6DXU

Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 2, TIM barrel domain proteinB [auth A],
C [auth B],
D [auth C],
A [auth D]
830Parabacteroides merdae ATCC 43184Mutation(s): 0 
Gene Names: PARMER_02407
UniProt
Find proteins for A7AG62 (Parabacteroides merdae ATCC 43184)
Explore A7AG62 
Go to UniProtKB:  A7AG62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7AG62
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.371α = 90
b = 163.393β = 103.351
c = 120.607γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesCA098468
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesCA207416

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence