1KEH

Precursor structure of cephalosporin acylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Precursor structure of cephalosporin acylase. Insights into autoproteolytic activation in a new N-terminal hydrolase family

Kim, Y.Kim, S.Earnest, T.N.Hol, W.G.

(2002) J Biol Chem 277: 2823-2829

  • DOI: 10.1074/jbc.M108888200
  • Primary Citation of Related Structures:  
    1KEH

  • PubMed Abstract: 
  • Autocatalytic proteolytic cleavage is a frequently observed post-translational modification in proteins. Cephalosporin acylase (CA) is a recently identified member of the N-terminal hydrolase family that is activated from an inactive precursor by autoproteolytic processing, generating a new N-terminal residue, which is either a Ser or a Thr ...

    Autocatalytic proteolytic cleavage is a frequently observed post-translational modification in proteins. Cephalosporin acylase (CA) is a recently identified member of the N-terminal hydrolase family that is activated from an inactive precursor by autoproteolytic processing, generating a new N-terminal residue, which is either a Ser or a Thr. The N-terminal Ser or Thr becomes a nucleophilic catalytic center for intramolecular and intermolecular amide cleavages. The gene structure of the open reading frame of CAs generally consists of a signal peptide followed by the alpha-subunit, a spacer sequence, and the beta-subunit, which are all translated into a single polypeptide chain, the CA precursor. The precursor is post-translationally modified into an active heterodimeric enzyme with alpha- and beta-subunits, first by intramolecular cleavage and second by intermolecular cleavage. We solved the first CA precursor structure (code 1KEH) from a class I CA from Pseudomonas diminuta at a 2.5-A resolution that provides insight into the mechanism of intramolecular cleavage. A conserved water molecule, stabilized by four hydrogen bonds in unusual pseudotetrahedral geometry, plays a key role to assist the OG atom of Ser(1beta) to generate a strong nucleophile. In addition, the site of the secondary intermolecular cleavage of CA is proposed to be the carbonyl carbon of Gly(158alpha) (Kim, S., and Kim, Y., (2001) J. Biol. Chem., 276, 48376-48381), which is different from the situation in two other class I CAs.


    Organizational Affiliation

    School of Chemical Engineering, Yeungnam University, Dae-Dong, Kyungsan 712-749, Korea. ykim1@yu.ac.kr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
precursor of cephalosporin acylaseA689Brevundimonas diminutaMutation(s): 2 
EC: 3.5.1 (PDB Primary Data), 3.5.1.93 (UniProt)
UniProt
Find proteins for Q9L5D6 (Brevundimonas diminuta)
Explore Q9L5D6 
Go to UniProtKB:  Q9L5D6
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.7α = 90
b = 73.7β = 90
c = 381γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-11-16 
  • Released Date: 2002-05-16 
  • Deposition Author(s): Kim, Y., Kim, S.

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance