8GDU

Crystal structure of a mutant methyl transferase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium (NESG) Target MvR53-11M

8GDU の概要

• エントリーDOI: 10.2210/pdb8gdu/pdb
• 分子名称: Methyltransferase domain-containing protein, S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total)
• 機能のキーワード: sam-binding protein, transferase
• 由来する生物種: Methanosarcina acetivorans C2A
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23755.90

構造登録者

Forouhar, F.,Banayan, N.E.,Loughlin, B.L.,Singh, S.,Wong, V.,Hunt, H.S.,Handelman, S.K.,Price, N.,Hunt, J.F. (登録日: 2023-03-06, 公開日: 2024-01-24, 最終更新日: 2024-03-20)

主引用文献

Banayan, N.E.,Loughlin, B.J.,Singh, S.,Forouhar, F.,Lu, G.,Wong, K.H.,Neky, M.,Hunt, H.S.,Bateman Jr., L.B.,Tamez, A.,Handelman, S.K.,Price, W.N.,Hunt, J.F.
Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution.
Protein Sci., 33:e4898-e4898, 2024

PubMed Abstract: Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.

PubMed: 38358135
DOI: 10.1002/pro.4898

実験手法

X-RAY DIFFRACTION (2.01 Å)