6W2I

Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A

6W2I の概要

• エントリーDOI: 10.2210/pdb6w2i/pdb
• 分子名称: UV excision repair protein RAD23 homolog A, GLYCEROL (3 entities in total)
• 機能のキーワード: ubiquitin associated domain, uba domain, dna binding protein, helical bundle
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 5626.34

構造登録者

Bowler, B.E.,Zeng, B.,Becht, D.C.,Rothfuss, M.,Sprang, S.R.,Mou, T.-C. (登録日: 2020-03-05, 公開日: 2021-03-10, 最終更新日: 2023-11-01)

主引用文献

Rothfuss, M.T.,Becht, D.C.,Zeng, B.,McClelland, L.J.,Yates-Hansen, C.,Bowler, B.E.
High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST.
J.Am.Chem.Soc., 145:22979-22992, 2023

PubMed Abstract: The accurate modeling of energetic contributions to protein structure is a fundamental challenge in computational approaches to protein analysis and design. We describe a general computational method, EmCAST (empirical Cα stabilization), to score and optimize the sequence to the structure in proteins. The method relies on an empirical potential derived from the database of the Cα dihedral angle preferences for all possible four-residue sequences, using the data available in the Protein Data Bank. Our method produces stability predictions that naturally correlate one-to-one with the experimental results for solvent-exposed mutation sites. EmCAST predicted four mutations that increased the stability of a three-helix bundle, UBA(1), from 2.4 to 4.8 kcal/mol by optimizing residues in both helices and turns. For a set of eight variants, the predicted and experimental stabilizations correlate very well ( = 0.97) with a slope near 1 and with a 0.16 kcal/mol standard error for EmCAST predictions. Tests against literature data for the stability effects of surface-exposed mutations show that EmCAST outperforms the existing stability prediction methods. UBA(1) variants were crystallized to verify and analyze their structures at an atomic resolution. Thermodynamic and kinetic folding experiments were performed to determine the magnitude and mechanism of stabilization. Our method has the potential to enable the rapid, rational optimization of natural proteins, expand the analysis of the sequence/structure relationship, and supplement the existing protein design strategies.

PubMed: 37815921
DOI: 10.1021/jacs.3c04966

実験手法

X-RAY DIFFRACTION (1.45 Å)