5OHS

A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases.

Abayakoon, P.Jin, Y.Lingford, J.P.Petricevic, M.John, A.Ryan, E.Wai-Ying Mui, J.Pires, D.E.V.Ascher, D.B.Davies, G.J.Goddard-Borger, E.D.Williams, S.J.

(2018) ACS Cent Sci 4: 1266-1273

  • DOI: https://doi.org/10.1021/acscentsci.8b00453
  • Primary Citation of Related Structures:  
    5OHS, 5OHT, 5OHY

  • PubMed Abstract: 

    An estimated 10 billion tonnes of sulfoquinovose (SQ) are produced and degraded each year. Prokaryotic sulfoglycolytic pathways catabolize sulfoquinovose (SQ) liberated from plant sulfolipid, or its delipidated form α-d-sulfoquinovosyl glycerol (SQGro), through the action of a sulfoquinovosidase (SQase), but little is known about the capacity of SQ glycosides to support growth. Structural studies of the first reported SQase ( Escherichia coli YihQ) have identified three conserved residues that are essential for substrate recognition, but crossover mutations exploring active-site residues of predicted SQases from other organisms have yielded inactive mutants casting doubt on bioinformatic functional assignment. Here, we show that SQGro can support the growth of E. coli on par with d-glucose, and that the E. coli SQase prefers the naturally occurring diastereomer of SQGro. A predicted, but divergent, SQase from Agrobacterium tumefaciens proved to have highly specific activity toward SQ glycosides, and structural, mutagenic, and bioinformatic analyses revealed the molecular coevolution of catalytically important amino acid pairs directly involved in substrate recognition, as well as structurally important pairs distal to the active site. Understanding the defining features of SQases empowers bioinformatic approaches for mapping sulfur metabolism in diverse microbial communities and sheds light on this poorly understood arm of the biosulfur cycle.


  • Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-glucosidase yihQ
A, B, C, D, E
A, B, C, D, E, F, G, H
672Agrobacterium tumefaciensMutation(s): 3 
Gene Names: SY94_3281
EC: 3.2.1.20 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for A9CEZ0 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CEZ0 
Go to UniProtKB:  A9CEZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CEZ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NSQ
Query on NSQ

Download Ideal Coordinates CCD File 
CB [auth G]
GA [auth D]
GB [auth H]
LA [auth E]
Q [auth A]
CB [auth G],
GA [auth D],
GB [auth H],
LA [auth E],
Q [auth A],
V [auth B],
WA [auth F],
Y [auth C]
4-nitrophenyl alpha-D-6-sulfoquinovoside
C12 H15 N O10 S
JRVQBBIDMNDOQV-ZIQFBCGOSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
IA [auth E]
K [auth A]
L [auth A]
BA [auth D],
CA [auth D],
IA [auth E],
K [auth A],
L [auth A],
M [auth A],
OA [auth F],
PA [auth F],
R [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
DA [auth D]
EA [auth D]
FA [auth D]
AB [auth G],
BB [auth G],
DA [auth D],
EA [auth D],
FA [auth D],
FB [auth H],
KA [auth E],
O [auth A],
P [auth A],
RA [auth F],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
VA [auth F],
X [auth C],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
AA [auth D]
DB [auth H]
HA [auth E]
I [auth A]
J [auth A]
AA [auth D],
DB [auth H],
HA [auth E],
I [auth A],
J [auth A],
MA [auth F],
NA [auth F],
XA [auth G]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
W [auth C],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EB [auth H]
JA [auth E]
N [auth A]
QA [auth F]
S [auth B]
EB [auth H],
JA [auth E],
N [auth A],
QA [auth F],
S [auth B],
YA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.2α = 90
b = 169.19β = 92.8
c = 169.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomAdG-322942

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary