7BYW

Crystal structure of Acidovorax avenae L-fucose mutarotase (L-fucose-bound form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional and structural characterization of a novel L-fucose mutarotase involved in non-phosphorylative pathway of L-fucose metabolism.

Watanabe, Y.Watanabe, S.Fukui, Y.Nishiwaki, H.

(2020) Biochem Biophys Res Commun 528: 21-27

  • DOI: 10.1016/j.bbrc.2020.05.094
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mutarotases catalyze the α-β anomeric conversion of monosaccharide, and play a key role in utilizing sugar as enzymes involved in sugar metabolism have specificity for the α- or β-anomer. In spite of the sequential similarity to l-rhamnose mutarotase ...

    Mutarotases catalyze the α-β anomeric conversion of monosaccharide, and play a key role in utilizing sugar as enzymes involved in sugar metabolism have specificity for the α- or β-anomer. In spite of the sequential similarity to l-rhamnose mutarotase protein superfamily (COG3254: RhaM), the ACAV_RS08160 gene in Acidovorax avenae ATCC 19860 (AaFucM) is located in a gene cluster related to non-phosphorylative l-fucose and l-galactose metabolism, and transcriptionally induced by these carbon sources; therefore, the physiological role remains unclear. Here, we report that AaFucM possesses mutarotation activity only toward l-fucose by saturation difference (SD) NMR experiments. Moreover, we determined the crystal structures of AaFucM in the apo form and in the l-fucose-bound form at resolutions of 2.21 and 1.75 Å, respectively. The overall structural folding was clearly similar to the RhaM members, differed from the known l-fucose mutarotase (COG4154: FucU), strongly indicating their convergent evolution. The structure-based mutational analyses suggest that Tyr18 is important for catalytic action, and that Gln87 and Trp99 are involved in the l-fucose-specific recognition.


    Organizational Affiliation

    Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-fucose mutarotase
A, B
120Acidovorax avenae subsp. avenae ATCC 19860Mutation(s): 0 
Gene Names: Acav_1655
Find proteins for F0Q4R9 (Acidovorax avenae (strain ATCC 19860 / DSM 7227 / JCM 20985 / NCPPB 1011))
Go to UniProtKB:  F0Q4R9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download CCD File 
A, B
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.398α = 90
b = 68.398β = 90
c = 69.102γ = 120
Software Package:
Software NamePurpose
XDSdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references