PDBsum entry 5v3c

Transferase

PDB id: 5v3c

Contents

Protein chain

373 a.a.

Ligands

AMH

PEG ×2

DMS ×2

PGE

Metals

_ZN

Waters ×226

PDB id:

5v3c

Name:

Transferase

Title:

Crystal structure of tgt in complex with 4-(aminomethane)cyclohexane- 1-carboxylic acid

Structure:

Queuine tRNA-ribosyltransferase. Chain: a. Synonym: guanine insertion enzyme,tRNA-guanine transglycosylase. Engineered: yes

Source:

Zymomonas mobilis. Organism_taxid: 542. Gene: tgt, zmo0363. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: codonplus.

Resolution:

1.42Å R-factor: 0.135 R-free: 0.155

Authors:

E.Hassaan,A.Heine,G.Klebe

Key ref:

E.Hassaan et al. (2020). Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. ChemMedChem, 15, 324-337. PubMed id: 31808981 DOI: 10.1002/cmdc.201900604

Date:

07-Mar-17 Release date: 16-May-18

Protein chain

P28720  (TGT_ZYMMO) -  Queuine tRNA-ribosyltransferase from Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

Seq: 386 a.a.

Struc: 373 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.4.2.29 - tRNA-guanosine(34) preQ1 transglycosylase.
• Reaction: 7-aminomethyl-7-carbaguanine + guanosine₃₄ in tRNA = 7-aminomethyl-7- carbaguanosine₃₄ in tRNA + guanine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/cmdc.201900604

ChemMedChem 15:324-337 (2020)

PubMed id: 31808981

Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies.

E.Hassaan, P.O.Eriksson, S.Geschwindner, A.Heine, G.Klebe.

ABSTRACT

Crystallography provides structural information crucial for fragment optimization, however several criteria must be met to screen directly on protein crystals as soakable, well-diffracting specimen must be available. We screened a 96-fragment library against the tRNA-modifying enzyme TGT using crystallography. Eight hits, some with surprising binding poses, were detected. However, the amount of data collection, reduction and refinement is assumed substantial. Therefore, having a reliable cascade of fast and cost-efficient methods available for pre-screening before embarking to elaborate crystallographic screening appears beneficial. This allows filtering of compounds to the most promising hits, available to rapidly progress from hit-to-lead. But how to ensure that this workflow is reliable? To answer this question, we also applied SPR and NMR to the same screening sample to study whether identical hits are retrieved. Upon hit-list comparisons, crystallography shows with NMR and SPR, only one overlapping hit and all three methods shared no common hits. This questions a cascade-type screening protocol at least in the current example. Compared to crystallography, SPR and NMR detected higher percentages of non-active-site binders suggesting the importance of running reporter ligand-based competitive screens in SPR and NMR, a requirement not needed in crystallography. Although not specific, NMR proved a more sensitive method relative to SPR and crystallography, as it picked up the highest numbers of binders.