1EKB

THE SERINE PROTEASE DOMAIN OF ENTEROPEPTIDASE BOUND TO INHIBITOR VAL-ASP-ASP-ASP-ASP-LYS-CHLOROMETHANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of enteropeptidase light chain complexed with an analog of the trypsinogen activation peptide.

Lu, D.Futterer, K.Korolev, S.Zheng, X.Tan, K.Waksman, G.Sadler, J.E.

(1999) J.Mol.Biol. 292: 361-373

  • DOI: 10.1006/jmbi.1999.3089

  • PubMed Abstract: 
  • Enteropeptidase is a membrane-bound serine protease that initiates the activation of pancreatic hydrolases by cleaving and activating trypsinogen. The enzyme is remarkably specific and cleaves after lysine residues of peptidyl substrates that resembl ...

    Enteropeptidase is a membrane-bound serine protease that initiates the activation of pancreatic hydrolases by cleaving and activating trypsinogen. The enzyme is remarkably specific and cleaves after lysine residues of peptidyl substrates that resemble trypsinogen activation peptides such as Val-(Asp)4-Lys. To characterize the determinants of substrate specificity, we solved the crystal structure of the bovine enteropeptidase catalytic domain to 2.3 A resolution in complex with the inhibitor Val-(Asp)4-Lys-chloromethane. The catalytic mechanism and contacts with lysine at substrate position P1 are conserved with other trypsin-like serine proteases. However, the aspartyl residues at positions P2-P4 of the inhibitor interact with the enzyme surface mainly through salt bridges with the Nzeta atom of Lys99. Mutation of Lys99 to Ala, or acetylation with acetic anhydride, specifically prevented the cleavage of trypsinogen or Gly-(Asp)4-Lys-beta-naphthylamide and reduced the rate of inhibition by Val-(Asp)4-Lys-chloromethane 22 to 90-fold. For these reactions, Lys99 was calculated to account for 1.8 to 2.5 kcal mol(-1) of the free energy of transition state binding. Thus, a unique basic exosite on the enteropeptidase surface has evolved to facilitate the cleavage of its physiological substrate, trypsinogen.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENTEROPEPTIDASE
A
13Bos taurusMutation(s): 0 
Gene Names: TMPRSS15 (ENTK, PRSS7)
EC: 3.4.21.9
Find proteins for P98072 (Bos taurus)
Go to Gene View: TMPRSS15
Go to UniProtKB:  P98072
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENTEROPEPTIDASE
B
235Bos taurusMutation(s): 0 
Gene Names: TMPRSS15 (ENTK, PRSS7)
EC: 3.4.21.9
Find proteins for P98072 (Bos taurus)
Go to Gene View: TMPRSS15
Go to UniProtKB:  P98072
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VAL-ASP-ASP-ASP-ASP-LYK PEPTIDE
C
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LYK
Query on LYK
C
peptide-likeC6 H16 N2 O2LYS
0QE
Query on 0QE
C
NON-POLYMERC H3 Cl

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.990α = 90.00
b = 70.650β = 90.00
c = 85.220γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    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