1HB0

Snapshots of serine protease catalysis: (D) acyl-enzyme intermediate between porcine pancreatic elastase and human beta-casomorphin-7 jumped to pH 10 for 2 minutes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Snapshots of Serine Protease Catalysis Reveal a Tetrahedral Intermediate

Wilmouth, R.C.Edman, K.Neutze, R.Wright, P.A.Clifton, I.J.Schneider, T.R.Schofield, C.J.Hajdu, J.

(2001) Nat.Struct.Mol.Biol. 8: 689

  • DOI: 10.1038/90401
  • Primary Citation of Related Structures:  1HAX, 1HAY, 1HAZ
  • Also Cited By: 2BB4, 2BD2, 2BD3, 2BD4, 2BD5, 2BD7, 2BD8, 2BD9, 2BDA, 2BDB, 2BDC

  • PubMed Abstract: 
  • Studies on the catalytic mechanism and inhibition of serine proteases are widely used as paradigms for teaching enzyme catalysis. Ground-breaking work on the structures of chymotrypsin and subtilisin led to the idea of a conserved catalytic triad for ...

    Studies on the catalytic mechanism and inhibition of serine proteases are widely used as paradigms for teaching enzyme catalysis. Ground-breaking work on the structures of chymotrypsin and subtilisin led to the idea of a conserved catalytic triad formed by the active site Ser, His and Asp residues. An oxyanion hole, consisting of the peptide amide of the active site serine and a neighbouring glycine, was identified, and hydrogen bonding in the oxyanion hole was suggested to stabilize the two proposed tetrahedral intermediates on the catalytic pathway. Here we show electron density changes consistent with the formation of a tetrahedral intermediate during the hydrolysis of an acyl-enzyme complex formed between a natural heptapeptide and elastase. No electron density for an enzyme-product complex was observed. The structures also suggest a mechanism for the synchronization of hydrolysis and peptide release triggered by the conversion of the sp2 hybridized carbonyl carbon to an sp3 carbon in the tetrahedral intermediate. This affects the location of the peptide in the active site cleft, triggering the collapse of a hydrogen bonding network between the peptide and the beta-sheet of the active site.


    Related Citations: 
    • Structure of a Specific Acyl-Enzyme Complex Formed between Beta-Casomorphin-7 and Porcine Pancreatic Elastase
      Wilmouth, R.C.,Clifton, I.J.,Robinson, C.V.,Roach, P.L.,Aplin, R.T.,Westwood, N.J.,Hajdu, J.,Schofield, C.J.
      (1997) Nat.Struct.Mol.Biol. 4: 456
    • Structure of Native Porcine Pancreatic Elastase at 1.65A Resolution
      Meyer, E.,Cole, G.,Radhakrishnan, R.,Epp, O.
      (1988) Acta Crystallogr.,Sect.B 44: 26


    Organizational Affiliation

    The Dyson Perrins Laboratory and Oxford Centre for Molecular Sciences, University of Oxford, South Parks Road, Oxford OX1 3QY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELASTASE 1
B
240Sus scrofaGene Names: CELA1 (ELA1)
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Go to Gene View: CELA1
Go to UniProtKB:  P00772
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.630α = 90.00
b = 57.600β = 90.00
c = 73.440γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-02
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance