3SOI

Crystallographic structure of Bacillus licheniformis beta-lactamase W210F/W229F/W251F at 1.73 angstrom resolution

3SOI の概要

• エントリーDOI: 10.2210/pdb3soi/pdb
• 関連するPDBエントリー: 4BLM
• 分子名称: Beta-lactamase, CITRIC ACID (3 entities in total)
• 機能のキーワード: hydrolase, (acting in cyclic amides)
• 由来する生物種: Bacillus licheniformis
• 細胞内の位置: Cell membrane; Lipid-anchor (Probable): P00808
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 57653.07

構造登録者

Acierno, J.P.,Capaldi, S.,Risso, V.A.,Monaco, H.L.,Ermacora, M.R. (登録日: 2011-06-30, 公開日: 2011-12-14, 最終更新日: 2023-09-13)

主引用文献

Risso, V.A.,Acierno, J.P.,Capaldi, S.,Monaco, H.L.,Ermacora, M.R.
X-ray evidence of a native state with increased compactness populated by tryptophan-less B. licheniformis beta-lactamase.
Protein Sci., 21:964-976, 2012

PubMed Abstract: β-lactamases confer antibiotic resistance, one of the most serious world-wide health problems, and are an excellent theoretical and experimental model in the study of protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class-A β-lactamase with three tryptophan residues located in the protein core. Here, we report the 1.7-Å resolution X-ray structure, catalytic parameters, and thermodynamic stability of ESP(ΔW), an engineered mutant of ESP in which phenylalanine replaces the wild-type tryptophan residues. The structure revealed no qualitative conformational changes compared with thirteen previously reported structures of B. licheniformis β-lactamases (RMSD = 0.4-1.2 Å). However, a closer scrutiny showed that the mutations result in an overall more compact structure, with most atoms shifted toward the geometric center of the molecule. Thus, ESP(ΔW) has a significantly smaller radius of gyration (R(g)) than the other B. licheniformis β-lactamases characterized so far. Indeed, ESP(ΔW) has the smallest R(g) among 126 Class-A β-lactamases in the Protein Data Bank (PDB). Other measures of compactness, like the number of atoms in fixed volumes and the number and average of noncovalent distances, confirmed the effect. ESP(ΔW) proves that the compactness of the native state can be enhanced by protein engineering and establishes a new lower limit to the compactness of the Class-A β-lactamase fold. As the condensation achieved by the native state is a paramount notion in protein folding, this result may contribute to a better understanding of how the sequence determines the conformational variability and thermodynamic stability of a given fold.

PubMed: 22496053
DOI: 10.1002/pro.2076

実験手法

X-RAY DIFFRACTION (1.729 Å)