8Q59

Crystal structure of metal-dependent class II sulfofructose phosphate aldolase from Yersinia aldovae in complex with sulfofructose phosphate (YaSqiA-Zn-SFP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases.

Sharma, M.Kaur, A.Madiedo Soler, N.Lingford, J.P.Epa, R.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2023) J Biol Chem 299: 105338-105338

  • DOI: https://doi.org/10.1016/j.jbc.2023.105338
  • Primary Citation of Related Structures:  
    8Q57, 8Q58, 8Q59, 8Q5A

  • PubMed Abstract: 

    Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant, algal, and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for SQ breakdown is the sulfoglycolytic Embden-Meyerhof-Parnas pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is understood for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures of complexes with substrate SFP and product dihydroxyacetone phosphate reveal a dimer-of-dimers (tetrameric) assembly, the sulfonate-binding pocket, two metal-binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal-dependent and exhibited high K M values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfoglycolytic Embden-Meyerhof-Parnas gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases have mututally exclusive occurrence within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tagatose-1,6-bisphosphate aldolase kbaY
A, B
309Yersinia aldovaeMutation(s): 0 
Gene Names: kbaY
EC: 4.1.2.40
UniProt
Find proteins for A0A0T9TPS2 (Yersinia aldovae)
Explore A0A0T9TPS2 
Go to UniProtKB:  A0A0T9TPS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0T9TPS2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JP9 (Subject of Investigation/LOI)
Query on JP9

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-oxidanylidene-6-phosphonooxy-hexane-1-sulfonic acid
C6 H13 O11 P S
BXFAKMQEOMYBNM-HSUXUTPPSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.637α = 90
b = 87.739β = 110.66
c = 91.008γ = 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: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Database references