PDBsum entry: 3c2u

Hydrolase

PDB id: 3c2u

Contents

Protein chains

538 a.a. *

Ligands

B3P ×4

Waters ×2050

* Residue conservation analysis

PDB id:

3c2u

Name:

Hydrolase

Title:

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

Structure:

Xylosidase/arabinosidase. Chain: a, b, c, d. Engineered: yes

Source:

Selenomonas ruminantium. Organism_taxid: 971. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.30Å R-factor: 0.136 R-free: 0.163

Authors:

J.S.Brunzelle,D.B.Jordan,D.R.Mccaslin,A.Olczak,A.Wawrzak

Key ref:

J.S.Brunzelle et al. (2008). 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. PubMed id: 18374656 DOI: 10.1016/j.abb.2008.03.007

Date:

25-Jan-08 Release date: 22-Apr-08

Protein chains

O52575  (O52575_SELRU) -  Xylosidase/arabinosidase

Seq: 538 a.a.

Struc: 538 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: hydrolase activity, hydrolyzing O-glycosyl compounds (1 term)

DOI no: 10.1016/j.abb.2008.03.007

Arch Biochem Biophys 474:157-166 (2008)

PubMed id: 18374656

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

J.S.Brunzelle, D.B.Jordan, D.R.McCaslin, A.Olczak, Z.Wawrzak.

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.