3CPA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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 U S A 83: 7568-7572

  • DOI: 10.1073/pnas.83.20.7568
  • Primary Citation of Related Structures:  
    3CPA

  • 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-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 ...

    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: 
    • Crystallographic Studies on Apocarboxypeptidase a and the Complex with Glycyl-L-Tyrosine
      Rees, D.C., Lipscomb, W.N.
      (1983) Proc Natl Acad Sci U S A 80: 7151
    • 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
    • Binding of Ligands to the Active Site of Carboxypeptidase A
      Rees, D.C., Lipscomb, W.N.
      (1981) Proc Natl Acad Sci U S A 78: 5455
    • 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 U S A 78: 3408
    • Carboxypeptidase a Mechanisms
      Lipscomb, W.N.
      (1980) Proc Natl Acad Sci U S A 77: 3875
    • Carboxypeptidase A,A Protein and an Enzyme
      Quiocho, F.A., Lipscomb, W.N.
      (1971) Adv Protein Chem 25: 1
    • Structure and Mechanism in the Enzymatic Activity of Carboxypeptidase a and Relations to Chemical Sequence
      Lipscomb, W.N.
      (1970) Acc Chem Res 3: 81
    • 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

    Organizational Affiliation

    Department of Biochemistry, University of Missouri, Columbia, Missouri, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE AA307Bos taurusMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Explore P00730 
Go to UniProtKB:  P00730
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download Ideal Coordinates CCD File 
C [auth A]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
GLY
Query on GLY

Download Ideal Coordinates CCD File 
B [auth A]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.6α = 90
b = 60.27β = 97.27
c = 47.25γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



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  (Full details and data files)

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