3C2U

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

Summary for 3C2U

• Entry DOI: 10.2210/pdb3c2u/pdb
• Descriptor: Xylosidase/arabinosidase, 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (3 entities in total)
• Functional Keywords: tetramer; glycoside hydrolase; gh43; alpha-l-arabinofuranosidase, hydrolase
• Biological source: Selenomonas ruminantium
• Total number of polymer chains: 4
• Total formula weight: 245929.80

Authors

Brunzelle, J.S.,Jordan, D.B.,McCaslin, D.R.,Olczak, A.,Wawrzak, A. (deposition date: 2008-01-25, release date: 2008-04-22, Last modification date: 2024-02-21)

Primary citation

Brunzelle, J.S.,Jordan, D.B.,McCaslin, D.R.,Olczak, A.,Wawrzak, Z.
Structure of the two-subsite beta-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane.
Arch.Biochem.Biophys., 474:157-166, 2008

PubMed Abstract: The three-dimensional structure of the catalytically efficient beta-xylosidase from Selenomonas ruminantium in complex with competitive inhibitor 1,3-bis[tris(hydroxymethyl)methylamino]propane (BTP) was determined by using X-ray crystallography (1.3A 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 (pK(a) 7.2) serves as catalytic acid. The pH (6-10) profile for 1/K(i)((BTP)) is bell-shaped with pK(a)'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 pK(a) 7.8, strongly suggesting that the BTP monocation binds to the dianionic enzyme D14(-)E186(-). A sedimentation equilibrium experiment estimates a K(d) ([dimer](2)/[tetramer]) of 7 x 10(-9)M. Similar k(cat) and k(cat)/K(m) values were determined when the tetramer/dimer ratio changes from 0.0028 to 26 suggesting that dimers and tetramers are equally active forms.

PubMed: 18374656
DOI: 10.1016/j.abb.2008.03.007

Experimental method

X-RAY DIFFRACTION (1.3 Å)