2FV9

Crystal structure of TACE in complex with JMV 390-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Stabilization of the autoproteolysis of TNF-alpha converting enzyme (TACE) results in a novel crystal form suitable for structure-based drug design studies.

Ingram, R.N.Orth, P.Strickland, C.L.Le, H.V.Madison, V.Beyer, B.M.

(2006) Protein Eng.Des.Sel. 19: 155-161

  • DOI: 10.1093/protein/gzj014
  • Primary Citation of Related Structures:  2DDF

  • PubMed Abstract: 
  • The crystallization of TNF-alpha converting enzyme (TACE) has been useful in understanding the structure-activity relationships of new chemical entities. However, the propensity of TACE to undergo autoproteolysis has made enzyme handling difficult an ...

    The crystallization of TNF-alpha converting enzyme (TACE) has been useful in understanding the structure-activity relationships of new chemical entities. However, the propensity of TACE to undergo autoproteolysis has made enzyme handling difficult and impeded the identification of inhibitor soakable crystal forms. The autoproteolysis of TACE was found to be specific (Y352-V353) and occurred within a flexible loop that is in close proximity to the P-side of the active site. The rate of autoproteolysis was found to be proportional to the concentration of TACE, suggesting a bimolecular reaction mechanism. A limited specificity study of the S(1)' subsite was conducted using surrogate peptides and suggested substitutions that would stabilize the proteolysis of the loop at positions Y352-V353. Two mutant proteases (V353G and V353S) were generated and proved to be highly resistant to autoproteolysis. The kinetics of the more resistant mutant (V353G) and wild-type TACE were compared and demonstrated virtually identical IC(50) values for a panel of competitive inhibitors. However, the k(cat)/K(m) of the mutant for a larger substrate (P6 - P(6)') was approximately 5-fold lower than that for the wild-type enzyme. Comparison of the complexed wild-type and mutant structures indicated a subtle shift in a peripheral P-side loop (comprising the mutation site) that may be involved in substrate binding/turnover and might explain the mild kinetic difference. The characterization of this stabilized form of TACE has yielded an enzyme with similar native kinetic properties and identified a novel crystal form that is suitable for inhibitor soaking and structure determination.


    Organizational Affiliation

    Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADAM 17
A, B
258Homo sapiensGene Names: ADAM17 (CSVP, TACE)
EC: 3.4.24.86
Find proteins for P78536 (Homo sapiens)
Go to Gene View: ADAM17
Go to UniProtKB:  P78536
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
INN
Query on INN

Download SDF File 
Download CCD File 
A
N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide
C19 H37 N5 O5
LMIQCBIEAHJAMZ-GZBFAFLISA-N
 Ligand Interaction
002
Query on 002

Download SDF File 
Download CCD File 
B
N-[(2R)-2-BENZYL-4-(HYDROXYAMINO)-4-OXOBUTANOYL]-L-ISOLEUCYL-L-LEUCINE
C23 H35 N3 O6
MWZOULASPWUGJJ-NFBUACBFSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000919 (INN)
Query on PRD_000919
A3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINEPeptide-like / Enzyme inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
002IC50: 60 nM BINDINGMOAD
2IC50: 60 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.799α = 90.00
b = 76.221β = 90.00
c = 102.092γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-01-30 
  • Released Date: 2006-03-14 
  • Deposition Author(s): Orth, P.

Revision History 

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2013-02-27
    Type: Other
  • Version 1.4: 2017-02-01
    Type: Structure summary
  • Version 1.5: 2017-10-18
    Type: Refinement description