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: 126.13 kDa 
• Atom Count: 8,661 
• Modelled Residue Count: 1,038 
• Deposited Residue Count: 1,105 
• Unique protein chains: 1

 5MQM

Glycoside hydrolase BT_0986

• PDB DOI:  https://doi.org/10.2210/pdb5MQM/pdb

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


• Deposited: 2016-12-20 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.
• Funding Organization(s): iotechnology and Biological Research Council, Wellcome Trust, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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 of 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolases family 2, sugar binding domain	A	1,105	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: Btheta7330_02599
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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A], G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
RPQ	E [auth A]	D-rhamnopyranose tetrazole C6 H10 N4 O3 RGTARVZVTUMUSY-QMKXCQHVSA-N
PGE	H [auth A], I [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.05	α = 90
b = 84.81	β = 99.2
c = 120.63	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

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.

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Funding Organization	Location	Grant Number
iotechnology and Biological Research Council	United Kingdom	BB/K020358/1
iotechnology and Biological Research Council	United Kingdom	BB/K001949/1
Wellcome Trust	United Kingdom	WT097907MA
European Research Council	United Kingdom	322820

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 1.3: 2017-08-23
  Changes: Author supporting evidence