4L1G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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 139: 5330-5337

  • DOI: https://doi.org/10.1021/jacs.6b12209
  • Primary Citation of Related Structures:  
    4L1G

  • 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 bacterial pathogens, modifying the protein backbone at the C α 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan N-acetylglucosamine deacetylase
A, B, C, D
273Bacillus cereus ATCC 14579Mutation(s): 0 
Gene Names: bc1960BC_1960
EC: 3.5.1 (PDB Primary Data), 3.5.1.104 (UniProt)
UniProt
Find proteins for Q81EK9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q81EK9 
Go to UniProtKB:  Q81EK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81EK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
I [auth C]
J [auth C]
L [auth D]
E [auth A],
G [auth B],
I [auth C],
J [auth C],
L [auth D],
M [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
N [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 2.34 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.657α = 90
b = 92.657β = 90
c = 242.947γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection