5OLR

Rhamnogalacturonan lyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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:  
    5OLP, 5OLQ, 5OLR, 5OLS, 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhamnogalacturonan lyaseA, B, C522Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: HMPREF2534_01516
UniProt
Find proteins for Q8A051 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A051 
Go to UniProtKB:  Q8A051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A051
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranoseD, E, F 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G70933BG
GlyCosmos:  G70933BG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.458α = 90
b = 123.872β = 90
c = 137.628γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary