. Structural analysis of ClAgl29B in complex with l-glucose showed that these enzymes have an active-site pocket that preferentially binds α-l-glucoside, but excludes α-l-fucoside. These results suggest that ClAgl29A and ClAgl29B evolved to hydrolyze α-l-glucoside, implying the existence of α-l-glucoside in nature. Furthermore, α-l-glucosidic linkages (α-l-Glc-(1 → 3)-l-Glc, α-l-Glc-(1 → 2)-l-Glc, and α-l-Glc-(1 → 6)-l-Glc) were synthesized by the transglucosylation activity of ClAgl29A and ClAgl29B. We believe that this study will lead to new research on α-l-glucosides, including determining the physiological effects on humans, and the discovery of novel α-l-glucoside-related enzymes.


  • Organizational Affiliation

    Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-L-fucosidase
A, B
587Cecembia lonarensis LW9Mutation(s): 0 
Gene Names: B879_03287
UniProt
Find proteins for K1KV82 (Cecembia lonarensis (strain CCUG 58316 / KCTC 22772 / LW9))
Explore K1KV82 
Go to UniProtKB:  K1KV82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK1KV82
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Z8T (Subject of Investigation/LOI)
Query on Z8T

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
beta-L-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-QYESYBIKSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
M [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.393α = 90
b = 121.583β = 90
c = 166.372γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K19159

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description