8QC6

Crystal Structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ and sulfoquinovose (SQ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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This is version 1.1 of the entry. See complete history


Literature

Widespread Family of NAD + -Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism.

Kaur, A.Pickles, I.B.Sharma, M.Madeido Soler, N.Scott, N.E.Pidot, S.J.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2023) J Am Chem Soc 145: 28216-28223

  • DOI: https://doi.org/10.1021/jacs.3c11126
  • Primary Citation of Related Structures:  
    8QC2, 8QC3, 8QC5, 8QC6, 8QC8

  • PubMed Abstract: 

    The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD + as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD + provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD + -dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.


  • Organizational Affiliation

    School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase
A, B
392Arthrobacter sp. U41Mutation(s): 0 
Gene Names: ASPU41_10185
UniProt
Find proteins for A0A1C9WRL0 (Arthrobacter sp. U41)
Explore A0A1C9WRL0 
Go to UniProtKB:  A0A1C9WRL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C9WRL0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.561α = 90
b = 73.017β = 90
c = 199.502γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W003805/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Database references