5TA5

Crystal structure of BuGH86wt in complex with neoagarooctaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont.

Pluvinage, B.Grondin, J.M.Amundsen, C.Klassen, L.Moote, P.E.Xiao, Y.Thomas, D.Pudlo, N.A.Anele, A.Martens, E.C.Inglis, G.D.Uwiera, R.E.R.Boraston, A.B.Abbott, D.W.

(2018) Nat Commun 9: 1043-1043

  • DOI: 10.1038/s41467-018-03366-x
  • Primary Citation of Related Structures:  
    5T98, 5T99, 5T9A, 5T9G, 5T9X, 5TA0, 5TA1, 5TA5, 5TA7, 5TA9

  • PubMed Abstract: 
  • In red algae, the most abundant principal cell wall polysaccharides are mixed galactan agars, of which agarose is a common component. While bioconversion of agarose is predominantly catalyzed by bacteria that live in the oceans, agarases have been discovered in microorganisms that inhabit diverse terrestrial ecosystems, including human intestines ...

    In red algae, the most abundant principal cell wall polysaccharides are mixed galactan agars, of which agarose is a common component. While bioconversion of agarose is predominantly catalyzed by bacteria that live in the oceans, agarases have been discovered in microorganisms that inhabit diverse terrestrial ecosystems, including human intestines. Here we comprehensively define the structure-function relationship of the agarolytic pathway from the human intestinal bacterium Bacteroides uniformis (Bu) NP1. Using recombinant agarases from Bu NP1 to completely depolymerize agarose, we demonstrate that a non-agarolytic Bu strain can grow on GAL released from agarose. This relationship underscores that rare nutrient utilization by intestinal bacteria is facilitated by the acquisition of highly specific enzymes that unlock inaccessible carbohydrate resources contained within unusual polysaccharides. Intriguingly, the agarolytic pathway is differentially distributed throughout geographically distinct human microbiomes, reflecting a complex historical context for agarose consumption by human beings.


    Organizational Affiliation

    Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada. wade.abbott@agr.gc.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside HydrolaseA, B649Bacteroides uniformisMutation(s): 0 
UniProt
Find proteins for A0A2D0TCD3 (Bacteroides uniformis)
Explore A0A2D0TCD3 
Go to UniProtKB:  A0A2D0TCD3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G45207BN
GlyCosmos:  G45207BN
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranoseD2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84576DT
GlyCosmos:  G84576DT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth B], DA [auth B], E [auth A], EA [auth B], FA [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth B] , BB [auth B] , F [auth A] , G [auth A] , GA [auth B] , H [auth A] , HA [auth B] , I [auth A] , 
AB [auth B], BB [auth B], F [auth A], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A], BA [auth A], CB [auth B], DB [auth B], EB [auth B], Z [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.741α = 85.84
b = 73.601β = 86.19
c = 83.39γ = 71.82
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2019-03-27
    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