3CPA

X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARBOXYPEPTIDASE A AT SUBZERO TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature.

Christianson, D.W.Lipscomb, W.N.

(1986) Proc.Natl.Acad.Sci.USA 83: 7568-7572


  • PubMed Abstract: 
  • A high-resolution x-ray crystallographic investigation of the complex between carboxypeptidase A (CPA; peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) and the slowly hydrolyzed substrate glycyl-L-tyrosine was done at -9 degrees C. Although this enzyme- ...

    A high-resolution x-ray crystallographic investigation of the complex between carboxypeptidase A (CPA; peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) and the slowly hydrolyzed substrate glycyl-L-tyrosine was done at -9 degrees C. Although this enzyme-substrate complex has been the subject of earlier crystallographic investigation, a higher resolution electron-density map of the complex with greater occupancy of the substrate was desired. All crystal chemistry (i.e., crystal soaking and x-ray data collection) was performed on a diffractometer-mounted flow cell, in which the crystal was immobilized. The x-ray data to 1.6-A resolution have yielded a well-resolved structure in which the zinc ion of the active site is five-coordinate: three enzyme residues (glutamate-72, histidine-69, and histidine-196) and the carbonyl oxygen and amino terminus of glycyl-L-tyrosine complete the coordination polyhedron of the metal. These results confirm that this substrate may be bound in a nonproductive manner, because the hydrolytically important zinc-bound water has been displaced and excluded from the active site. It is likely that all dipeptide substrates of carboxypeptidase A that carry an unprotected amino terminus are poor substrates because of such favorable bidentate coordination to the metal ion of the active site.


    Related Citations: 
    • Carboxypeptidase A,A Protein and an Enzyme
      Quiocho, F.A.,Lipscomb, W.N.
      (1971) Adv.Protein Chem. 25: 1
    • Binding of Ligands to the Active Site of Carboxypeptidase A
      Rees, D.C.,Lipscomb, W.N.
      (1981) Proc.Natl.Acad.Sci.USA 78: 5455
    • Refined Crystal Structure of Carboxypeptidase a at 1.54 Angstroms Resolution.
      Rees, D.C.,Lewis, M.,Lipscomb, W.N.
      (1983) J.Mol.Biol. 168: 367
    • Carboxypeptidase a Mechanisms
      Lipscomb, W.N.
      (1980) Proc.Natl.Acad.Sci.USA 77: 3875
    • Zinc Environment and Cis Peptide Bonds in Carboxypeptidase a at 1.75-Angstroms Resolution
      Rees, D.C.,Lewis, M.,Honzatko, R.B.,Lipscomb, W.N.,Hardman, K.D.
      (1981) Proc.Natl.Acad.Sci.USA 78: 3408
    • Crystallographic Studies on Apocarboxypeptidase a and the Complex with Glycyl-L-Tyrosine
      Rees, D.C.,Lipscomb, W.N.
      (1983) Proc.Natl.Acad.Sci.USA 80: 7151
    • The Structure of Carboxypeptidase A, Vii.The 2.0-Angstroms Resolution Studies of the Enzyme and of its Complex with Glycyltyrosine,and Mechanistic Deductions
      Lipscomb, W.N.,Hartsuck, J.A.,Reekejunior, G.N.,Quiocho, F.A.,Bethge, P.H.,Ludwig, M.L.,Steitz, T.A.,Muirhead, H.,Coppola, J.C.
      (1969) Brookhaven Symposia in Biology 21: 24
    • Structure and Mechanism in the Enzymatic Activity of Carboxypeptidase a and Relations to Chemical Sequence
      Lipscomb, W.N.
      (1970) Acc.Chem.Res. 3: 81



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE A
A
307Bos 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
Small Molecules
Ligands 3 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
GLY
Query on GLY

Download SDF File 
Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
TYR
Query on TYR

Download SDF File 
Download CCD File 
A
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.600α = 90.00
b = 60.270β = 97.27
c = 47.250γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1982-03-24 
  • Released Date: 1982-07-29 
  • Deposition Author(s): Lipscomb, W.N.
  • This entry supersedes: 1CPA

Revision History 

  • Version 1.0: 1982-07-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other