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 4L1G | pdb_00004l1g

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 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4L1G

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 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.

Macromolecule Content 

  • Total Structure Weight: 126.61 kDa 
  • Atom Count: 7,688 
  • Modeled Residue Count: 855 
  • Deposited Residue Count: 1,092 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidoglycan N-acetylglucosamine deacetylase
A, B, C, D
273Bacillus cereus ATCC 14579Mutation(s): 0 
Gene Names: bc1960, BC_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
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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 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
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