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 
  • R-Value Observed: 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

  • DOI: 10.1021/bi00028a033
  • Primary Citation of Related Structures:  
    1LCP

  • 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 and Mechanism of Bovine Lens Leucine Aminopeptidase
      Kim, H., Lipscomb, W.N.
      (1994) Adv Enzymol Relat Subj Biochem 68: 153
    • 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
    • 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 U S A 90: 5006
    • 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 U S A 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 U S A 87: 6878

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCINE AMINOPEPTIDASEAB484Bos taurusMutation(s): 0 
Gene Names: LAP3
EC: 3.4.11.1 (PDB Primary Data), 3.4.11.5 (UniProt)
Find proteins for P00727 (Bos taurus)
Explore P00727 
Go to UniProtKB:  P00727
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLU
Query on PLU

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

Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PLUKi:  230   nM  Binding MOAD
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 
  • R-Value Observed: 0.160 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.4α = 90
b = 130.4β = 90
c = 125.4γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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