1WL7

Structure of the thermostable arabinanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3.

Yamaguchi, A.Tada, T.Wada, K.Nakaniwa, T.Kitatani, T.Sogabe, Y.Takao, M.Sakai, T.Nishimura, K.

(2005) J.Biochem.(Tokyo) 137: 587-592

  • DOI: 10.1093/jb/mvi078

  • PubMed Abstract: 
  • The crystal structure of a thermostable endo-1,5-alpha-L-arabinanase, ABN-TS, from Bacillus thermodenitrificans TS-3 was determined at 1.9 A to an R-factor of 18.3% and an R-free-factor of 22.5%. The enzyme molecule has a five-bladed beta-propeller f ...

    The crystal structure of a thermostable endo-1,5-alpha-L-arabinanase, ABN-TS, from Bacillus thermodenitrificans TS-3 was determined at 1.9 A to an R-factor of 18.3% and an R-free-factor of 22.5%. The enzyme molecule has a five-bladed beta-propeller fold. The substrate-binding cleft formed across one face of the propeller is open on both sides to allow random binding of several sugar units in the polymeric substrate arabinan. The beta-propeller fold is stabilized through a ring closure. ABN-TS exhibits a new closure-mode involving residues in the N-terminal region: Phe7 to Gly21 exhibit hydrogen bonds and hydrophobic interactions with the first and last blades, and Phe4 links the second and third blades through a hydrogen bond and an aromatic stacking interaction, respectively. The role of the N-terminal region in the thermostability was confirmed with a mutant lacking 16 amino acid residues from the N-terminus of ABN-TS.


    Organizational Affiliation

    Research Institute for Advanced Science and Technology, Osaka Prefecture University, Sakai, Osaka 599-8570.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
arabinanase-TS
A
312Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: abn-ts
EC: 3.2.1.99
Find proteins for Q93HT9 (Geobacillus thermodenitrificans)
Go to UniProtKB:  Q93HT9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.270α = 90.00
b = 77.810β = 90.00
c = 89.680γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance