1KWM

Human procarboxypeptidase B: Three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI).

Barbosa Pereira, P.J.Segura-Martin, S.Oliva, B.Ferrer-Orta, C.Aviles, F.X.Coll, M.Gomis-Ruth, F.X.Vendrell, J.

(2002) J.Mol.Biol. 321: 537-547

  • Also Cited By: 3D4U

  • PubMed Abstract: 
  • Besides their classical role in alimentary protein degradation, zinc-dependant carboxypeptidases also participate in more selective regulatory processes like prohormone and neuropeptide processing or fibrinolysis inhibition in blood plasma. Human pan ...

    Besides their classical role in alimentary protein degradation, zinc-dependant carboxypeptidases also participate in more selective regulatory processes like prohormone and neuropeptide processing or fibrinolysis inhibition in blood plasma. Human pancreatic procarboxypeptidase B (PCPB) is the prototype for those human exopeptidases that cleave off basic C-terminal residues and are secreted as inactive zymogens. One such protein is thrombin-activatable fibrinolysis inhibitor (TAFI), also known as plasma PCPB, which circulates in human plasma as a zymogen bound to plasminogen. The structure of human pancreatic PCPB displays a 95-residue pro-segment consisting of a globular region with an open-sandwich antiparallel-alpha antiparallel-beta topology and a C-terminal alpha-helix, which connects to the enzyme moiety. The latter is a 309-amino acid residue catalytic domain with alpha/beta hydrolase topology and a preformed active site, which is shielded by the globular domain of the pro-segment. The fold of the proenzyme is similar to previously reported procarboxypeptidase structures, also in that the most variable region is the connecting segment that links both globular moieties. However, the empty active site of human procarboxypeptidase B has two alternate conformations in one of the zinc-binding residues, which account for subtle differences in some of the key residues for substrate binding. The reported crystal structure, refined with data to 1.6A resolution, permits in the absence of an experimental structure, accurate homology modelling of TAFI, which may help to explain its properties.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, C.I.D. - C.S.I.C., Jordi Girona, 18-26, E-08034, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Procarboxypeptidase B
A, B
402Homo sapiensMutation(s): 0 
Gene Names: CPB1 (CPB, PCPB)
EC: 3.4.17.2
Find proteins for P15086 (Homo sapiens)
Go to Gene View: CPB1
Go to UniProtKB:  P15086
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
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.135 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.959α = 90.00
b = 83.558β = 99.12
c = 127.447γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CCP4data scaling
SHELXL-97refinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance