5MQS | pdb_00005mqs

Sialidase BT_1020

• PDB DOI: https://doi.org/10.2210/pdb5MQS/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: 3.00 Å
• R-Value Free: 
  0.262 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.210 (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: 127.75 kDa 
• Atom Count: 8,806 
• Modeled Residue Count: 1,082 
• Deposited Residue Count: 1,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-L-arabinobiosidase	A	1,108	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: hypBA2, Btheta7330_02635 EC: 3.2.1.187
UniProt
Find proteins for Q8A8Z7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A8Z7  Go to UniProtKB:  Q8A8Z7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHR	B [auth A]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.262 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.433	α = 90
b = 318.194	β = 90
c = 90.579	γ = 90

Software Package:

Software Name	Purpose
XDS	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
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary