Abstract
The three-dimensional structure of the catalytically efficient β-xylosidase from Selenomonas ruminantium in complex with competitive inhibitor 1,3-bis[tris(hydroxymethyl)methylamino]propane (BTP) was determined by using X-ray crystallography (1.3 Å resolution). Most H bonds between inhibitor and protein occur within subsite -1, including one between the carboxyl group of E186 and an N group of BTP. The other N of BTP occupies subsite +1 near K99. E186 (pKa 7.2) serves as catalytic acid. The pH (6-10) profile for 1 / Ki(BTP) is bell-shaped with pKa's 6.8 and 7.8 on the acidic limb assigned to E186 and inhibitor groups and 9.9 on the basic limb assigned to inhibitor. Mutation K99A eliminates pKa 7.8, strongly suggesting that the BTP monocation binds to the dianionic enzyme D14-E186-. A sedimentation equilibrium experiment estimates a Kd ([dimer]2/[tetramer]) of 7 × 10-9 M. Similar kcat and kcat/Km values were determined when the tetramer/dimer ratio changes from 0.0028 to 26 suggesting that dimers and tetramers are equally active forms.
Original language | English (US) |
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Pages (from-to) | 157-166 |
Number of pages | 10 |
Journal | Archives of biochemistry and biophysics |
Volume | 474 |
Issue number | 1 |
DOIs | |
State | Published - Jun 1 2008 |
Funding
We thank Jay D. Braker for excellent technical assistance. Sedimentation equilibrium data was collected in Biophysics Instrumentation Facility at the University of Wisconsin (Madison), which was established with support from the University of Wisconsin, and Grants BIR-9512577 (NSF) and S10 RR13790 (NIH). This work was supported by USDA funding of CRIS 3620-41000-118-00D. The mention of firm names or trade products does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned.
Keywords
- GH43
- Glycoside hydrolase
- Protein crystallography
- Sedimentation equilibrium
- Structure-function
- α-l-Arabinofuranosidase
ASJC Scopus subject areas
- Molecular Biology
- Biophysics
- Biochemistry
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Dive into the research topics of 'Structure of the two-subsite β-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane'. Together they form a unique fingerprint.Datasets
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Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane
Brunzelle, J. S. (Contributor), Jordan, D. B. (Contributor), McCaslin, D. R. (Contributor), Olczak, A. (Contributor) & Wawrzak, Z. (Contributor), Protein Data Bank (PDB), Apr 22 2008
DOI: 10.2210/pdb3C2U/pdb, https://www.wwpdb.org/pdb?id=pdb_00003c2u
Dataset