2AE3

Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries.

Kim, J.K.Yang, I.S.Shin, H.J.Cho, K.J.Ryu, E.K.Kim, S.H.Park, S.S.Kim, K.H.

(2006) Proc.Natl.Acad.Sci.USA 103: 1732-1737

  • DOI: 10.1073/pnas.0507862103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cephalosporin acylase (CA), a member of the N-terminal nucleophile hydrolase family, is activated through sequential primary and secondary autoproteolytic reactions with the release of a pro segment. We have determined crystal structures of four CA m ...

    Cephalosporin acylase (CA), a member of the N-terminal nucleophile hydrolase family, is activated through sequential primary and secondary autoproteolytic reactions with the release of a pro segment. We have determined crystal structures of four CA mutants. Two mutants are trapped after the primary cleavage, and the other two undergo secondary cleavage slowly. These structures provide a look at pro-segment conformation during activation in N-terminal nucleophile hydrolases. The highly strained helical pro segment of precursor is transformed into a relaxed loop in the intermediates, suggesting that the relaxation of structural constraints drives the primary cleavage reaction. The secondary autoproteolytic step has been proposed to be intermolecular. However, our analysis provides evidence that CA is processed in two sequential steps of intramolecular autoproteolysis involving two distinct residues in the active site, the first a serine and the second a glutamate.


    Organizational Affiliation

    Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaryl 7-Aminocephalosporanic Acid Acylase
A
166Pseudomonas sp. (strain SY-77)Mutation(s): 0 
EC: 3.5.1.93
Find proteins for P07662 (Pseudomonas sp. (strain SY-77))
Go to UniProtKB:  P07662
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutaryl 7-Aminocephalosporanic Acid Acylase
B
528Pseudomonas sp. (strain SY-77)Mutation(s): 0 
EC: 3.5.1.93
Find proteins for P07662 (Pseudomonas sp. (strain SY-77))
Go to UniProtKB:  P07662
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.387α = 90.00
b = 73.387β = 90.00
c = 379.684γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description