6S2M

Perdeuterated human myelin protein P2 at 0.72-A resolution

6S2M の概要

• エントリーDOI: 10.2210/pdb6s2m/pdb
• 分子名称: Myelin P2 protein, PALMITIC ACID, VACCENIC ACID, ... (4 entities in total)
• 機能のキーワード: fabp, beta barrel, deuteration, fatty acid, lipid binding protein
• 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: 15562.35

構造登録者

Laulumaa, S.,Kursula, P. (登録日: 2019-06-21, 公開日: 2019-08-28, 最終更新日: 2024-11-20)

主引用文献

Laulumaa, S.,Kursula, P.
Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites.
Molecules, 24:-, 2019

PubMed Abstract: Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C-H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C-H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.

PubMed: 31443388
DOI: 10.3390/molecules24173044

実験手法

X-RAY DIFFRACTION (0.72 Å)