1PYB

Crystal Structure of Aquifex aeolicus Trbp111: a Structure-Specific tRNA Binding Protein

Summary for 1PYB

• Entry DOI: 10.2210/pdb1pyb/pdb
• Related: 1PXF
• Descriptor: tRNA-binding protein Trbp111 (2 entities in total)
• Functional Keywords: oligonucleotide, oligosaccharide-binding fold, ob-fold, beta-barrel, rna binding protein
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 4
• Total formula weight: 48448.53

Authors

Swairjo, M.A.,Morales, A.J.,Wang, C.C.,Ortiz, A.R.,Schimmel, P. (deposition date: 2003-07-08, release date: 2003-08-05, Last modification date: 2023-08-16)

Primary citation

Swairjo, M.A.,Morales, A.J.,Wang, C.C.,Ortiz, A.R.,Schimmel, P.
Crystal structure of trbp111: a structure-specific tRNA-binding protein.
Embo J., 19:6287-6298, 2000

PubMed 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.

PubMed: 11101501
DOI: 10.1093/emboj/19.23.6287

Experimental method

X-RAY DIFFRACTION (2.5 Å)