5MWK | pdb_00005mwk

Glycoside hydrolase BT_0986

• PDB DOI: https://doi.org/10.2210/pdb5MWK/pdb

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


• Deposited: 2017-01-18 Released: 2017-03-22 
• Deposition Author(s): Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Basle, A., Gray, J., Venditto, I., Briggs, J., Zhang, X., Labourel, A., Terrapon, N., Buffetto, F., Nepogodiev, S., Xiao, Y., Field, R.A., Zhu, Y., O'Neill, M.A., Urbanowicz, B.R., York, W.S., Davies, G.J., Abbott, D.W., Ralet, M.C., Martens, E.C., Henrissat, B., Gilbert, H.J.

(2017) Nature 544: 65-70

• PubMed: 28329766 
• DOI: https://doi.org/10.1038/nature21725
• Primary Citation Related Structures: 
  5MQM, 5MQN, 5MQO, 5MQR, 5MQS, 5MSX, 5MSY, 5MT2, 5MUI, 5MUJ, 5MWK


• PubMed Abstract: 
  

  The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.

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Organizational Affiliation: 
• Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K.
Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, F-13288 Marseille, France.
INRA, UR1268 Biopolymères Interactions Assemblages, 44300 Nantes, France.
Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich NR4 7UH, UK.
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
Department of Chemistry, University of York, York YO10 5DD, U.K.
Lethbridge Research Centre, Lethbridge, AB, Canada.
INRA, USC 1408 AFMB, F-13288 Marseille, France.
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 126.43 kDa 
• Atom Count: 8,765 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 2, sugar binding protein	A	1,105	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: BT_0986
UniProt
Find proteins for Q8A931 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A931  Go to UniProtKB:  Q8A931

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-rhamnopyranose-(1-2)-alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose-(1-2)]beta-D-galactopyranose-(1-2)-alpha-D-aceric acid-(1-3)-alpha-L-rhamnopyranose	B	6	N/A	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
BR	E [auth A], F [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.254	α = 90
b = 86.216	β = 99.38
c = 123.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-04-05
  Changes: Database references
• Version 1.2: 2017-04-12
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary