5XGZ

Metagenomic glucose-tolerant glycosidase

PDB DOI: https://doi.org/10.2210/pdb5XGZ/pdb

Classification: HYDROLASE
Organism(s): uncultured microorganism
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-19 Released: 2018-05-02
Deposition Author(s): Watanabe, M., Matsuzawa, T., Yaoi, K.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.255
R-Value Work: 0.206
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Improved thermostability of a metagenomic glucose-tolerant beta-glycosidase based on its X-ray crystal structure.

Matsuzawa, T., Watanabe, M., Yaoi, K.

(2017) Appl Microbiol Biotechnol 101: 8353-8363

PubMed: 29063172 Search on PubMed
DOI: https://doi.org/10.1007/s00253-017-8525-9
Primary Citation of Related Structures:
5XGZ

PubMed Abstract:
MeBglD2, a metagenomic β-glycosidase, is stimulated by various saccharides, including D-glucose, D-xylose, and maltose, and it promotes the enzymatic saccharification of plant biomass. To improve the thermostability of MeBglD2, its X-ray crystal structure was analyzed, and the amino acid residues responsible for its thermostability were identified using the structural information. Mutations in His8, Asn59, and Gly295 improved the thermostability of MeBglD2, and the combination of these mutations resulted in the highest thermostability. Compared with wild-type MeBglD2, thermostable MeBglD2 mutants promoted plant biomass saccharification using Trichoderma reesei cellulase. In addition to thermostability, the thermostable mutants exhibited higher tolerance to ethanol, dimethyl sulfoxide, and copper ions, indicating that the MeBglD2 mutants generated in this study were improved in their tolerance to not only high temperature but also to organic solvents and metal ions.

Organizational Affiliation

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan. [email protected].

Macromolecule Content

Total Structure Weight: 105.98 kDa
Atom Count: 7,882
Modelled Residue Count: 890
Deposited Residue Count: 914
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glycosidase	A, B	457	uncultured microorganism	Mutation(s): 0 EC: 3.2.1.21
UniProt
Find proteins for A0A1E1FFN6 (uncultured microorganism) Explore A0A1E1FFN6 Go to UniProtKB: A0A1E1FFN6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1E1FFN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain W [auth B]	L [auth A], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	J [auth A], K [auth A], U [auth B], V [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.255
R-Value Work: 0.206
R-Value Observed: 0.209
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.427	α = 90
b = 202.427	β = 90
c = 202.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Watanabe, M.

Matsuzawa, T.

Yaoi, K.

Funding Organization	Location	Grant Number
JSPS	Japan	26850067

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2019-11-13
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5XGZ

Metagenomic glucose-tolerant glycosidase

Improved thermostability of a metagenomic glucose-tolerant beta-glycosidase based on its X-ray crystal structure.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)