6A8I

Crystal structure of endo-arabinanase ABN-TS D147N mutant in complex with arabinohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides.

Yamaguchi, A.Sogabe, Y.Fukuoka, S.Sakai, T.Tada, T.

(2018) Acta Crystallogr F Struct Biol Commun 74: 774-780

  • DOI: 10.1107/S2053230X18015947
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The thermostable endo-1,5-α-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined ...

    The thermostable endo-1,5-α-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates.


    Organizational Affiliation

    IGA Bio Research, Sakai, Osaka 590-0004, Japan.,Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
endo-alpha-(1->5)-L-arabinanase
A, B
321Geobacillus thermodenitrificansMutation(s): 1 
Gene Names: abn-ts
EC: 3.2.1.99
Find proteins for Q93HT9 (Geobacillus thermodenitrificans)
Go to UniProtKB:  Q93HT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHR
Query on AHR

Download SDF File 
Download CCD File 
A, B
ALPHA-L-ARABINOFURANOSE
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.809α = 90.00
b = 92.260β = 91.52
c = 78.673γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release