5XXM | pdb_00005xxm

Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.208 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.

Ishiguro, R., Tanaka, N., Abe, K., Nakajima, M., Maeda, T., Miyanaga, A., Takahashi, Y., Sugimoto, N., Nakai, H., Taguchi, H.

(2017) FEBS Lett 591: 3926-3936

  • DOI: https://doi.org/10.1002/1873-3468.12911
  • Primary Citation Related Structures: 
    5XXL, 5XXM, 5XXN, 5XXO

  • PubMed Abstract: 

    BT_3567 protein, a putative β-glucosidase from Bacteroides thetaiotaomicron, exhibits higher activity toward Sop 3-5 (Sop n , n: degree of polymerization of β-1,2-glucooligosaccharides) than toward Sop 2 , unlike a known β-glucosidase from Listeria innocua which predominantly prefers Sop 2 . In the complex structure determined by soaking of a D286N mutant crystal with Sop 4 , a Sop 3 moiety was observed at subsites -1 to +2. The glucose moiety at subsite +2 forms a hydrogen bond with Asn81, which is replaced with Gly in the L. innocua β-glucosidase. The K m values of the N81G mutant for Sop 3-5 are much higher than those of the wild-type, suggesting that Asn81 contributes to the binding to substrates longer than Sop 3 .

    • Organizational Affiliation: 
    • Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.

Macromolecule Content 

  • Total Structure Weight: 168.64 kDa 
  • Atom Count: 12,778 
  • Modeled Residue Count: 1,493 
  • Deposited Residue Count: 1,520 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic beta-glucosidase
A, B
760Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_3567
EC: 3.2.1.21
UniProt
Find proteins for Q8A1U1 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A1U1 
Go to UniProtKB:  Q8A1U1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A1U1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.208 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.82α = 90
b = 167.69β = 90
c = 224.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Structure summary