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.

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

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 22313787 Search on PubMed
DOI: https://doi.org/10.1271/bbb.110902
Primary Citation of Related Structures:
3UG3

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.

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-arabinofuranosidase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DB [auth F] SDF format, chain G [auth A] SDF format, chain S [auth B] SDF format, chain TA [auth D] SDF format, chain UA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth E]	BA [auth C] DB [auth F] G [auth A] S [auth B] TA [auth D] 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		Interactions Focus chain BA [auth C] Focus chain DB [auth F] Focus chain G [auth A] Focus chain S [auth B] Focus chain TA [auth D] Focus chain UA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain DB [auth F] Focus chain G [auth A] Focus chain S [auth B] Focus chain TA [auth D] Focus chain UA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CA [auth C] SDF format, chain CB [auth E] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] SDF format, chain GA [auth C] SDF format, chain Q [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	AA [auth B] AB [auth E] BB [auth E] CA [auth C] CB [auth E] 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		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A]	R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description