PDBsum entry 2zxh

Fad-binding protein

PDB id: 2zxh

Contents

Protein chains

603 a.a. *

Ligands

FAD ×2

PO4 ×3

* Residue conservation analysis

PDB id:

2zxh

Name:

Fad-binding protein

Title:

Structure of aquifex aeolicus gida in the form i crystal

Structure:

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg. Chain: a, b. Synonym: gida, glucose-inhibited division protein a. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: aq_761. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

3.20Å R-factor: 0.242 R-free: 0.271

Authors:

T.Numata,T.Osawa

Key ref:

T.Osawa et al. (2009). Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure, 17, 713-724. PubMed id: 19446527

Date:

24-Dec-08 Release date: 19-May-09

Protein chains

O66962  (MNMG_AQUAE) -  tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG from Aquifex aeolicus (strain VF5)

Seq: 617 a.a.

Struc: 603 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Structure 17:713-724 (2009)

PubMed id: 19446527

Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon.

T.Osawa, K.Ito, H.Inanaga, O.Nureki, K.Tomita, T.Numata.

ABSTRACT

The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the anticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restricting codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in the cmnm(5)U modification process. Here we determined the crystal structure of Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight interaction of GidA with FAD. Structure-based mutation analyses allowed us to identify two conserved Cys residues in the vicinity of the FAD-binding site that are essential for the cmnm(5)U modification in vivo. Together with mutational analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogous to that of thymidylate synthase. We also present a tRNA-docking model that provides structural insights into the tRNA recognition mechanism for efficient modification.