1IAE | pdb_00001iae

CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 
    0.143 (Depositor) 
  • R-Value Observed: 
    0.143 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of structure and proteolytic activity.

Gomis-Ruth, F.X.Grams, F.Yiallouros, I.Nar, H.Kusthardt, U.Zwilling, R.Bode, W.Stocker, W.

(1994) J Biological Chem 269: 17111-17117

  • Primary Citation Related Structures: 
    1IAA, 1IAB, 1IAE

  • PubMed Abstract: 

    The catalytic zinc ion of astacin, a prototypical metalloproteinase from crayfish, has been substituted by Co(II), Cu(II), Hg(II), and Ni(II) in order to probe the role of the metal for both catalysis and structure. Compared to Zn(II)-astacin, Co(II)- and Cu(II)-astacin display enzymatic activities of about 140 and 37%, respectively, while Ni(II)- and Hg(II)-astacin are almost inactive. The electron paramagnetic resonance spectrum of Cu(II)-astacin is typical of 5-fold coordinated copper(II), and its intense absorption maxima at 445 and 325 nm are probably due to ligand-metal charge-transfer transitions involving Tyr-149. This residue had been identified previously by x-ray crystallography of the zinc enzyme as a zinc ligand, in addition to three imidazoles and a glutamic acid-bound water molecule. We present now the refined high-resolution x-ray crystal structures of Cu(II)-, Co(II)-, and Ni(II)-astacin, which exhibit a virtually identical protein framework to the previously analyzed structures of Zn(II)-, apo-, and Hg(II)-astacin. In Co(II)- and Cu(II)-astacin, the metal is penta-coordinated similarly to the native zinc enzyme. In the Ni(II) derivative, however, an additional solvent molecule expands the metal coordination sphere to a distorted octahedral ligand geometry, while in Hg(II)-astacin, no ordered solvent molecule at all is observed in the inner coordination sphere of the metal. This indicates a close correlation between catalytic properties and ground-state metal coordination of astacin.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 22.68 kDa 
  • Atom Count: 1,776 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ASTACIN200Astacus astacusMutation(s): 0 
EC: 3.4.24.21
UniProt
Find proteins for P07584 (Astacus astacus)
Explore P07584 
Go to UniProtKB:  P07584
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07584
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI

Query on NI



Download:Ideal Coordinates CCD File
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work:  0.143 (Depositor) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.89α = 90
b = 61.89β = 90
c = 98.55γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-11-13
    Changes: Structure summary