1BPM

DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 5006-5010

  • Primary Citation of Related Structures:  1BPN

  • PubMed Abstract: 
  • The tightly binding and readily exchanging metal binding sites in the active site of bovine lens leucine aminopeptidase (blLAP; EC 3.4.11.1) have been differentiated and identified by x-ray crystallography. In native blLAP,Zn2+ occupies both binding ...

    The tightly binding and readily exchanging metal binding sites in the active site of bovine lens leucine aminopeptidase (blLAP; EC 3.4.11.1) have been differentiated and identified by x-ray crystallography. In native blLAP,Zn2+ occupies both binding sites. In solution, site 1 readily exchanges Zn2+ for other divalent cations, including Mg2+. The Zn2+ in site 2 is unavailable for metal exchange under conditions which allow exchange at site 1. The Zn2+/Mg2+ metal hybrid of blLAP (Mg-blLAP) was prepared in solution and crystallized. X-ray diffraction data to 2.9-A resolution were collected at -150 degrees C from single crystals of Mg-blLAP and native blLAP. Comparisons of omit maps calculated from the Mg-blLAP data with analogous maps calculated from the native blLAP data show electron density in one of the metal binding sites in Mg-blLAP which is much weaker than the electron density in the other binding site. Since there are fewer electrons associated with Mg2+ than with Zn2+, the difference in electron density between the two metal binding sites is consistent with occupancy of the weaker electron density site by Mg2+ and identifies this metal binding site as site 1, defined as the readily exchanging site. The present identification of the metal binding sites reverses the previous presumptive assignment of the metal binding sites which was based on the structure of native blLAP [Burley, S. K., David, P. R., Sweet, R. M., Taylor, A. & Lipscomb, W. N. (1992) J. Mol. Biol. 224, 113-140]. According to the residue-numbering convention of native blLAP, the new assignment of the metal binding sites identifies the readily exchanging site 1 with Zn-488, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-332, and Glu-334 and the main-chain carbonyl oxygen of Asp-332. The more tightly binding site 2 is identified with Zn-489, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-273, and Glu-334 and the side-chain amine nitrogen of Lys-250.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCINE AMINOPEPTIDASE
A
487Bos 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 2 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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.189 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 129.100α = 90.00
b = 129.100β = 90.00
c = 120.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    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