6CCI

The Crystal Structure of XOAT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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This is version 2.1 of the entry. See complete history


Literature

Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis XylanO-acetyltransferase XOAT1.

Lunin, V.V.Wang, H.T.Bharadwaj, V.S.Alahuhta, M.Pena, M.J.Yang, J.Y.Archer-Hartmann, S.A.Azadi, P.Himmel, M.E.Moremen, K.W.York, W.S.Bomble, Y.J.Urbanowicz, B.R.

(2020) Plant Cell 32: 2367-2382

  • DOI: https://doi.org/10.1105/tpc.20.00028
  • Primary Citation of Related Structures:  
    6CCI

  • PubMed Abstract: 

    Xylans are a major component of plant cell walls. O -Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis ( Arabidopsis thaliana ) xylan O -acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2- O -acetylation of xylan, followed by nonenzymatic acetyl migration to the O -3 position, resulting in products that are monoacetylated at both O -2 and O -3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the α/β/α topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac-Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.


  • Organizational Affiliation

    Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ESKIMO 1487Arabidopsis thalianaMutation(s): 0 
Gene Names: ESK1TBL29At3g55990F27K19.170
UniProt
Find proteins for Q9LY46 (Arabidopsis thaliana)
Explore Q9LY46 
Go to UniProtKB:  Q9LY46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LY46
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.431α = 90
b = 58.169β = 90
c = 138.528γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
SAINTdata reduction
CRANK2phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-02
    Changes: Database references, Structure summary