1ESB

DIRECT STRUCTURE OBSERVATION OF AN ACYL-ENZYME INTERMEDIATE IN THE HYDROLYSIS OF AN ESTER SUBSTRATE BY ELASTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase.

Ding, X.Rasmussen, B.F.Petsko, G.A.Ringe, D.

(1994) Biochemistry 33: 9285-9293

  • Primary Citation of Related Structures:  1ESA

  • PubMed Abstract: 
  • The method of X-ray crystallographic cryoenzymology has been used to determine the crystal structure of a kinetically significant species on the reaction pathway of a crystalline enzyme. The structure of a specific acyl-enzyme intermediate in the ela ...

    The method of X-ray crystallographic cryoenzymology has been used to determine the crystal structure of a kinetically significant species on the reaction pathway of a crystalline enzyme. The structure of a specific acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of the N-carbobenzoxy-L-alanine p-nitrophenyl ester has been determined and refined against X-ray diffraction data at 2.3-A resolution. The difference Fourier electron density map clearly shows electron density for the trapped acyl-enzyme. The acyl-enzyme was formed at -26 degrees C and was stabilized at -55 degrees C during data collection, taking advantage of the glass transition in protein dynamics that occurs at around -50 degrees C.


    Related Citations: 
    • Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78 Angstroms Resolution
      Takahashi, L.H.,Radhakrishnan, R.,Rosenfield Junior, R.E.,Meyer Junior, E.F.,Trainor, D.A.
      (1989) J.Am.Chem.Soc. 111: 3368
    • Structures of Product and Inhibitor Complexes of Streptomyces Griseus Protease a at 1.8 Angstroms Resolution
      James, M.N.G.,Sielecki, A.R.,Brayer, G.D.,Delbaere, L.T.J.
      (1980) J.Mol.Biol. 144: 43
    • Structure of Native Procine Pancreatic Elastase at 1.65 Angstroms Resolution
      Meyer, E.,Cole, G.,Radhakrishnan, R.,Epp, O.
      (1988) Acta Crystallogr.,Sect.B 44: 26
    • Crystal Structure of Elastase-Substrate Complex at-55 Degc
      Alber, T.,Petsko, G.A.,Tsernoglou, D.
      (1976) Nature 263: 297
    • Formation of Stable Crystalline Enzyme-Substrate Intermediates at Sub-Zero Temperatures
      Fink, A.L.,Ahmed, A.I.
      (1976) Nature 263: 294


    Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PORCINE PANCREATIC ELASTASE
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BBL
Query on BBL

Download SDF File 
Download CCD File 
A
N-[(BENZYLOXY)CARBONYL]-L-ALANINE
N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE
C11 H13 N O4
TYRGLVWXHJRKMT-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.020α = 90.00
b = 57.220β = 90.00
c = 74.660γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance