Glycoside hydrolase BT_0996

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Ndeh, D.Rogowski, A.Cartmell, A.Luis, A.S.Basle, A.Gray, J.Venditto, I.Briggs, J.Zhang, X.Labourel, A.Terrapon, N.Buffetto, F.Nepogodiev, S.Xiao, Y.Field, R.A.Zhu, Y.O'Neill, M.A.Urbanowicz, B.R.York, W.S.Davies, G.J.Abbott, D.W.Ralet, M.C.Martens, E.C.Henrissat, B.Gilbert, H.J.

(2017) Nature 544: 65-70

  • DOI: https://doi.org/10.1038/nature21725
  • Primary Citation of Related Structures:  
    5MQM, 5MQN, 5MQO, 5MQR, 5MQS, 5MSX, 5MSY, 5MT2, 5MUI, 5MUJ, 5MWK

  • PubMed Abstract: 

    The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.

  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase381Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_0996
Find proteins for Q8A921 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A921 
Go to UniProtKB:  Q8A921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A921
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-L-arabinofuranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-3)]alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose-(1-2)]beta-D-galactopyranose-(1-2)-alpha-D-aceric acid-(1-3)-alpha-L-rhamnopyranose
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.18α = 90
b = 80.74β = 114.99
c = 51.41γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
iotechnology and Biological Research CouncilUnited KingdomBB/K020358/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K001949/1
European Research CouncilUnited Kingdom322820
Wellcome TrustUnited KingdomWT097907MA

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary