3DFK | pdb_00003dfk

The crystal structure of teicoplanin pseudoaglycone deacetylase Orf2* bound to one of its products decanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.220 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

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This is version 1.2 of the entry. See complete history

Literature

Crystal structures of lipoglycopeptide antibiotic deacetylases: implications for the biosynthesis of a40926 and teicoplanin.

Zou, Y.Brunzelle, J.S.Nair, S.K.

(2008) Chem Biol 15: 533-545

  • DOI: https://doi.org/10.1016/j.chembiol.2008.05.009
  • Primary Citation Related Structures: 
    3DFF, 3DFI, 3DFK, 3DFM

  • PubMed Abstract: 

    The lipoglycopeptide antibiotics teicoplanin and A40926 have proven efficacy against Gram-positive pathogens. These drugs are distinguished from glycopeptide antibiotics by N-linked long chain acyl-D-glucosamine decorations that contribute to antibacterial efficacy. During the biosynthesis of lipoglycopeptides, tailoring glycosyltransferases attach an N-acetyl-D-glucosamine to the aglycone, and this N-acetyl-glucosaminyl pseudoaglycone is deacetylated prior to long chain hydrocarbon attachment. Here we present several high-resolution crystal structures of the pseudoaglycone deacetylases from the biosynthetic pathways of teicoplanin and A40926. The cocrystal structure of the teicoplanin pseudoaglycone deacetylase with a fatty acid product provides further insights into the roles of active-site residues, and suggests mechanistic similarities with structurally distinct zinc deacetylases, such as peptidoglycan deacetylase and LpxC. A unique, structurally mobile capping lid, located at the apex of these pseudoaglycone deacetylases, likely serves as a determinant of substrate specificity.


  • Organizational Affiliation
    • Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 30.53 kDa 
  • Atom Count: 2,338 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 273 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Teicoplanin pseudoaglycone deacetylase Orf2273Actinoplanes teichomyceticusMutation(s): 0 
Gene Names: tcp14
UniProt
Find proteins for Q6ZZJ1 (Actinoplanes teichomyceticus)
Explore Q6ZZJ1 
Go to UniProtKB:  Q6ZZJ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZZJ1
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.220 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.53α = 90
b = 64.263β = 99.01
c = 50.375γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary