2PCU

Human carboxypeptidase A4 in complex with a cleaved hexapeptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Caught after the Act: a human A-type metallocarboxypeptidase in a product complex with a cleaved hexapeptide.

Bayes, A.Fernandez, D.Sola, M.Marrero, A.Garcia-Pique, S.Aviles, F.X.Vendrell, J.Gomis-Ruth, F.X.

(2007) Biochemistry 46: 6921-6930

  • DOI: 10.1021/bi700480b

  • PubMed Abstract: 
  • A/B-type metallocarboxypeptidases (MCPs) are among the most thoroughly studied proteolytic enzymes, and their catalytic mechanisms have been considered as prototypes even for several unrelated metalloprote(in)ase families. It has long been postulated ...

    A/B-type metallocarboxypeptidases (MCPs) are among the most thoroughly studied proteolytic enzymes, and their catalytic mechanisms have been considered as prototypes even for several unrelated metalloprote(in)ase families. It has long been postulated that the nature of the side chains of at least five substrate residues, i.e., P4-P1', influence Km and kcat and that once the peptide or protein substrate is cleaved, both products remain in the first instance bound to the active-site cleft of the enzyme in a double-product complex. Structural details of binding of substrate to the nonprimed side of the cleft have largely relied on complexes with protein inhibitors and peptidomimetic small-molecule inhibitors that do not span the entire groove. In the former, the presence of N-terminal globular protein domains participating in large-scale interactions with the surface of the cognate catalytic domain outside the active-site cleft mostly conditions the way their C-terminal tails bind to the cleft. Accordingly, they may not be accurate models for a product complex. We hereby provide the structural details of a true cleaved double-product complex with a hexapeptide of an MCP engaged in prostate cancer, human carboxypeptidase A4, employing diffraction data to 1.6 A resolution (Rcryst and Rfree = 0.159 and 0.176, respectively). These studies provide detailed information about subsites S5-S1' and contribute to our knowledge of the cleavage mechanism, which is revisited in light of these new structural insights.


    Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autonoma de Barcelona, E-08193 Bellaterra, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A4
A
305Homo 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
peptide
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 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
SCN
Query on SCN

Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ASP
Query on ASP

Download SDF File 
Download CCD File 
B
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.304α = 90.00
b = 72.494β = 90.00
c = 81.575γ = 90.00
Software Package:
Software NamePurpose
ProDCdata collection
REFMACrefinement
AMoREphasing
CCP4data scaling
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description