1BLL

X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: FORMULATION OF A CATALYTIC MECHANISM FEATURING A GEM-DIOLATE TRANSITION STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state.

Kim, H.Lipscomb, W.N.

(1993) Biochemistry 32: 8465-8478


  • PubMed Abstract: 
  • The structure of the complex of bovine lens leucine aminopeptidase (blLAP) with the slow-, tight-binding inhibitor amastatin has been determined by X-ray crystallography. X-ray diffraction data were collected at -150 degrees C from a single blLAP-ama ...

    The structure of the complex of bovine lens leucine aminopeptidase (blLAP) with the slow-, tight-binding inhibitor amastatin has been determined by X-ray crystallography. X-ray diffraction data were collected at -150 degrees C from a single blLAP-amastatin crystal which under the data collection conditions was of the space group P6(3)22 with unit cell parameters a = 130.3 A and c = 121.9 A. The structure of the blLAP-amastatin complex was determined by molecular replacement, using the structure of native blLAP as the starting model. Refinement of the blLAP-amastatin model plus 132 water molecules against data from 10.0- to 2.4-A resolution resulted in a final structure with a crystallographic residual of 0.198. The binding mode of amastatin is similar to that of bestatin, the structure of whose complex with blLAP has previously been determined. Of particular note, the N-terminus-to-C-terminus orientation of the two bound inhibitors is the same. The two N-terminal residues of amastatin and bestatin occupy the same binding sites, which are most likely S1 and S'1. The slow binding of amastatin and bestatin may be partially attributable to a binding mechanism in which the two active site metals are sequentially coordinated by the P1 amino and hydroxyl groups of these inhibitors. A catalytic mechanism for blLAP is proposed based on the binding modes of amastatin and bestatin and plausible binding modes of a dipeptide substrate and its putative gem-diolate transition state which were modeled into the active site of blLAP after the binding mode of amastatin. The proposed catalytic mechanism invokes roles for the catalytic metals in binding and activating the substrate and in stabilizing the transition state. The mechanism also includes roles for Asp-255 as a general base, Arg-336 as an additional electrophilic substrate activator and transition state stabilizer, and Lys-262 as a proton shuttle.


    Related Citations: 
    • Structure Determination and Refinement of Bovine Lens Leucine Aminopeptidase and its Complex with Bestatin
      Burley, S.K.,David, P.R.,Sweet, R.M.,Taylor, A.,Lipscomb, W.N.
      (1992) J.Mol.Biol. 224: 113
    • Leucine Aminopeptidase: Bestatin Inhibition and a Model for Enzyme-Catalyzed Peptide Hydrolysis
      Burley, S.K.,David, P.R.,Lipscomb, W.N.
      (1991) Proc.Natl.Acad.Sci.USA 88: 6916
    • Molecular Structure of Leucine Aminopeptidase at 2.7 Angstroms Resolution
      Burley, S.K.,David, P.R.,Taylor, A.,Lipscomb, W.N.
      (1990) Proc.Natl.Acad.Sci.USA 87: 6878


    Organizational Affiliation

    Gibbs Chemical Laboratory, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCINE AMINOPEPTIDASE
E
488Bos taurusGene Names: LAP3
EC: 3.4.11.5, 3.4.11.1
Find proteins for P00727 (Bos taurus)
Go to Gene View: LAP3
Go to UniProtKB:  P00727
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AMASTATIN
I
4N/AN/A
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 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000415
Query on PRD_000415
IAmastatinPeptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
E
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.198 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 130.300α = 90.00
b = 130.300β = 90.00
c = 121.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    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
  • Version 1.3: 2012-12-12
    Type: Other