7XSH | pdb_00007xsh

Crystal structure of ClAgl29B bound with L-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.202 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.190 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7XSH

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 135.56 kDa 
  • Atom Count: 9,706 
  • Modeled Residue Count: 1,096 
  • Deposited Residue Count: 1,174 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-L-fucosidase
A, B
587Cecembia lonarensis LW9Mutation(s): 0 
Gene Names: B879_03287
EC: 3.2.1.51
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
Expand
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 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
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

View Full Validation Report



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