PDBsum entry 1q2s

Transferase/RNA

PDB id: 1q2s

Contents

Protein chains

376 a.a. *

DNA/RNA

Ligands

9DG

Metals

_ZN ×4

Waters ×93

* Residue conservation analysis

PDB id:

1q2s

Name:

Transferase/RNA

Title:

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Structure:

5'-r( Ap Gp Cp Ap Cp Gp Gp Cp Up (Pq1) p Up Ap Ap Ap Cp Cp Gp Up Gp C)-3'. Chain: e. Engineered: yes. RNA (5'-r( Ap Gp Cp Ap Cp Gp Gp Cp Up (N) p Up Ap Ap Ap Cp Cp Gp Up Gp C)-3'). Chain: f. Engineered: yes. Queuine tRNA-ribosyltransferase.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Zymomonas mobilis. Organism_taxid: 542. Strain: zm4-cp4. Atcc: 31821. Gene: tgt. Expressed in: escherichia coli.

Biol. unit:

Trimer (from PQS)

Resolution:

3.20Å R-factor: 0.180 R-free: 0.235

Authors:

W.Xie,X.Liu,R.H.Huang

Key ref:

W.Xie et al. (2003). Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate. Nat Struct Biol, 10, 781-788. PubMed id: 12949492 DOI: 10.1038/nsb976

Date:

25-Jul-03 Release date: 09-Sep-03

Protein chains

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

Seq: 386 a.a.

Struc: 376 a.a.*

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

DNA/RNA chains

A-G-C-A-C-G-G-C-U-PQ1-U-A-A-A-C-C-G-U-G-C 20 bases

A-G-C-A-C-G-G-C-U-__N-U-A-A-A-C-C-G-U-G-C 20 bases

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 + guanosine(34) in tRNA = 7-aminomethyl-7- carbaguanosine(34) in tRNA + guanine (Bound ligand (Het Group name = 9DG) matches with 83.33% similarity)

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

Added reference

DOI no: 10.1038/nsb976

Nat Struct Biol 10:781-788 (2003)

PubMed id: 12949492

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.

W.Xie, X.Liu, R.H.Huang.

ABSTRACT

Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.

Selected figure(s)

Figure 3.
Figure 3. Overall structure of the trapped covalent intermediate. (a) Ribbon representation of the TGT -RNA -9dzG ternary complex. TGT is colored according to the assignment of the secondary structures in Figure 2. The RNA is dark green. 9dzG is shown in ball-and-stick model in red, and a zinc ion is represented by a ball in magenta. (b) Summary of TGT -RNA, TGT -9dzG and RNA -RNA interactions. TGT, RNA and 9dzG are colored as in a except the phosphate groups of RNA are in magenta. The conserved RNA nucleotides 33 -35, 9dzG and Asp280 are highlighted with color-filled boxes. Arrows in blue represent hydrogen bonds between RNA and TGT, RNA and water, or 9dzG and TGT. Arrows in red show stacking of amino acid side chains from TGT on bases of RNA or on 9dzG. Two arrows in green represent intramolecular interactions in RNA. 'W' in a circle represents well-positioned water molecules in the structure.

Figure 5.
Figure 5. The active site and molecular basis of substrate specificity. (a) Stereo view of TGT active site. The main chains of TGT are grayish blue, the side chains of TGT are orange and the RNA and 9dzG are green. The hetero-atoms are colored individually, with nitrogen in blue, oxygen in red and phosphate in magenta. The C9 of 9dzG is highlighted in black. A water molecule is shown as a small ball in red and labeled 'W'. Hydrogen bonds are indicated with dashed lines. The side chains of Asp106 and Cys158, which block 9dzG from the top, are omitted for clarity. (b,c) Recognition of U33 (b) and U35 (c) in RNA substrate by TGT. The color schemes are the same as in a. The structure of the phosphate group of A38 in c is omitted but labeled for clarity.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 781-788) copyright 2003.

Figures were selected by an automated process.