Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 348.15 kDa 
• Atom Count: 24,750 
• Modelled Residue Count: 2,892 
• Deposited Residue Count: 3,024 
• Unique protein chains: 1

 3UG5

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

• PDB DOI: 10.2210/pdb3UG5/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-02 Released: 2012-03-07 
• Deposition Author(s): Im, D.-H., Miyazaki, K., Wakagi, T., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.209 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

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

• PubMed: 22313787 
• DOI: 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.

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Related Citations: 

• Hyperthermophilic alpha-L: -arabinofuranosidase from Thermotoga maritima MSB8: molecular cloning, gene expression, and characterization of the recombinant protein
  Miyazaki, K.
  (2005) Extremophiles 9: 399

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-arabinofuranosidase	A, B, C, D, E, F	504	Thermotoga maritima	Mutation(s): 1  Gene Names: TM_0281 EC: 3.2.1.55
UniProt
Find proteins for Q9WYB7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYB7  Go to UniProtKB:  Q9WYB7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	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]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
TRS	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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 102.2	α = 90
b = 160.933	β = 91.84
c = 156.172	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Im, D.-H., Miyazaki, K., Wakagi, T., Fushinobu, S.

Revision History  

• 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