3UG4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-L-arabinofuranosidase
A, B, C, D, E
A, B, C, D, E, F
504Thermotoga maritimaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYB7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AHR
Query on AHR

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth D]
FA [auth D]
GA [auth D]
AA [auth C],
BA [auth C],
CA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
OA [auth E],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
V [auth B],
VA [auth F],
X [auth C],
Y [auth C],
Z [auth C]
alpha-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
G [auth A]
H [auth A]
KA [auth E]
DA [auth D],
EA [auth D],
G [auth A],
H [auth A],
KA [auth E],
LA [auth E],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
W [auth C]
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: 2.15 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.483α = 90
b = 160.639β = 92.44
c = 154.841γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
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