5AED | pdb_00005aed

A bacterial protein structure in glycoside hydrolase family 31

• PDB DOI: https://doi.org/10.2210/pdb5AED/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-28 Released: 2016-02-10 
• Deposition Author(s): Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

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

• PubMed: 26878550 
• DOI: https://doi.org/10.1038/nchembio.2023
• Primary Citation Related Structures: 
  5AED, 5AEE, 5AEG


• 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 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.

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Organizational Affiliation: 
• School of Chemistry, University of Melbourne, Parkville, Victoria, Australia.
Bio21 Molecular Science and Biotechnology Institute, 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.
Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.32 kDa 
• Atom Count: 11,533 
• Modeled Residue Count: 1,345 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCOSIDASE YIHQ	A, B	686	Escherichia coli K-12	Mutation(s): 0  EC: 3.2.1 (PDB Primary Data), 3.2.1.199 (UniProt)
UniProt
Find proteins for P32138 (Escherichia coli (strain K12)) Explore P32138  Go to UniProtKB:  P32138

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], E [auth B], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.71	α = 90
b = 113.177	β = 109.23
c = 111.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Database references
• Version 1.2: 2016-03-30
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other