6D7J

The Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) with Glycerol in Active-Site

• PDB DOI:  https://doi.org/10.2210/pdb6D7J/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides merdae CL03T12C32
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-04-24 Released: 2019-05-01 
• Deposition Author(s): Little, M.S., Redinbo, M.R.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.200 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome.

Little, M.S., Ervin, S.M., Walton, W.G., Tripathy, A., Xu, Y., Liu, J., Redinbo, M.R.

(2018) Protein Sci 27: 2010-2022

• PubMed: 30230652 
• DOI: https://doi.org/10.1002/pro.3507
• Primary Citation of Related Structures:  
  6D7J, 6DXU


• PubMed Abstract: 
  

β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs.

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Related Citations: 

• Gut microbial beta-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens.
  Ervin, S.M., Li, H., Lim, L., Roberts, L.R., Liang, X., Mani, S., Redinbo, M.R.
  (2019) J Biol Chem 294: 18586

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Organizational Affiliation: 

The Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, 27599-3290.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 384.86 kDa 
• Atom Count: 27,403 
• Modelled Residue Count: 3,163 
• Deposited Residue Count: 3,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Glucuronidase	A, B, C, D	830	Parabacteroides merdae CL03T12C32	Mutation(s): 0  Gene Names: HMPREF1060_00403
UniProt
Find proteins for K5ZWV5 (Parabacteroides merdae CL03T12C32) Explore K5ZWV5  Go to UniProtKB:  K5ZWV5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO	NB [auth D], R [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
GOL	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], EA [auth B], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KB [auth D], L [auth A], LB [auth D], M [auth A], MA [auth C], MB [auth D], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A], EB [auth D], LA [auth C], T [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	DB [auth C], KA [auth B], OB [auth D], S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.200 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.92	α = 90
b = 171.968	β = 107.84
c = 125.322	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Little, M.S., Redinbo, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	CA098468
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	CA207416

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-05-13
  Changes: Database references
• Version 1.3: 2020-05-20
  Changes: Database references