8DHL | pdb_00008dhl

Tannerella forsythia beta-glucuronidase (L2)

  • Classification: HYDROLASE
  • Organism(s): Tannerella forsythia
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-06-27 Released: 2023-05-17 
  • Deposition Author(s): Lietzan, A.D., Redinbo, M.R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.170 (Depositor) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8DHL

This is version 1.1 of the entry. See complete history

Literature

Microbial beta-glucuronidases drive human periodontal disease etiology.

Lietzan, A.D.Simpson, J.B.Walton, W.G.Jariwala, P.B.Xu, Y.Boynton, M.H.Liu, J.Redinbo, M.R.

(2023) Sci Adv 9: eadg3390-eadg3390

  • DOI: https://doi.org/10.1126/sciadv.adg3390
  • Primary Citation Related Structures: 
    8DHE, 8DHL, 8DHV, 8DHW, 8E72

  • PubMed Abstract: 

    Periodontitis is a chronic inflammatory disease associated with persistent oral microbial dysbiosis. The human β-glucuronidase (GUS) degrades constituents of the periodontium and is used as a biomarker for periodontitis severity. However, the human microbiome also encodes GUS enzymes, and the role of these factors in periodontal disease is poorly understood. Here, we define the 53 unique GUSs in the human oral microbiome and examine diverse GUS orthologs from periodontitis-associated pathogens. Oral bacterial GUS enzymes are more efficient polysaccharide degraders and processers of biomarker substrates than the human enzyme, particularly at pHs associated with disease progression. Using a microbial GUS-selective inhibitor, we show that GUS activity is reduced in clinical samples obtained from individuals with untreated periodontitis and that the degree of inhibition correlates with disease severity. Together, these results establish oral GUS activity as a biomarker that captures both host and microbial contributions to periodontitis, facilitating more efficient clinical monitoring and treatment paradigms for this common inflammatory disease.


  • Organizational Affiliation
    • Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 202.3 kDa 
  • Atom Count: 14,047 
  • Modeled Residue Count: 1,680 
  • Deposited Residue Count: 1,778 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycosyl hydrolase family 2, sugar binding domain protein
A, B
889Tannerella forsythiaMutation(s): 0 
UniProt
Find proteins for G8UKC1 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338))
Explore G8UKC1 
Go to UniProtKB:  G8UKC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8UKC1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
H [auth A],
O [auth B],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.170 (Depositor) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.983α = 90
b = 119.209β = 90
c = 209.883γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137286
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesTR002489

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description