9PMY | pdb_00009pmy

Crystal Structure of an ATP-Binding Cassette (ABC) Transporter Associated, Xyloglucan-Binding Protein from the Extremely Thermophilic, Lignocellulose Degrading Bacterium Anaerocellum (f. Caldicellulosiruptor) bescii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium.

Tjo, H.Jiang, V.Jeffrey, P.D.Zhu, A.Link, A.J.Joseph, J.A.Conway, J.M.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70667
  • Primary Citation Related Structures: 
    9PMY

  • PubMed Abstract: 

    Xyloglucan (an α-1,6-xylosyl-substituted β-1,4-glucan) is a major hemicellulose of the primary cell wall of many plants and an important growth substrate for biomass-degrading bacteria in diverse ecological niches, including the gut microbiome and hot springs. In Gram-positive bacteria, xyloglucan is deconstructed into soluble oligosaccharides in the extracytoplasmic space before import by ATP-Binding Cassette (ABC) transporters, but the structural basis for this process remains poorly understood. Here, we identified an ABC transporter for xyloglucan uptake (Athe_2052-2054) in the Gram-positive, plant biomass-degrading thermophile Anaerocellum bescii, which is conserved across the Anaerocellum genus. We solved the apo crystal structure of its extracellular substrate-binding protein (SBP), Athe_2052, revealing a unique tertiary fold found only in a small subset of SBPs that bind complex oligosaccharides. To our knowledge, Athe_2052 is the first structurally characterized ABC SBP known to recognize xyloglucan oligosaccharides. Biophysical analysis showed that while Athe_2052 binds unsubstituted β-glucan chains, recognition of xyloglucan side chains in the binding pocket markedly increases affinity (K d  = 14 nm) for xyloglucan heptasaccharide (XXXG), the principal oligosaccharide released during xyloglucan deconstruction. Molecular modeling revealed that xyloglucan heptasaccharide, owing to its branched substitutions, is bound in a distinct conformation compared to unsubstituted β-glucans. This represents a unique mode of xyloglucan recognition driven by α-linked side chain interactions rather than β-glucan backbone recognition alone. Together, these findings provide the first structural basis for xyloglucan oligosaccharide recognition by an ABC transporter in Gram-positive bacteria.


  • Organizational Affiliation
    • Department of Chemical and Biological Engineering, Princeton University, NJ, USA.

Macromolecule Content 

  • Total Structure Weight: 126.28 kDa 
  • Atom Count: 8,989 
  • Modeled Residue Count: 1,066 
  • Deposited Residue Count: 1,100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular solute-binding protein family 1
A, B
550Caldicellulosiruptor besciiMutation(s): 0 
Gene Names: Athe_2052
UniProt
Find proteins for B9MLD9 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320))
Explore B9MLD9 
Go to UniProtKB:  B9MLD9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9MLD9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.291α = 90
b = 129.997β = 93.611
c = 111.249γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references