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: 348.36 kDa 
• Atom Count: 25,934 
• Modelled Residue Count: 2,892 
• Deposited Residue Count: 3,024 
• Unique protein chains: 1

 3UG3

Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form

• PDB DOI:  https://doi.org/10.2210/pdb3UG3/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: 1.80 Å
• R-Value Free: 0.197 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

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: 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.

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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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	BA [auth C], DB [auth F], G [auth A], S [auth B], TA [auth D], UA [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	AA [auth B], AB [auth E], BB [auth E], CA [auth C], CB [auth E], DA [auth C], EA [auth C], EB [auth F], FA [auth C], FB [auth F], GA [auth C], GB [auth F], H [auth A], HA [auth C], HB [auth F], I [auth A], IA [auth C], IB [auth F], J [auth A], JA [auth C], JB [auth F], K [auth A], KA [auth D], KB [auth F], L [auth A], LA [auth D], LB [auth F], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], RA [auth D], SA [auth D], T [auth B], U [auth B], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth E], Y [auth B], YA [auth E], Z [auth B], ZA [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.197 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.515	α = 90
b = 160.647	β = 91.75
c = 155.735	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