9HUC | pdb_00009huc

The glucuronyl esterase OtCE15A from Opitutus terrae in complex with a heptasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.245 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.175 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Interaction of a glucuronoyl esterase with complex fragments of the plant cell wall hemicellulose.

Zaghini, A.Ostberg, E.B.Banerjee, S.Mazurkewich, S.Yu, L.Dupree, P.Larsbrink, J.Lo Leggio, L.

(2026) Int J Biol Macromol 352: 151020-151020

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.151020
  • Primary Citation Related Structures: 
    9HUC, 9HVR

  • PubMed Abstract: 

    Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant cell walls and are promising biochemical tools for industrial processing of these recalcitrant natural resources. However, details on how GEs interact with and catalyze degradation of their natural substrates are sparse. Using well-diffracting crystals of the model GE OtCE15A, we sought to structurally elucidate its interactions with fragments and analogues of the lignin carbohydrate complex, including commercially available oligosaccharides, digests of complex polysaccharides, and chemical fragments representing building blocks of lignin. While most compounds failed to bind in crystals, the analysis uncovered the structure of a complex with a heptasaccharide (a decorated xylopentaose), the largest ligand bound to a GE experimental structure to date. Most hydrogen bonding interactions are with the glucuronic acid moiety, which is almost totally buried upon binding; however, the rest of the saccharide chain also has a significant contact surface. The structure shows for the first time that OtCE15A can accommodate an arabinose decoration on the glucuronoxylan chain it attacks. Structural comparison suggests that the polysaccharide conformation may influence specificity, reinforcing the view of GEs as true carbohydrate-active enzymes rather than opportunistic promiscuous esterases.


  • Organizational Affiliation
    • Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 48.87 kDa 
  • Atom Count: 3,292 
  • Modeled Residue Count: 395 
  • Deposited Residue Count: 437 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative acetyl xylan esterase437Opitutus terrae PB90-1Mutation(s): 0 
Gene Names: Oter_0116
UniProt
Find proteins for B1ZMF4 (Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1))
Explore B1ZMF4 
Go to UniProtKB:  B1ZMF4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1ZMF4
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
B
7N/A

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.245 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.77α = 90
b = 65.43β = 90
c = 118.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF21OC0071611

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Database references
  • Version 1.2: 2026-03-18
    Changes: Database references