2VAV

Crystal structure of deacetylcephalosporin C acetyltransferase (DAC-Soak)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

The last step in cephalosporin C formation revealed: crystal structures of deacetylcephalosporin C acetyltransferase from Acremonium chrysogenum in complexes with reaction intermediates.

Lejon, S.Ellis, J.Valegard, K.

(2008) J Mol Biol 377: 935-944

  • DOI: https://doi.org/10.1016/j.jmb.2008.01.047
  • Primary Citation of Related Structures:  
    2VAT, 2VAV, 2VAX

  • PubMed Abstract: 

    Deacetylcephalosporin C acetyltransferase (DAC-AT) catalyses the last step in the biosynthesis of cephalosporin C, a broad-spectrum beta-lactam antibiotic of large clinical importance. The acetyl transfer step has been suggested to be limiting for cephalosporin C biosynthesis, but has so far escaped detailed structural analysis. We present here the crystal structures of DAC-AT in complexes with reaction intermediates, providing crystallographic snapshots of the reaction mechanism. The enzyme is found to belong to the alpha/beta hydrolase class of acetyltransferases, and the structures support previous observations of a double displacement mechanism for the acetyl transfer reaction in other members of this class of enzymes. The structures of DAC-AT reported here provide evidence of a stable acyl-enzyme complex, thus underpinning a mechanism involving acetylation of a catalytic serine residue by acetyl coenzyme A, followed by transfer of the acetyl group to deacetylcephalosporin C through a suggested tetrahedral transition state.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, S-751 24 Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
A, B, C, D, E
444Hapsidospora chrysogenaMutation(s): 0 
EC: 2.3.1.175
UniProt
Find proteins for P39058 (Hapsidospora chrysogena)
Explore P39058 
Go to UniProtKB:  P39058
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39058
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CSC
Query on CSC

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth I]
JA [auth J]
KA [auth K]
4-(3-ACETOXYMETHYL-2-CARBOXY-8-OXO-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-EN-7-YLCARBAMOYL)-1-CARBOXY-BUTYL-AMMONIUM
C16 H22 N3 O8 S
HOKIDJSKDBPKTQ-GLXFQSAKSA-O
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
HA [auth I]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OAS
Query on OAS
A, B, C, D, E
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.065α = 90
b = 108.865β = 90.03
c = 195.792γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CSCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-12-12
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary