7TOK

Crystal structure of the CBM domain of carbohydrate esterase FjoAcXE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans.

Penttinen, L.Kouhi, V.Faure, R.Skarina, T.Stogios, P.Master, E.Jurak, E.

(2022) Molecules 27

  • DOI: https://doi.org/10.3390/molecules27092655
  • Primary Citation of Related Structures:  
    7TOG, 7TOH, 7TOI, 7TOJ, 7TOK

  • PubMed Abstract: 

    Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xyl p ) backbone that can be substituted with an acetyl group at O -2 and O- 3 positions, and α-(1→2)-linked 4- O -methylglucopyranosyluronic acid (MeGlc p A). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xyl p are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae ( Fjo AcXE) was the first to remove the acetyl group from 2- O -MeGlc p A-3- O -acetyl-substituted Xyl p units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of Fjo AcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlc p A and another with acetate. All homologs were confirmed to release acetate from 2- O -MeGlc p A-3- O -acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In Fjo AcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlc p A-Xyl p ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.


  • Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, 80130 Joensuu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylxylan esterase I
A, B
150Flavobacterium johnsoniaeMutation(s): 2 
Gene Names: axeA
EC: 3.1.1.72
UniProt
Find proteins for A0A5P6A8B9 (Flavobacterium johnsoniae)
Explore A0A5P6A8B9 
Go to UniProtKB:  A0A5P6A8B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P6A8B9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.084α = 90
b = 120.964β = 90
c = 86.645γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
HKL-3000phasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references