2AE5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 

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 U S A 103: 1732-1737

  • DOI: 10.1073/pnas.0507862103
  • Primary Citation of Related Structures:  
    2AE5, 2AE4, 2AE3, 2ADV

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutaryl 7-Aminocephalosporanic Acid AcylaseA166Pseudomonas sp. GK16Mutation(s): 0 
EC: 3.5.1.11 (PDB Primary Data), 3.5.1.93 (UniProt)
Find proteins for P07662 (Pseudomonas sp. (strain SY-77))
Explore P07662 
Go to UniProtKB:  P07662
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutaryl 7-Aminocephalosporanic Acid AcylaseB528Pseudomonas sp. GK16Mutation(s): 0 
EC: 3.5.1.11 (PDB Primary Data), 3.5.1.93 (UniProt)
Find proteins for P07662 (Pseudomonas sp. (strain SY-77))
Explore P07662 
Go to UniProtKB:  P07662
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.736α = 90
b = 73.736β = 90
c = 383.349γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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