4A94

Structure of the carboxypeptidase inhibitor from Nerita versicolor in complex with human CPA4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Novel Metallo-Carboxypeptidase Inhibitor from the Marine Mollusk Nerita Versicolor in Complex with Human Carboxypeptidase A4.

Covaleda, G.Alonso Del Rivero, M.Chavez, M.A.Aviles, F.X.Reverter, D.

(2012) J.Biol.Chem. 287: 9250

  • DOI: 10.1074/jbc.M111.330100

  • PubMed Abstract: 
  • NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure ...

    NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure defines a distinctive protein fold basically composed of a two-stranded antiparallel β-sheet connected by three loops and the inhibitory C-terminal tail and stabilized by three disulfide bridges. NvCI is a tight-binding inhibitor that interacts with the active site of the enzyme in a substrate-like manner. NvCI displays an extended and novel interface with human carboxypeptidase A4, responsible for inhibitory constants in the picomolar range for some members of the M14A subfamily of carboxypeptidases. This makes NvCI the strongest inhibitor reported so far for this family. The structural homology displayed by the C-terminal tails of different carboxypeptidase inhibitors represents a relevant example of convergent evolution.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE A4
A, B
310Homo sapiensMutation(s): 0 
Gene Names: CPA4 (CPA3)
EC: 3.4.17.-
Find proteins for Q9UI42 (Homo sapiens)
Go to Gene View: CPA4
Go to UniProtKB:  Q9UI42
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE INHIBITOR
C, D
53Nerita versicolorMutation(s): 0 
Find proteins for P86912 (Nerita versicolor)
Go to UniProtKB:  P86912
Small Molecules
Ligands 2 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
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B, C, D
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.220α = 90.00
b = 71.980β = 108.84
c = 79.840γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-02-15
    Type: Other
  • Version 1.2: 2012-03-28
    Type: Other