3C2U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2008) Arch.Biochem.Biophys. 474: 157-166

  • DOI: 10.1016/j.abb.2008.03.007

  • 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 ...

    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.


    Organizational Affiliation

    Northwestern University Center for Synchrotron Research, Life Sciences Collaborative Access Team, Department of Molecular Pharmacology and Biological Chemistry, 9700 South Cass Avenue, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylosidase/arabinosidase
A, B, C, D
538Selenomonas ruminantiumMutation(s): 0 
Gene Names: Xsa
Find proteins for O52575 (Selenomonas ruminantium)
Go to UniProtKB:  O52575
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download SDF File 
Download CCD File 
A, B, C, D
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTPKi: 1250000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.579α = 67.84
b = 84.401β = 81.31
c = 94.039γ = 75.08
Software Package:
Software NamePurpose
MAR345data collection
SnBphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description