PDBsum entry: 2z2u

Metal binding protein

PDB id: 2z2u

Contents

Protein chain

279 a.a. *

Waters ×77

* Residue conservation analysis

PDB id:

2z2u

Name:

Metal binding protein

Title:

Crystal structure of archaeal tyw1

Structure:

Upf0026 protein mj0257. Chain: a. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.220 R-free: 0.296

Authors:

Y.Suzuki,R.Ishitani,O.Nureki

Key ref:

Y.Suzuki et al. (2007). Crystal Structure of the Radical SAM Enzyme Catalyzing Tricyclic Modified Base Formation in tRNA. J Mol Biol, 372, 1204-1214. PubMed id: 17727881 DOI: 10.1016/j.jmb.2007.07.024

Date:

28-May-07 Release date: 23-Oct-07

Protein chain

Q57705  (TYW1_METJA) -  tRNA wyosine derivatives biosynthesis protein Taw1

Seq: 311 a.a.

Struc: 279 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: tRNA processing (1 term)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1016/j.jmb.2007.07.024

J Mol Biol 372:1204-1214 (2007)

PubMed id: 17727881

Crystal Structure of the Radical SAM Enzyme Catalyzing Tricyclic Modified Base Formation in tRNA.

Y.Suzuki, A.Noma, T.Suzuki, M.Senda, T.Senda, R.Ishitani, O.Nureki.

ABSTRACT

Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue. Among these steps, TYW1 catalyzes the second step to form the tricyclic ring structure, by cyclizing N(1)-methylguanosine. In this study, we solved the crystal structure of TYW1 from Methanocaldococcus jannaschii at 2.4 A resolution. TYW1 assumes an incomplete TIM barrel with (alpha/beta)(6) topology, which closely resembles the reported structures of radical SAM enzymes. Hence, TYW1 was considered to catalyze the cyclization reaction by utilizing the radical intermediate. Comparison with other radical SAM enzymes allowed us to build a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters. Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base.

Selected figure(s)

Figure 1.
Figure 1. Biosynthetic pathway of the wyosine derivatives. (a) Chemical structure of N^1-methylguanosine (m^1G). TRM5 methylates G37 to produce m^1G37, utilizing Ado-Met as a methyl donor. (b) Chemical structure of 4-demethylwyosine (imG-14). The carbon and nitrogen atoms in the tricyclic 1H-imidazo[1,2-α]purine base are numbered. TYW1 catalyzes the cyclization reaction using an unknown substrate X. The carbon atoms from this substrate X are shadowed in red. (c) The chemical structure of wybutosine (yW). TYW2, 3, and 4 attach methyl groups and a side-chain (shadowed in red) using SAM to form yW.

Figure 5.
Figure 5. Unbiased F[o]–F[c] electron density map around the first [4Fe-4S] cluster, contoured at 3.0 σ. Structure factors (F[o]) collected from the crystal soaked in a buffer containing FeCl[3] and Na[2]S were used for the Fourier synthesis.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 372, 1204-1214) copyright 2007.

Figures were selected by an automated process.