3C1U

D192N mutant of Rhamnogalacturonan acetylesterase

3C1U の概要

• エントリーDOI: 10.2210/pdb3c1u/pdb
• 関連するPDBエントリー: 1DEO 1DEX 1K7C 1PP4
• 分子名称: Rhamnogalacturonan acetylesterase, 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ... (4 entities in total)
• 機能のキーワード: sgnh hydrolase, pectin degradation, glycoprotein, hydrolase
• 由来する生物種: Aspergillus aculeatus (FUNGI)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25123.36

構造登録者

Langkilde, A.,Lo Leggio, L.,Navarro Poulsen, J.C.,Molgaard, A.,Larsen, S. (登録日: 2008-01-24, 公開日: 2008-08-05, 最終更新日: 2024-11-20)

主引用文献

Langkilde, A.,Kristensen, S.M.,Lo Leggio, L.,Jensen, J.H.,Houk, A.R.,Navarro Poulsen, J.C.,Kauppinen, S.,Larsen, S.
Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase
ACTA CRYSTALLOGR.,SECT.D, 64:851-863, 2008

PubMed Abstract: An extremely low-field signal (at approximately 18 p.p.m.) in the (1)H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental (1)H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 A resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 A) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor-acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK(a) values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins.

PubMed: 18645234
DOI: 10.1107/S0907444908017083

実験手法

X-RAY DIFFRACTION (1.33 Å)