1ODT

cephalosporin C deacetylase mutated, in complex with acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Multifunctional Xylooligosaccharide/Cephalosporin C Deacetylase Revealed by the Hexameric Structure of the Bacillus Subtilis Enzyme at 1.9A Resolution

Vincent, F.Charnock, S.J.Verschueren, K.H.G.Turkenburg, J.P.Scott, D.J.Offen, W.A.Roberts, S.Pell, G.Gilbert, H.J.Davies, G.J.Brannigan, J.A.

(2003) J Mol Biol 330: 593

  • DOI: 10.1016/s0022-2836(03)00632-6
  • Primary Citation of Related Structures:  
    1ODS, 1ODT

  • PubMed Abstract: 
  • Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C ...

    Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C. The 1.9A structure of the multifunctional CE-7 esterase (hereinafter CAH) from Bacillus subtilis 168 reveals a classical alpha/beta hydrolase fold encased within a 32 hexamer. This is the first example of a hexameric alpha/beta hydrolase and is further evidence of the versatility of this particular fold, which is used in a wide variety of biological contexts. A narrow entrance tunnel leads to the centre of the molecule, where the six active-centre catalytic triads point towards the tunnel interior and thus are sequestered away from cytoplasmic contents. By analogy to self-compartmentalising proteases, the tunnel entrance may function to hinder access of large substrates to the poly-specific active centre. This would explain the observation that the enzyme is active on a variety of small, acetylated molecules. The structure of an active site mutant in complex with the reaction product, acetate, reveals details of the putative oxyanion binding site, and suggests that substrates bind predominantly through non-specific contacts with protein hydrophobic residues. Protein residues involved in catalysis are tethered by interactions with protein excursions from the canonical alpha/beta hydrolase fold. These excursions also mediate quaternary structure maintenance, so it would appear that catalytic competence is only achieved on protein multimerisation. We suggest that the acetyl xylan esterase (EC 3.1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CEPHALOSPORIN C DEACETYLASEA [auth C],
B [auth H]
318Bacillus subtilisMutation(s): 1 
EC: 3.1.1.41 (PDB Primary Data), 3.1.1.72 (UniProt)
UniProt
Find proteins for P94388 (Bacillus subtilis (strain 168))
Explore P94388 
Go to UniProtKB:  P94388
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94388
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C,
D [auth H]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.167α = 90
b = 157.17β = 90
c = 132.098γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance