Structure of the thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structure of a novel thermostable GH51 Alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

Souza, T.A.Santos, C.R.Souza, A.R.Oldiges, D.P.Ruller, R.Prade, R.A.Squina, F.M.Murakami, M.T.

(2011) Protein Sci 20: 1632-1637

  • DOI: https://doi.org/10.1002/pro.693
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    α-L-arabinofuranosidases (EC participate in the degradation of a variety of L-arabinose-containing polysaccharides and interact synergistically with other hemicellulases in the production of oligosaccharides and bioconversion of lignocellulosic biomass into biofuels. In this work, the structure of a novel thermostable family 51 (GH51) α-L-arabinofuranosidase from Thermotoga petrophila RKU-1 (TpAraF) was determined at 3.1 Å resolution. The TpAraF tertiary structure consists of an (α/β)-barrel catalytic core associated with a C-terminal β-sandwich domain, which is stabilized by hydrophobic contacts. In contrast to other structurally characterized GH51 AraFs, the accessory domain of TpAraF is intimately linked to the active site by a long β-hairpin motif, which modifies the catalytic cavity in shape and volume. Sequence and structural analyses indicate that this motif is unique to Thermotoga AraFs. Small angle X-ray scattering investigation showed that TpAraF assembles as a hexamer in solution and is preserved at the optimum catalytic temperature, 65°C, suggesting functional significance. Crystal packing analysis shows that the biological hexamer encompasses a dimer of trimers and the multiple oligomeric interfaces are predominantly fashioned by polar and electrostatic contacts.

  • Organizational Affiliation

    Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
484Thermotoga petrophila RKU-1Mutation(s): 0 
Gene Names: Tpet_0631
Find proteins for A5IKC8 (Thermotoga petrophila (strain ATCC BAA-488 / DSM 13995 / JCM 10881 / RKU-1))
Explore A5IKC8 
Go to UniProtKB:  A5IKC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5IKC8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.95α = 90
b = 187.292β = 90.87
c = 180.636γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description