PDBsum entry: 1r3e

Lyase/RNA

PDB id: 1r3e

Contents

Protein chain

305 a.a. *

DNA/RNA

Waters ×263

* Residue conservation analysis

PDB id:

1r3e

Name:

Lyase/RNA

Title:

Crystal structure of tRNA pseudouridine synthase trub and it complex: RNA-protein recognition through a combination of r docking and induced fit

Structure:

5'-r( Cp Up Gp Up Gp Up (Fhu) p Cp Gp Ap Up Cp Cp Ap Cp Ap G)-3'. Chain: c. Engineered: yes. 5'-r( Cp Up Gp Up Gp Up Up Cp Gp Ap Up Cp Cp Ap C 3'. Chain: d, e. Engineered: yes. tRNA pseudouridine synthase b.

Source:

Synthetic: yes. Thermotoga maritima. Organism_taxid: 2336. Gene: trub. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.10Å R-factor: 0.223 R-free: 0.273

Authors:

H.Pan,S.Agarwalla,D.T.Moustakas,J.Finer-Moore,R.M.Stroud

Key ref:

H.Pan et al. (2003). Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc Natl Acad Sci U S A, 100, 12648-12653. PubMed id: 14566049 DOI: 10.1073/pnas.2135585100

Date:

01-Oct-03 Release date: 04-Nov-03

Protein chain

Q9WZW0  (TRUB_THEMA) -  tRNA pseudouridine synthase B

Seq: 309 a.a.

Struc: 305 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.99.25 - tRNA pseudouridine(55) synthase.
• Reaction: tRNA uridine₅₅ = tRNA pseudouridine₅₅

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (4 terms)
• Biochemical function: isomerase activity (3 terms)

DOI no: 10.1073/pnas.2135585100

Proc Natl Acad Sci U S A 100:12648-12653 (2003)

PubMed id: 14566049

Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

H.Pan, S.Agarwalla, D.T.Moustakas, J.Finer-Moore, R.M.Stroud.

ABSTRACT

RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.

Selected figure(s)

Figure 2.
Fig. 2. Protein-RNA interactions and conformational changes on RNA binding. (A) Schematic representation of protein-RNA interactions. 55 is highlighted with red, and the backbones of the RNA molecules A, B, and C are shown in blue, yellow, and green, respectively. Water-mediated contacts are shown in dashed blue lines, directed interactions to the RNA bases are shown in dashed red lines, interactions to the RNA backbones are shown in dashed black lines, and stacking interactions are shown in dashed green lines. (B) Superposition of E. coli apo TruB (yellow), tmTruB-RNA complex (gray), and E. coli TruB-RNA complex (cyan) (14). (C) Interactions between the three flipped-out bases and the protein residues. Hydrogen bonds are shown as green dashed lines, and hydrophobic interactions are shown as red "eyelashes." The figure was generated by using the program LIGPLOT (27). (D) Detailed view of the specific protein-RNA interactions. (E) Superposition of the T arm bound to TruB (lavender) with corresponding residues from the structure of tRNA^Phe (acceptor stem shown in green, D loop shown in blue). (F) Superposition of the catalytic residues of apo TruB (yellow) and the corresponding residues from tmTruB-RNA complex (blue).

Figure 3.
Fig. 3. Electrostatic surface potential of TruB. The protein surfaces are colored by their electrostatic potentials, from red (-10 kT) to blue (+10 kT). (A) The front and back surfaces of apo TruB. (B) The front surface of apo TruB with 17-base RNA (shown in green with U55 in magenta) docked into the active site and the view 90° away. (C) The front surface of tmTruB with bound RNA substrate and the view 90° away. The RNA molecules A, B, and C are shown in green, yellow, and blue, respectively. The figure was prepared by using GRASP (28).

Figures were selected by the author.