6H9X

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily.

De Ruysscher, D.Pang, L.De Graef, S.Nautiyal, M.De Borggraeve, W.M.Rozenski, J.Strelkov, S.V.Weeks, S.D.Van Aerschot, A.

(2019) Eur.J.Med.Chem. 174: 252-264

  • DOI: 10.1016/j.ejmech.2019.04.045

  • PubMed Abstract: 
  • The superfamily of adenylate-forming enzymes all share a common chemistry. They activate a carboxylate group, on a specific substrate, by catalyzing the formation of a high energy mixed phosphoanhydride-linked nucleoside intermediate. Members of this ...

    The superfamily of adenylate-forming enzymes all share a common chemistry. They activate a carboxylate group, on a specific substrate, by catalyzing the formation of a high energy mixed phosphoanhydride-linked nucleoside intermediate. Members of this diverse enzymatic family play key roles in a variety of metabolic pathways and therefore many have been regarded as drug targets. A generic approach to inhibit such enzymes is the use of non-hydrolysable sulfur-based bioisosteres of the adenylate intermediate. Here we compare the activity of compounds containing a sulfamoyl and sulfonamide linker respectively. An improved synthetic strategy was developed to generate inhibitors containing the latter that target isoleucyl- (IleRS) and seryl-tRNA synthetase (SerRS), two structurally distinct representatives of Class I and II aminoacyl-tRNA synthetases (aaRSs). These enzymes attach their respective amino acid to its cognate tRNA and are indispensable for protein translation. Evaluation of the ability of the two similar isosteres to inhibit serRS revealed a remarkable difference, with an almost complete loss of activity for seryl-sulfonamide 15 (SerSoHA) compared to its sulfamoyl analogue (SerSA), while inhibition of IleRS was unaffected. To explain these observations, we have determined a 2.1 Å crystal structure of Klebsiella pneumoniae SerRS in complex with SerSA. Using this structure as a template, modelling of 15 in the active site predicts an unfavourable eclipsed conformation. We extended the same modelling strategy to representative members of the whole adenylate-forming enzyme superfamily, and were able to disclose a new classification system for adenylating enzymes, based on their protein fold. The results suggest that, other than for the structural and functional orthologues of the Class II aaRSs, the O to C substitution within the sulfur-sugar link should generally preserve the inhibitory potency.


    Organizational Affiliation

    KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium; KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Biocrystallography, Herestraat 49 BOX 822, 3000 Leuven, Belgium.,KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium.,KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Biocrystallography, Herestraat 49 BOX 822, 3000 Leuven, Belgium.,KU Leuven, Department of Chemistry, Molecular Design and Synthesis, Celestijnenlaan 200F BOX 2404, 3001 Leuven, Belgium.,KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 BOX 1030, 3000 Leuven, Belgium. Electronic address: arthur.vanaerschot@kuleuven.be.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine--tRNA ligase
A
430Klebsiella pneumoniaeMutation(s): 0 
Gene Names: serS (serS_1, serS_2)
EC: 6.1.1.11
Find proteins for W9BNU9 (Klebsiella pneumoniae)
Go to UniProtKB:  W9BNU9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA
Query on SSA

Download SDF File 
Download CCD File 
A
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.407α = 90.00
b = 84.407β = 90.00
c = 229.874γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG077814N
Research Foundation - FlandersBelgiumG0A4616N
Research Foundation - FlandersBelgium1109117N

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release