6SGF

Molecular insight into a new low affinity xylan binding module CBM86, from the xylanolytic gut symbiont Roseburia intestinalis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.756 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


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Literature

Molecular insight into a new low affinity xylan binding module from the xylanolytic gut symbiont Roseburia intestinalis.

Leth, M.L.Ejby, M.Madland, E.Kitaoku, Y.Slotboom, D.J.Guskov, A.Aachmann, F.L.Abou Hachem, M.

(2019) Febs J. --: --

  • DOI: 10.1111/febs.15117

  • PubMed Abstract: 
  • Efficient capture of glycans, the prime metabolic resources in the human gut, confers a key competitive advantage for gut microbiota members equipped with extracellular glycoside hydrolases (GHs) to target these substrates. The association of glycans ...

    Efficient capture of glycans, the prime metabolic resources in the human gut, confers a key competitive advantage for gut microbiota members equipped with extracellular glycoside hydrolases (GHs) to target these substrates. The association of glycans to the bacterial cell surface is typically mediated by carbohydrate binding modules (CBMs). Here, we report the structure of RiCBM86 appended to a GH family 10 xylanase from Roseburia intestinalis. This CBM represents a new family of xylan binding CBMs present in xylanases from abundant and prevalent healthy human gut Clostridiales. RiCBM86 adopts a canonical β-sandwich fold, but shows structural divergence from known CBMs. The structure of RiCBM86 has been determined with a bound xylohexaose, which revealed an open and shallow binding site. RiCBM86 recognizes only a single xylosyl ring with direct hydrogen bonds. This mode of recognition is unprecedented amongst previously reported xylan binding type-B CBMs that display more extensive hydrogen-bonding patterns to their ligands or employ Ca 2+ to mediate ligand-binding. The architecture of RiCBM86 is consistent with an atypically low binding affinity (K about 0.5 mm for xylohexaose) compared to most xylan binding CBMs. Analyses using NMR spectroscopy corroborated the observations from the complex structure and the preference of RiCBM86 to arabinoxylan over glucuronoxylan, consistent with the largely negatively charged surface flanking the binding site. Mutational analysis and affinity electrophoresis established the importance of key binding residues, which are conserved in the family. This study provides novel insight into the structural features that shape low-affinity CBMs that mediate extended bacterial glycan capture in the human gut niche. DATABASES: Structural data are available in the protein data bank database under the accession number 6SGF. Sequence data are available in the GenBank database under the accession number EEV01588.1. The assignment of the Roseburia intestinalis xylan binding module into the CBM86 new family is available in the CAZy database (http://www.cazy.org/CBM86.html).


    Organizational Affiliation

    Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.,NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.,Membrane Enzymology, Institute for Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-xylanase
A, B, C, D, E, F
141Roseburia intestinalis L1-82Mutation(s): 0 
EC: 3.2.1.8
Find proteins for C7G9B5 (Roseburia intestinalis L1-82)
Go to UniProtKB:  C7G9B5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C, D, E
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.756 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 141.870α = 90.00
b = 141.870β = 90.00
c = 60.600γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark4002-00297B

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release