5AED

A bacterial protein structure in glycoside hydrolase family 31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Yihq is a Sulfoquinovosidase that Cleaves Sulfoquinovosyl Diacylglyceride Sulfolipids.

Speciale, G.Jin, Y.Davies, G.J.Williams, S.J.Goddard-Borger, E.D.

(2016) Nat.Chem.Biol. 12: 215

  • DOI: 10.1038/nchembio.2023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sulfoquinovose is produced by photosynthetic organisms at a rate of 10(10) tons per annum and is degraded by bacteria as a source of carbon and sulfur. We have identified Escherichia coli YihQ as the first dedicated sulfoquinovosidase and the gateway ...

    Sulfoquinovose is produced by photosynthetic organisms at a rate of 10(10) tons per annum and is degraded by bacteria as a source of carbon and sulfur. We have identified Escherichia coli YihQ as the first dedicated sulfoquinovosidase and the gateway enzyme to sulfoglycolytic pathways. Structural and mutagenesis studies unveiled the sequence signatures for binding the distinguishing sulfonate residue and revealed that sulfoquinovoside degradation is widespread across the tree of life.


    Organizational Affiliation

    School of Chemistry, University of Melbourne, Parkville, Victoria, Australia.,Department of Chemistry, University of York, Heslington, York, UK.,ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-GLUCOSIDASE YIHQ
A, B
686Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yihQ (squQ)
EC: 3.2.1.199
Find proteins for P32138 (Escherichia coli (strain K12))
Go to UniProtKB:  P32138
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.710α = 90.00
b = 113.177β = 109.23
c = 111.720γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Aimlessdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Database references
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other