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Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase.

Langkilde A, Kristensen SM, Lo Leggio L, Mølgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S - Acta Crystallogr. D Biol. Crystallogr. (2008)

Bottom Line: 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.The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.

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.

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1H NMR spectra of wild-type RGAE (a) and RGAE D192N (b) at various pH values.
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fig4: 1H NMR spectra of wild-type RGAE (a) and RGAE D192N (b) at various pH values.

Mentions: Spectra for wild-type RGAE were measured at eight different pH values ranging from pH 3.67 to 10.2 (Fig. 4a ▶). The 18.2 p.p.m. signal was present over the entire pH range. At pH 10.2 denaturation results in reduced signals in the whole spectrum. A second low-field signal at approximately 14 p.p.m. appeared at pH 7.4. Spectra for RGAE D192N were measured at seven different pH values between pH 6.0 and 10.1 and are shown in Fig. 4 ▶(b). A low-field signal at 18.2 p.p.m. was also present in these spectra as observed for the wild type. The activity measurements on the D192N sample ruled out deamidation of Asn192 as the source of the 18 p.p.m. signal. The signal observed around 14 p.p.m. at pH 7.4 and above in the spectra of the wild type could not be detected in the spectra of the mutant.


Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase.

Langkilde A, Kristensen SM, Lo Leggio L, Mølgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S - Acta Crystallogr. D Biol. Crystallogr. (2008)

1H NMR spectra of wild-type RGAE (a) and RGAE D192N (b) at various pH values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483496&req=5

fig4: 1H NMR spectra of wild-type RGAE (a) and RGAE D192N (b) at various pH values.
Mentions: Spectra for wild-type RGAE were measured at eight different pH values ranging from pH 3.67 to 10.2 (Fig. 4a ▶). The 18.2 p.p.m. signal was present over the entire pH range. At pH 10.2 denaturation results in reduced signals in the whole spectrum. A second low-field signal at approximately 14 p.p.m. appeared at pH 7.4. Spectra for RGAE D192N were measured at seven different pH values between pH 6.0 and 10.1 and are shown in Fig. 4 ▶(b). A low-field signal at 18.2 p.p.m. was also present in these spectra as observed for the wild type. The activity measurements on the D192N sample ruled out deamidation of Asn192 as the source of the 18 p.p.m. signal. The signal observed around 14 p.p.m. at pH 7.4 and above in the spectra of the wild type could not be detected in the spectra of the mutant.

Bottom Line: 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.The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.

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.

Show MeSH
Related in: MedlinePlus