Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima xylose complex

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Crystal Structures of Glycoside Hydrolase Family 51 alpha-L-Arabinofuranosidase from Thermotoga maritima

Im, D.-H.Kimura, K.I.Hayasaka, F.Tanaka, T.Noguchi, M.Kobayashi, A.Shoda, S.Miyazaki, K.Wakagi, T.Fushinobu, S.

(2012) Biosci Biotechnol Biochem 76: 423-428

  • DOI: https://doi.org/10.1271/bbb.110902
  • Primary Citation of Related Structures:  
    3UG3, 3UG4, 3UG5

  • PubMed Abstract: 

    α-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-β-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3 Å resolution to determine the architecture of the substrate binding pocket. Subsite -1 of Tm-AFase is similar to that of α-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.

  • Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Tokyo, Japan.

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
504Thermotoga maritimaMutation(s): 1 
Gene Names: TM_0281
Find proteins for Q9WYB7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYB7 
Go to UniProtKB:  Q9WYB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYB7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on XYP

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
GA [auth F]
I [auth A]
J [auth A]
CA [auth E],
DA [auth E],
GA [auth F],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
C5 H10 O5
Query on TRS

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
EA [auth F]
FA [auth F]
G [auth A]
AA [auth E],
BA [auth E],
EA [auth F],
FA [auth F],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D]
C4 H12 N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.2α = 90
b = 160.933β = 91.84
c = 156.172γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary