6FUV | pdb_00006fuv

Structure of a manno-oligosaccharide specific solute binding protein, BlMnBP2 from Bifidobacterium animalis subsp. lactis ATCC 27673 in complex with mannotriose

• PDB DOI: https://doi.org/10.2210/pdb6FUV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bifidobacterium
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-02-27 Released: 2019-03-20 
• Deposition Author(s): Ejby, M., Abou Hachem, M., Guskov, A., Slotboom, D.J.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Two binding proteins of the ABC transporter that confers growth of Bifidobacterium animalis subsp. lactis ATCC27673 on beta-mannan possess distinct manno-oligosaccharide-binding profiles.

Ejby, M., Guskov, A., Pichler, M.J., Zanten, G.C., Schoof, E., Saburi, W., Slotboom, D.J., Abou Hachem, M.

(2019) Mol Microbiol 112: 114-130

• PubMed: 30947380 
• DOI: https://doi.org/10.1111/mmi.14257
• Primary Citation Related Structures: 
  6FUV, 6I5R, 6I5V, 6I5W


• PubMed Abstract: 
  

  Human gut bifidobacteria rely on ATP-binding cassette (ABC) transporters for oligosaccharide uptake. Multiple oligosaccharide-specific solute-binding protein (SBP) genes are occasionally associated with a single ABC transporter, but the significance of this multiplicity remains unclear. Here, we characterize BlMnBP1 and BlMnBP2, the two SBPs associated to the β-manno-oligosaccharide (MnOS) ABC transporter in Bifidobacterium animalis subsp. lactis. Despite similar overall specificity and preference to mannotriose (K _d ≈80 nM), affinity of BlMnBP1 is up to 2570-fold higher for disaccharides than BlMnBP2. Structural analysis revealed a substitution of an asparagine that recognizes the mannosyl at position 2 in BlMnBP1, by a glycine in BlMnBP2, which affects substrate affinity. Both substitution types occur in bifidobacterial SBPs, but BlMnBP1-like variants prevail in human gut isolates. B. animalis subsp. lactis ATCC27673 showed growth on gluco and galactomannans and was able to outcompete a mannan-degrading Bacteroides ovatus strain in co-cultures, attesting the efficiency of this ABC uptake system. By contrast, a strain that lacks this transporter failed to grow on mannan. This study highlights SBP diversification as a possible strategy to modulate oligosaccharide uptake preferences of bifidobacterial ABC-transporters during adaptation to specific ecological niches. Efficient metabolism of galactomannan by distinct bifidobacteria, merits evaluating this plant glycan as a potential prebiotic.

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Organizational Affiliation: 
• Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads building 224, Kgs Lyngby, 2800, Denmark.
Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands.
Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg C, Denmark.
Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 49.4 kDa 
• Atom Count: 3,959 
• Modeled Residue Count: 427 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute Binding Protein, BlMnBP1 in complex with mannotriose	A	427	Bifidobacterium	Mutation(s): 0  Gene Names: Blac_00785
UniProt
Find proteins for A0A4V8GZV8 (Bifidobacterium) Explore A0A4V8GZV8  Go to UniProtKB:  A0A4V8GZV8

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G26320VF GlyCosmos: G26320VF GlyGen: G26320VF

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	H [auth A], I [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
PGE	C [auth A], D [auth A], E [auth A], G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.17	α = 90
b = 64.59	β = 90
c = 133.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Ejby, M., Abou Hachem, M., Guskov, A., Slotboom, D.J.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	DFF-4002-00297

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-07-17
  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
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Structure summary