1LAN

LEUCINE AMINOPEPTIDASE COMPLEX WITH L-LEUCINAL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography.

Strater, N.Lipscomb, W.N.

(1995) Biochemistry 34: 14792-14800

  • Primary Citation of Related Structures:  1LAM

  • PubMed Abstract: 
  • The three-dimensional structures of bovine lens leucine aminopeptidase (blLAP) complexed with L-leucinal and of the unliganded enzyme have been determined at crystallographic resolutions of 1.9 and 1.6 A, respectively. Leucinal binds as a hydrated ge ...

    The three-dimensional structures of bovine lens leucine aminopeptidase (blLAP) complexed with L-leucinal and of the unliganded enzyme have been determined at crystallographic resolutions of 1.9 and 1.6 A, respectively. Leucinal binds as a hydrated gem-diol to the active site of b1LAP), resembling the presumed gem-diolated intermediate in the catalytic pathway. One hydroxyl group bridges the two active site metal ions, and the other OH group is coordinated to Zn1. The high-resolution structure of the unliganded enzyme reveals one metal-bound water ligand, which is bridging both zinc ions. Together, these structures support a mechanism in which the bridging water ligand is the attacking hydroxide ion nucleophile. The gem-diolate intermediate is probably stabilized by four coordinating bonds to the dizinc center and by interaction with Lys-262 and Arg-336. In the mechanism, Lys-262 polarizes the peptide carbonyl group, which is also coordinated to Zn1. The Arg-336 side chain interacts with the substrate and the gem-diolate intermediate via water molecules. Near Arg-336 in the b1LAP-leucinal structure, an unusually short hydrogen bond is found between two active site water molecules.


    Related Citations: 
    • Re-Refinement of the X-Ray Crystal Structure of Bovine Lens Leucine Aminopeptidase Complexed with Bestatin
      Kim, H.,Burley, S.K.,Lipscomb, W.N.
      (1993) J.Mol.Biol. 230: 722
    • 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
    • Transition State Analogue L-Leucinephosphonic Acid Bound to Bovine Lens Leucine Aminopeptidase: X-Ray Structure at 1.65 Angstroms Resolution in a New Crystal Form
      Straeter, N.,Lipscomb, W.N.
      (1995) Biochemistry 34: 9200
    • 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.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
    • 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


    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
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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
A
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LEUKi: 60 nM BINDINGMOAD
LEUKi: 60 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.200α = 90.00
b = 131.200β = 90.00
c = 120.900γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
X-PLORrefinement
XDSdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    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