Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.05 kDa 
• Atom Count: 3329 
• Modelled Residue Count: 425 
• Deposited Residue Count: 522 
• Unique protein chains: 1

5OLS

Rhamnogalacturonan lyase

• PDB DOI: 10.2210/pdb5OLS/pdb

• Classification: LYASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-28 Released: 2017-11-29 
• Deposition Author(s): Basle, A., Luis, A.S., Gilbert, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

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

• PubMed: 29255254 
• 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). 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.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhamnogalacturonan lyase	A	522	Bacteroides thetaiotaomicron	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G70933BG GlyCosmos:  G70933BG

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid	C	3		N/A
Glycosylation Resources
GlyTouCan:  G00781DD GlyCosmos:  G00781DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.42	α = 90
b = 76.6	β = 90
c = 122.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
XDS	data scaling
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-28 
• Released Date: 2017-11-29 
Deposition Author(s): Basle, A., Luis, A.S., Gilbert, H.J.

Revision History  

• 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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary