1LCP

BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSPHONIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 A resolution in a new crystal form.

Strater, N.Lipscomb, W.N.

(1995) Biochemistry 34: 9200-9210


  • PubMed Abstract: 
  • The three-dimensional structure of bovine lens leucine aminopeptidase (blLAP) complexed with L-Leucinephosphonic acid (LeuP) has been determined by molecular replacement using the structure of native blLAP as a starting model. Cocrystallization of th ...

    The three-dimensional structure of bovine lens leucine aminopeptidase (blLAP) complexed with L-Leucinephosphonic acid (LeuP) has been determined by molecular replacement using the structure of native blLAP as a starting model. Cocrystallization of the enzyme with the inhibitor yielded a new crystal form of space group P321 which has cell dimensions a = 130.4 A and c = 125.4 A. Refinement of the model against data from 7.0 to 1.65 A resolution resulted in a final structure with a crystallographic residual of 0.160 (R(free) = 0.191). The N-terminal amino group of LeuP is coordinated to Zn-489, one phosphoryl oxygen atom bridges both metal ions, and another phosphoryl oxygen atom is coordinated to Zn-488. The side chain of Arg-336 interacts with the inhibitor via three water molecules. LeuP resembles the presumed tetrahedral gem-diolate transition state after direct attack of a water or hydroxide ion nucleophile on the scissile peptide bond. On the basis of the LeuP binding mode and the previous structural and biochemical data, three plausible reaction pathways are evaluated. The two-metal ion mechanisms discussed herein share as common features a metal-bound hydroxide ion nucleophile and polarization of the carbonyl group by the zinc ions. Possible catalytic roles of Arg-336 and Lys-262 in the direct or indirect (through H2O) protonation of the leaving group, in the stabilization of a zinc-bound OH- nucleophile and in the stabilization of the negatively charged intermediate, are discussed. A site 3 metal ion approximately 12 A away from the active site 2 zinc ion probably serves a structural role.


    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
    • 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
    • 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
    • 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
    • Differentiation and Identification of the Two Catalytic Metal Binding Sites in Bovine Lens Leucine Aminopeptidase by X-Ray Crystallography
      Kim, H.,Lipscomb, W.N.
      (1993) Proc.Natl.Acad.Sci.USA 90: 5006
    • Structure and Mechanism of Bovine Lens Leucine Aminopeptidase
      Kim, H.,Lipscomb, W.N.
      (1994) Adv.Enzymol.Relat.Areas Mol.Biol. 68: 153


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCINE AMINOPEPTIDASE
A, B
484Bos 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
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
PLU
Query on PLU

Download SDF File 
Download CCD File 
A, B
LEUCINE PHOSPHONIC ACID
C5 H14 N O3 P
HGCAUCAWEADMPM-RXMQYKEDSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PLEKi: 230 nM (92) BINDINGDB
PLUKi: 230 nM BINDINGMOAD
PLUKi: 230 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.400α = 90.00
b = 130.400β = 90.00
c = 125.400γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata reduction
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model