5NS8 | pdb_00005ns8

Crystal structure of beta-glucosidase BglM-G1 mutant H75R from marine metagenome in complex with inhibitor 1-Deoxynojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.172 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5NS8

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments.

Mhaindarkar, D.Gasper, R.Lupilov, N.Hofmann, E.Leichert, L.I.

(2018) Commun Biol 1: 171-171

  • DOI: https://doi.org/10.1038/s42003-018-0167-7
  • Primary Citation Related Structures: 
    5NS6, 5NS7, 5NS8

  • PubMed Abstract: 

    Salt bridges are the strongest electrostatic interactions in proteins. They substantially contribute to a protein's structural stability. Thus, mutations of salt bridges are typically selected against. Here, we report on the evolutionary loss of a highly conserved salt bridge in the GH1 family glycosyl hydrolase BglM-G1. BglM-G1's gene was found in the bacterial metagenome of a temperate, seasonally cold marine habitat. In BglM-G1, arginine 75 is replaced by a histidine. While fully retaining β-glucosidase activity, BglM-G1 is less heat stable than an H75R variant, in which the salt bridge was artificially re-introduced. However, the K m toward its substrates was lower in wild type, leading to an overall higher catalytic efficiency. Our results indicate that this loss of the salt bridge leads to higher flexibility in BglM-G1's active site, trading structural stability at high temperatures, a trait not needed in a temperate, seasonally cold habitat, for a more effective catalytic activity.


  • Organizational Affiliation
    • Ruhr University Bochum, Fakultät für Medizin, Institute for Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany.

Macromolecule Content 

  • Total Structure Weight: 157.8 kDa 
  • Atom Count: 11,612 
  • Modeled Residue Count: 1,320 
  • Deposited Residue Count: 1,362 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
beta-glucosidase M - G1
A, B, C
454marine metagenomeMutation(s): 0 
EC: 3.2.1.21

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NOJ

Query on NOJ



Download:Ideal Coordinates CCD File
I [auth A],
S [auth B],
Y [auth C]
1-DEOXYNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
J [auth B]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
J [auth B],
K [auth B],
L [auth B],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
V [auth C],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.172 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.75α = 90
b = 137.75β = 90
c = 97.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany281384

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Refinement description