PDBsum entry 2qii

Transferase

PDB id: 2qii

Contents

Protein chain

368 a.a. *

Ligands

PQ0

GOL ×3

Metals

_ZN

Waters ×307

* Residue conservation analysis

PDB id:

2qii

Name:

Transferase

Title:

Crystal structure of tRNA-guanine transglycosylase (tgt) from zymomonas mobilis complexed with archaeosine precursor, preq0

Structure:

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

Source:

Zymomonas mobilis. Organism_taxid: 542. Strain: zymomonas mobilis. Gene: tgt. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.166 R-free: 0.213

Authors:

N.Tidten,R.Brenk,A.Heine,K.Reuter,G.Klebe

Key ref:

N.Tidten et al. (2007). Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies. J Mol Biol, 374, 764-776. PubMed id: 17949745 DOI: 10.1016/j.jmb.2007.09.062

Date:

04-Jul-07 Release date: 17-Jul-07

Protein chain

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

Seq: 386 a.a.

Struc: 368 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

7-aminomethyl-7-carbaguanine (Bound ligand (Het Group name = PQ0) corresponds exactly) + guanosine(34) in tRNA = 7-aminomethyl-7- carbaguanosine(34) in tRNA + guanine

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

Added reference

DOI no: 10.1016/j.jmb.2007.09.062

J Mol Biol 374:764-776 (2007)

PubMed id: 17949745

Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.

N.Tidten, B.Stengl, A.Heine, G.A.Garcia, G.Klebe, K.Reuter.

ABSTRACT

Bacterial tRNA-guanine transglycosylase (Tgt) catalyses the exchange of guanine in the wobble position of particular tRNAs by the modified base preQ(1). In vitro, however, the enzyme is also able to insert the immediate biosynthetic precursor, preQ(0), into those tRNAs. This substrate promiscuity is based on a peptide switch in the active site, gated by the general acid/base Glu235. The switch alters the properties of the binding pocket to allow either the accommodation of guanine or preQ(1). The peptide conformer recognising guanine, however, is also able to bind preQ(0). To investigate selectivity regulation, kinetic data for Zymomonas mobilis Tgt were recorded. They show that selectivity in favour of the actual substrate preQ(1) over preQ(0) is not achieved by a difference in affinity but via a higher turnover rate. Moreover, a Tgt(Glu235Gln) variant was constructed. The mutation was intended to stabilise the peptide switch in the conformation favouring guanine and preQ(0) binding. Kinetic characterisation of the mutated enzyme revealed that the Glu235Gln exchange has, with respect to all substrate bases, no significant influence on k(cat). In contrast, K(M)(preQ(1)) is drastically increased, while K(M)(preQ(0)) seems to be decreased. Hence, regarding k(cat)/K(M) as an indicator for catalytic efficiency, selectivity of Tgt in favour of preQ(1) is abolished or even inverted in favour of preQ(0) for Tgt(Glu235Gln). Crystal structures of the mutated enzyme confirm that the mutation strongly favours the binding pocket conformation required for the accommodation of guanine and preQ(0). The way this is achieved, however, significantly differs from that predicted based on crystal structures of wild-type Tgt.

Selected figure(s)

Figure 1.
Fig. 1. Queuine modification pathway. GTP, guanosine triphosphate AdoMet, S-adenosylmethionine; B[12], coenzyme B[12]; oQ, epoxyqueuine.

Figure 2.
Fig. 2. Base exchange mechanism in bacterial Tgt.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 374, 764-776) copyright 2007.

Figures were selected by an automated process.