5MQM

Glycoside hydrolase BT_0986


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/nature21725
  • Primary Citation of Related Structures:  

  • 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 bac ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyl hydrolases family 2, sugar binding domain
A
1105Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A931 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A931
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
RPQ
Query on RPQ

Download SDF File 
Download CCD File 
A
D-rhamnopyranose tetrazole
C6 H10 N4 O3
RGTARVZVTUMUSY-QMKXCQHVSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.050α = 90.00
b = 84.810β = 99.20
c = 120.630γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
REFMACrefinement
xia2data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-04-12
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Author supporting evidence