4OZO

Crystal structure of an a-L-fucosidase GH29 from Bacteroides thetaiotaomicron (BT2192) in complex with oNPTG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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This is version 1.4 of the entry. See complete history. 


Literature

Unraveling the substrate recognition mechanism and specificity of the unusual glycosyl hydrolase family 29 BT2192 from Bacteroides thetaiotaomicron.

Guillotin, L., Lafite, P., Daniellou, R.

(2014) Biochemistry 53: 1447-1455

  • DOI: 10.1021/bi400951q
  • Primary Citation of Related Structures:  
    4OUE, 4OZO

  • PubMed Abstract: 

    • Glycosyl hydrolase (GH) family 29 (CAZy database) consists of retaining α-l-fucosidases. We have identified BT2192, a protein from Bacteroides thetaiotaomicron, as the first GH29 representative exhibiting both weak α-l-fucosidase and β-d-galactosidase activities ...

    Glycosyl hydrolase (GH) family 29 (CAZy database) consists of retaining α-l-fucosidases. We have identified BT2192, a protein from Bacteroides thetaiotaomicron, as the first GH29 representative exhibiting both weak α-l-fucosidase and β-d-galactosidase activities. Determination and analysis of X-ray structures of BT2192 in complex with β-d-galactoside competitive inhibitors showed a new binding mode different from that of known GH29 enzymes. Three point mutations, specific to BT2192, prevent the canonical GH29 substrate α-l-fucose from binding efficiently to the fucosidase-like active site relative to other GH29 enzymes. β-d-Galactoside analogues bind and interact in a second pocket, which is not visible in other reported GH29 structures. Molecular simulations helped in the assessment of the flexibility of both substrates in their respective pocket. Hydrolysis of the fucosyl moiety from the putative natural substrates like 3-fucosyllactose or Lewis(X) antigen would be mainly due to the efficient interactions with the galactosyl moiety, in the second binding site, located more than 6-7 Å apart.

    Organizational Affiliation: 

    Université Orléans, CNRS, ICOA, UMR 7311 , F-45067 Orleans, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative lipoproteinA, B469Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2192
EC: 3.2.1.111
UniProt
Find proteins for Q8A5P6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A5P6 
Go to UniProtKB:  Q8A5P6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A5P6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OTN
Query on OTN
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		2-nitrophenyl 1-thio-beta-D-galactopyranoside
C12 H15 N O7 S
SZAOZNVCHHBUDZ-RUXWNWLUSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B],
G [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.3α = 90
b = 122.17β = 90
c = 159.65γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
R?gion CentreFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Data collection, Database references, Other, Structure summary
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Refinement description, Structure summary