5OPJ

Beta-L-arabinofuranosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.

Luis, A.S.Briggs, J.Zhang, X.Farnell, B.Ndeh, D.Labourel, A.Basle, A.Cartmell, A.Terrapon, N.Stott, K.Lowe, E.C.McLean, R.Shearer, K.Schuckel, J.Venditto, I.Ralet, M.C.Henrissat, B.Martens, E.C.Mosimann, S.C.Abbott, D.W.Gilbert, H.J.

(2018) Nat Microbiol 3: 210-219

  • DOI: 10.1038/s41564-017-0079-1
  • Primary Citation of Related Structures:  
    5OLQ, 5OLP, 5OLS, 5OLR, 5OPJ

  • PubMed Abstract: 
  • The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs) ...

    The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. harry.gilbert@ncl.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhamnogalacturonan lyaseA802Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: SAMN02910322_03495
UniProt
Find proteins for Q8AAW3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Explore Q8AAW3 
Go to UniProtKB:  Q8AAW3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHR
Query on AHR

Download Ideal Coordinates CCD File 
B [auth A]alpha-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.21α = 90
b = 96.21β = 90
c = 187.84γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
SHELXCDphasing
SHELXEmodel building
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary