1ESA

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

• PDB DOI: https://doi.org/10.2210/pdb1ESA/pdb

• Classification: HYDROLASE(SERINE PROTEINASE)
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1994-02-04 Released: 1994-04-30 
• Deposition Author(s): Ding, X., Rasmussen, B., Petsko, G.A., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Observed: 
  0.190 (Depositor) 

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

• PubMed: 8049229 
• Primary Citation of Related Structures:  
  1ESA, 1ESB


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.16 kDa 
• Atom Count: 1,967 
• Modelled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORCINE PANCREATIC ELASTASE	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.37	α = 90
b = 58.21	β = 90
c = 74.83	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Ding, X., Rasmussen, B., Petsko, G.A., Ringe, D.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary