2EWB

The crystal structure of Bovine Lens Leucine Aminopeptidase in complex with zofenoprilat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Metal Ion Substitution in the Catalytic Site Greatly Affects the Binding of Sulfhydryl-Containing Compounds to Leucyl Aminopeptidase.

Cappiello, M.Alterio, V.Amodeo, P.Del Corso, A.Scaloni, A.Pedone, C.Moschini, R.De Donatis, G.M.De Simone, G.Mura, U.

(2006) Biochemistry 45: 3226-3234

  • DOI: 10.1021/bi052069v
  • Primary Citation of Related Structures:  
    2EWB

  • PubMed Abstract: 
  • Bovine lens leucyl aminopeptidase (blLAP), a homohexameric metallopeptidase preferring bulky and hydrophobic amino acids at the N-terminus of (di)peptides, contains two Zn(2+) ions per subunit that are essential for catalytic activity. They may be replaced by other divalent cations with different exchange kinetics ...

    Bovine lens leucyl aminopeptidase (blLAP), a homohexameric metallopeptidase preferring bulky and hydrophobic amino acids at the N-terminus of (di)peptides, contains two Zn(2+) ions per subunit that are essential for catalytic activity. They may be replaced by other divalent cations with different exchange kinetics. The protein readily exchangeable site (site 1) can be occupied by Zn(2+), Mn(2+), Mg(2+), or Co(2+), while the tight binding site (site 2) can be occupied by Zn(2+) or Co(2+). We recently reported that introduction of Mn(2+) into site 1 generates a novel activity of blLAP toward CysGly [Cappiello, M., et al. (2004) Biochem. J. 378, 35-44], which in contrast is not hydrolyzed by the (Zn/Zn) enzyme. This finding, while disclosing a potential specific role for blLAP in glutathione metabolism, raised a question about the features required for molecules to be a substrate for the enzyme. To clarify the interaction of the enzyme with sulfhydryl-containing derivatives, (Zn/Zn)- and (Mn/Zn)blLAP forms were prepared and functional-structural studies were undertaken. Thus, a kinetic analysis of various compounds with both enzyme forms was performed; the crystal structure of (Zn/Zn)blLAP in complex with the peptidomimetic derivative Zofenoprilat was determined, and a modeling study on the CysGly-(Zn/Zn)blLAP complex was carried out. This combined approach provided insight into the interaction of blLAP with sulfhydryl-containing derivatives, showing that the metal exchange in site 1 modulates binding to these molecules that may result in enzyme substrates or inhibitors, depending on the nature of the metal.


    Organizational Affiliation

    Department of Physiology and Biochemistry, University of Pisa, I-56126 Pisa, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytosol aminopeptidaseA486Bos taurusMutation(s): 0 
Gene Names: LAP3
EC: 3.4.11.1 (PDB Primary Data), 3.4.13.23 (UniProt), 3.4.11.5 (UniProt)
UniProt
Find proteins for P00727 (Bos taurus)
Explore P00727 
Go to UniProtKB:  P00727
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZED
Query on ZED

Download Ideal Coordinates CCD File 
F [auth A]L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S
C15 H19 N O3 S2
UQWLOWFDKAFKAP-WXHSDQCUSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
E [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZEDKi:  800   nM  Binding MOAD
ZEDKi :  800   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.156 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.94α = 90
b = 128.94β = 90
c = 119.79γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description