PDBsum entry: 1ozm

Transferase

PDB id: 1ozm

Contents

Protein chain

372 a.a. *

Metals

_ZN

Waters ×343

* Residue conservation analysis

PDB id:

1ozm

Name:

Transferase

Title:

Y106f mutant of z. Mobilis tgt

Structure:

Queuine tRNA-ribosyltransferase. Chain: a. Synonym: tRNA-guanine transglycosylase, guanine insertion e engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.184 R-free: 0.198

Authors:

R.Brenk,M.T.Stubbs,A.Heine,K.Reuter,G.Klebe

Key ref:

R.Brenk et al. (2003). Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design. Chembiochem, 4, 1066-1077. PubMed id: 14523925 DOI: 10.1002/cbic.200300644

Date:

09-Apr-03 Release date: 30-Sep-03

Protein chain

P28720  (TGT_ZYMMO) -  Queuine tRNA-ribosyltransferase

Seq: 386 a.a.

Struc: 372 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.2.29 - tRNA-guanine transglycosylase.
• Reaction:
  1. [tRNA]-guanine + queuine = [tRNA]-queuine + guanine
  2. [tRNA]-guanine + 7-aminomethyl-7-carbaguanine = [tRNA]-7-aminomethyl- 7-carbaguanine + guanine

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

 Gene Ontology (GO) functional annotation 

• Biological process: tRNA processing (3 terms)
• Biochemical function: transferase activity (4 terms)

reference

DOI no: 10.1002/cbic.200300644

Chembiochem 4:1066-1077 (2003)

PubMed id: 14523925

Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design.

R.Brenk, M.T.Stubbs, A.Heine, K.Reuter, G.Klebe.

ABSTRACT

The enzyme tRNA-guanine transglycosylase (TGT, EC 2.4.2.29) catalyses a base-exchange reaction that leads to anticodon modifications of certain tRNAs. The TGT enzymes of the eubacteria Zymomonas mobilis (Z. mobilis TGT) and Escherichia coli (E. coli TGT) show a different behaviour in the presence of competitive inhibitors. The active sites of both enzymes are identical apart from a single conservative amino acid exchange, namely Tyr106 of Z. mobilis TGT is replaced by a Phe in E. coli TGT. Although Tyr106 is, in contrast to Phe106, hydrogen bonded in the ligand-free structure, we can show by a mutational study of TGT(Y106F) that this is not the reason for the different responses upon competition. The TGT enzymes of various species differ in their substrate selectivity. Depending on the applied pH conditions and/or induced by ligand binding, a peptide-bond flip modulates the recognition properties of the substrate binding site, which changes between donor and acceptor functionality. Furthermore interstitial water molecules play an important role in these adaptations of the pocket. The flip of the peptide bond is further stabilised by a glutamate residue that operates as general acid/base. An active-site aspartate residue, presumed to operate as a nucleophile through covalent bonding during the base-exchange reaction, shows different conformations depending on the nature of the bound ligand. The induced-fit adaptations observed in the various TGT complex structures by multiple crystal-structure analyses are in agreement with the functional properties of the enzyme. In consequence, full understanding of this plasticity can be exploited for drug design.