PDBsum entry 1pyb

RNA binding protein

PDB id: 1pyb

Contents

Protein chains

107 a.a. *

Waters ×174

* Residue conservation analysis

PDB id:

1pyb

Name:

RNA binding protein

Title:

Crystal structure of aquifex aeolicus trbp111: a structure-specific tRNA binding protein

Structure:

tRNA-binding protein trbp111. Chain: a, b, c, d. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: metg. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.208 R-free: 0.226

Authors:

M.A.Swairjo,A.J.Morales,C.C.Wang,A.R.Ortiz,P.Schimmel

Key ref:

M.A.Swairjo et al. (2000). Crystal structure of trbp111: a structure-specific tRNA-binding protein. EMBO J, 19, 6287-6298. PubMed id: 11101501 DOI: 10.1093/emboj/19.23.6287

Date:

08-Jul-03 Release date: 05-Aug-03

Protein chains

O66738  (O66738_AQUAE) -  Methionyl-tRNA synthetase beta subunit from Aquifex aeolicus (strain VF5)

Seq: 111 a.a.

Struc: 107 a.a.

DOI no: 10.1093/emboj/19.23.6287

EMBO J 19:6287-6298 (2000)

PubMed id: 11101501

Crystal structure of trbp111: a structure-specific tRNA-binding protein.

M.A.Swairjo, A.J.Morales, C.C.Wang, A.R.Ortiz, P.Schimmel.

ABSTRACT

Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the A.aeolicus protein and its Escherichia coli homolog at resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical dimer of two core domains and a central dimerization domain where the N- and C-terminal regions of Trbp111 form an extensive dimer interface. The core of the monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a five-stranded ss-barrel and a small capping helix. This structure is similar to that seen in the anticodon-binding domain of three class II tRNA synthetases and several other proteins. Mutational analysis identified sites important for interactions with tRNA. These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer.

Selected figure(s)

Figure 7.
Figure 7 Stereo view of a C[ ]trace of the Trbp111 dimeric structure with all single site mutations described in Figure 6 highlighted in ball-and-stick representation. Side chains of residues found to be important in tRNA binding are in black (on the top side of the dimer) and are labeled. Residues at which an alanine substitution did not correlate with a measurable effect on tRNA binding are shown in gray (bottom side of the dimer). Loops L2 and L6 are indicated. The figure was made with MOLSCRIPT (Kraulis, 1991).

Figure 8.
Figure 8 (A) Highest score docking model of the Trbp111–tRNA complex showing surface complementarity and tRNA binding mode. The protein dimer is shown in a Connolly surface representation (generated in the program InsightII; Molecular Simulations, San Diego, CA) of all non-hydrogen atoms, superimposed on a C[ ]trace. The monomers are shown in different colors. tRNA is shown as sticks. The asterisk denotes the observed cleft (putative tRNA-binding site). Loop L6 is also labeled. (B) Side view of (A) looking down the tRNA acceptor stem helix. The surface electrostatic potential on the Trbp111 dimer is shown. Positive charge potential is shown in blue and negative charge potential in red. The surface is superimposed on a ribbon diagram of the protein. The tRNA is shown in green as a ribbon through the backbone phosphate groups.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 6287-6298) copyright 2000.

Figures were selected by an automated process.