6M55

Crystal structure of the E496A mutant of HsBglA in complex with 4-galactosyllactose

PDB DOI: https://doi.org/10.2210/pdb6M55/pdb

Classification: HYDROLASE
Organism(s): Hamamotoa singularis
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2020-03-10 Released: 2020-09-02
Deposition Author(s): Uehara, R., Iwamoto, R., Aoki, S., Yoshizawa, T., Takano, K., Matsumura, H., Tanaka, S.-i.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.298
R-Value Work: 0.265
R-Value Observed: 0.266

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a GH1 beta-glucosidase from Hamamotoa singularis.

Uehara, R., Iwamoto, R., Aoki, S., Yoshizawa, T., Takano, K., Matsumura, H., Tanaka, S.I.

(2020) Protein Sci 29: 2000-2008

PubMed: 32713015 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.3916
Primary Citation of Related Structures:
6M4E, 6M4F, 6M55

PubMed Abstract:
A GH1 β-glucosidase from the fungus Hamamotoa singularis (HsBglA) has high transgalactosylation activity and efficiently converts lactose to galactooligosaccharides. Consequently, HsBglA is among the most widely used enzymes for industrial galactooligosaccharide production. Here, we present the first crystal structures of HsBglA with and without 4'-galactosyllactose, a tri-galactooligosaccharide, at 3.0 and 2.1 Å resolutions, respectively. These structures reveal details of the structural elements that define the catalytic activity and substrate binding of HsBglA, and provide a possible interpretation for its high catalytic potency for transgalactosylation reaction.

Organizational Affiliation

Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan.

Macromolecule Content

Total Structure Weight: 124.01 kDa
Atom Count: 8,773
Modelled Residue Count: 1,084
Deposited Residue Count: 1,084
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-galactosidase-like enzyme	A, B [auth D]	542	Hamamotoa singularis	Mutation(s): 1 Gene Names: bglA
UniProt
Find proteins for Q564N5 (Hamamotoa singularis) Explore Q564N5 Go to UniProtKB: Q564N5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q564N5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	C, D [auth F]	3		N/A	Interactions Focus chain C Focus chain D [auth F] Interactions & Density Focus chain C Focus chain D [auth F]
Glycosylation Resources
GlyTouCan: G33559CW GlyCosmos: G33559CW GlyGen: G33559CW

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth B], F [auth E]	2		N-Glycosylation	Interactions Focus chain E [auth B] Focus chain F [auth E] Interactions & Density Focus chain E [auth B] Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	I [auth D], J [auth D], K [auth D], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth D]	G [auth A], H [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.298
R-Value Work: 0.265
R-Value Observed: 0.266
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.686	α = 90
b = 67.116	β = 128.54
c = 117.585	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18K05445
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H05401

Revision History (Full details and data files)

Version 1.0: 2020-09-02
Type: Initial release
Version 1.1: 2020-12-16
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description