2ABZ

Crystal structure of C19A/C43A mutant of leech carboxypeptidase inhibitor in complex with bovine carboxypeptidase A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Study of a major intermediate in the oxidative folding of leech carboxypeptidase inhibitor: contribution of the fourth disulfide bond

Arolas, J.L.Popowicz, G.M.Bronsoms, S.Aviles, F.X.Huber, R.Holak, T.A.Ventura, S.

(2005) J.Mol.Biol. 352: 961-975

  • DOI: 10.1016/j.jmb.2005.07.065

  • PubMed Abstract: 
  • The oxidative folding pathway of leech carboxypeptidase inhibitor (LCI; four disulfide bonds) proceeds through the formation of two major intermediates (III-A and III-B) that contain three native disulfide bonds and act as strong kinetic traps in the ...

    The oxidative folding pathway of leech carboxypeptidase inhibitor (LCI; four disulfide bonds) proceeds through the formation of two major intermediates (III-A and III-B) that contain three native disulfide bonds and act as strong kinetic traps in the folding process. The III-B intermediate lacks the Cys19-Cys43 disulfide bond that links the beta-sheet core with the alpha-helix in wild-type LCI. Here, an analog of this intermediate was constructed by replacing Cys19 and Cys43 with alanine residues. Its oxidative folding follows a rapid sequential flow through one, two, and three disulfide species to reach the native form; the low accumulation of two disulfide intermediates and three disulfide (scrambled) isomers accounts for a highly efficient reaction. The three-dimensional structure of this analog, alone and in complex with carboxypeptidase A (CPA), was determined by X-ray crystallography at 2.2A resolution. Its overall structure is very similar to that of wild-type LCI, although the residues in the region adjacent to the mutation sites show an increased flexibility, which is strongly reduced upon binding to CPA. The structure of the complex also demonstrates that the analog and the wild-type LCI bind to the enzyme in the same manner, as expected by their inhibitory capabilities, which were similar for all enzymes tested. Equilibrium unfolding experiments showed that this mutant is destabilized by approximately 1.5 kcal mol(-1) (40%) relative to the wild-type protein. Together, the data indicate that the fourth disulfide bond provides LCI with both high stability and structural specificity.


    Related Citations: 
    • NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor
      Arolas, J.L.,D'Silva, L.,Popowicz, G.M.,Aviles, F.X.,Holak, T.A.,Ventura, S.
      (2005) Structure 13: 1193
    • Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2
      Reverter, D.,Fernandez-Catalan, C.,Baumgartner, R.,Pfander, R.,Huber, R.,Bode, W.,Vendrell, J.,Holak, T.A.,Aviles, F.X.
      (2000) Nat.Struct.Mol.Biol. 7: 322


    Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A1
A, B
309Bos taurusMutation(s): 0 
Gene Names: CPA1 (CPA)
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to Gene View: CPA1
Go to UniProtKB:  P00730
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metallocarboxypeptidase inhibitor
C, D, E, F
67Hirudo medicinalisMutation(s): 2 
Find proteins for P81511 (Hirudo medicinalis)
Go to UniProtKB:  P81511
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.930α = 90.00
b = 124.930β = 90.00
c = 154.980γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance