5LFZ | pdb_00005lfz

T48 deacetylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LFZ

This is version 1.6 of the entry. See complete history

Literature

Structure and function of a CE4 deacetylase isolated from a marine environment.

Tuveng, T.R.Rothweiler, U.Udatha, G.Vaaje-Kolstad, G.Smalas, A.Eijsink, V.G.H.

(2017) PLoS One 12: e0187544-e0187544

  • DOI: https://doi.org/10.1371/journal.pone.0187544
  • Primary Citation Related Structures: 
    5LFZ, 5LGC

  • PubMed Abstract: 

    Chitin, a polymer of β(1-4)-linked N-acetylglucosamine found in e.g. arthropods, is a valuable resource that may be used to produce chitosan and chitooligosaccharides, two compounds with considerable industrial and biomedical potential. Deacetylating enzymes may be used to tailor the properties of chitin and its derived products. Here, we describe a novel CE4 enzyme originating from a marine Arthrobacter species (ArCE4A). Crystal structures of this novel deacetylase were determined, with and without bound chitobiose [(GlcNAc)2], and refined to 2.1 Å and 1.6 Å, respectively. In-depth biochemical characterization showed that ArCE4A has broad substrate specificity, with higher activity against longer oligosaccharides. Mass spectrometry-based sequencing of reaction products generated from a fully acetylated pentamer showed that internal sugars are more prone to deacetylation than the ends. These enzyme properties are discussed in the light of the structure of the enzyme-ligand complex, which adds valuable information to our still rather limited knowledge on enzyme-substrate interactions in the CE4 family.


  • Organizational Affiliation
    • Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.

Macromolecule Content 

  • Total Structure Weight: 25.09 kDa 
  • Atom Count: 1,710 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 223 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ArCE4A223Arthrobacter sp. AW19M34-1Mutation(s): 0 
Gene Names: AA310_02990ATC04_16800

Small Molecules

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

Query on NI



Download:Ideal Coordinates CCD File
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.09α = 90
b = 56.77β = 90
c = 76.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norway--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Structure summary
  • Version 1.2: 2017-11-01
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Database references
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 1.5: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary