4L1G

Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase from Bacillus cereus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.336 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An unusual alpha-carbon hydroxylation of proline promotes active-site maturation.

Fadouloglou, V.E.Balomenou, S.Aivaliotis, M.Kotsifaki, D.Arnaouteli, S.Tomatsidou, A.Efstathiou, G.Kountourakis, N.Miliara, S.Griniezaki, M.Tsalafouta, A.Pergantis, S.A.Boneca, I.G.Glykos, N.M.Bouriotis, V.Kokkinidis, M.

(2017) J.Am.Chem.Soc. --: --

  • DOI: 10.1021/jacs.6b12209
  • Also Cited By: 5O6Y

  • PubMed Abstract: 
  • The full extent of proline (Pro) hydroxylation has yet to be established, as it is largely unexplored in bacteria. We describe here a so far unknown Pro hydroxylation activity which occurs in active sites of polysaccharide deacetylases (PDAs) from ba ...

    The full extent of proline (Pro) hydroxylation has yet to be established, as it is largely unexplored in bacteria. We describe here a so far unknown Pro hydroxylation activity which occurs in active sites of polysaccharide deacetylases (PDAs) from bacterial pathogens, modifying the protein backbone at the Cα atom of a Pro residue to produce 2-hydroxyproline (2-Hyp). This process modifies with high specificity a conserved Pro, shares with the deacetylation reaction the same active site and one catalytic residue, and utilizes molecular oxygen as source for the hydroxyl group oxygen of 2-Hyp. By providing additional hydrogen-bonding capacity, the Pro→2-Hyp conversion alters the active site and enhances significantly deacetylase activity, probably by creating a more favorable environment for transition-state stabilization. Our results classify this process as an active-site "maturation", which is highly atypical in being a protein backbone-modifying activity, rather than a side-chain-modifying one.


    Organizational Affiliation

    Institute of Molecular Biology and Biotechnology , 70013 Heraklion, Crete, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan N-acetylglucosamine deacetylase
A, B, C, D
273Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)Mutation(s): 0 
EC: 3.5.1.-
Find proteins for Q81EK9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q81EK9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PXU
Query on PXU
A, B, C, D
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.336 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.657α = 90.00
b = 92.657β = 90.00
c = 242.947γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references