5OLP

Galacturonidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 Bac ...

    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

    Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada. wade.abbott@agr.gc.ca.,Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. harry.gilbert@ncl.ac.uk.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.,INRA, USC 1408 AFMB, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada. wade.abbott@agr.gc.ca.,INRA, UR1268 Biopolymères Interactions Assemblages, Nantes, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pectate lyase
A, B
452Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A066 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A066
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.545α = 90.00
b = 127.545β = 90.00
c = 263.641γ = 90.00
Software Package:
Software NamePurpose
SHELXCDphasing
SHELXEmodel building
ARP/wARPmodel building
Aimlessdata scaling
XDSdata reduction
Cootmodel building
REFMACrefinement
BUCCANEERmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references