3UG4 | pdb_00003ug4

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

PDB DOI: https://doi.org/10.2210/pdb3UG4/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: 2.15 Å
R-Value Free:
0.207 (Depositor), 0.206 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 22313787 Search on PubMed
DOI: https://doi.org/10.1271/bbb.110902
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 350.43 kDa
Atom Count: 25,486
Modeled Residue Count: 2,893
Deposited Residue Count: 3,024
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHR Query on AHR Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain R [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain UA [auth F] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain RA [auth F] SDF format, chain NA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain QA [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain QA [auth F] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain QA [auth F]	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		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.207 (Depositor), 0.206 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.483	α = 90
b = 160.639	β = 92.44
c = 154.841	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

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Ligand Structure Quality Assessment

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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 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