7AGK

Crystal structure of E. coli SF kinase (YihV) in complex with product sulfofructose phosphate (SFP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis.

Sharma, M.Abayakoon, P.Epa, R.Jin, Y.Lingford, J.P.Shimada, T.Nakano, M.Mui, J.W.Ishihama, A.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2021) ACS Cent Sci 7: 476-487

  • DOI: https://doi.org/10.1021/acscentsci.0c01285
  • Primary Citation of Related Structures:  
    7AG1, 7AG4, 7AG6, 7AG7, 7AGH, 7AGK, 7NE2

  • PubMed Abstract: 

    The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolizes SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase, and sulfofructose-1-phosphate (SFP) aldolase. Our data show that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by three-dimensional structures of each enzyme, which reveal the presence of conserved sulfonate binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a derepressor for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites SQ, SLA, AMP, ADP, ATP, F6P, FBP, PEP, DHAP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity, and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfofructose kinaseA [auth D],
B [auth A],
C [auth B],
D [auth C]
306Escherichia coli K-12Mutation(s): 0 
Gene Names: yihVb3883JW5568
EC: 2.7.1.184
UniProt
Find proteins for P32143 (Escherichia coli (strain K12))
Explore P32143 
Go to UniProtKB:  P32143
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32143
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RAH (Subject of Investigation/LOI)
Query on RAH

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C]
[(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid
C6 H13 O11 P S
IZVMCURFIBVEOJ-ARQDHWQXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.548α = 90
b = 91.856β = 90
c = 312.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2017-190

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description