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: 2.30 Å
  • R-Value Work: 0.210 
  • R-Value Observed: 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:  
    1ESB, 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 elastase-catalyzed hydrolysis of the N-carbobenzoxy-L-alanine p-nitrophenyl ester has been determined and refined against X-ray diffraction data at 2 ...

    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
    • Structure of Native Procine Pancreatic Elastase at 1.65 Angstroms Resolution
      Meyer, E., Cole, G., Radhakrishnan, R., Epp, O.
      (1988) Acta Crystallogr B 44: 26
    • 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
    • Formation of Stable Crystalline Enzyme-Substrate Intermediates at Sub-Zero Temperatures
      Fink, A.L., Ahmed, A.I.
      (1976) Nature 263: 294
    • Crystal Structure of Elastase-Substrate Complex at-55 Degc
      Alber, T., Petsko, G.A., Tsernoglou, D.
      (1976) Nature 263: 297

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PORCINE PANCREATIC ELASTASEA240Sus scrofaMutation(s): 0 
Gene Names: CELA1ELA1
EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBL
Query on BBL

Download Ideal Coordinates CCD File 
B [auth A]N-[(BENZYLOXY)CARBONYL]-L-ALANINE
C11 H13 N O4
TYRGLVWXHJRKMT-QMMMGPOBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.02α = 90
b = 57.22β = 90
c = 74.66γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance