4Z65

Carboxypeptidase B with Sulphamoil Arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine.

Akparov, V.Sokolenko, N.Timofeev, V.Kuranova, I.

(2015) Acta Crystallogr.,Sect.F 71: 1335-1340

  • DOI: 10.1107/S2053230X15016799

  • PubMed Abstract: 
  • Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form b ...

    Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps. The enzyme-inhibitor complex and 329 water molecules were further refined to a crystallographic R factor of 0.159. The differences in conformation between the complexed and uncomplexed forms of carboxypeptidase B are shown. The inhibitor is bound in a curved conformation in the active-site cleft, and the sulfamide group is bound to the Zn ion in an asymmetric bidentate fashion. The complex is stabilized by hydrogen bonds between the N1/N2 guanidine group of the inhibitor and the Asp255 carboxyl of the enzyme. The side-chain CH2 groups of the inhibitor are in van der Waals contact with Leu203 and Ile247 in the enzyme. This study provides useful clues concerning how the transition state of arginine may bind to carboxypeptidase B and therefore provides an insight into the structural basis of carboxypeptidase B selectivity, which is useful for the rational design of a carboxypeptidase with improved selectivity for industrial recombinant pro-insulin processing.


    Organizational Affiliation

    Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd 1, 117545 Moscow, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase B
A
304Sus scrofaMutation(s): 0 
Gene Names: CPB1 (CPB)
EC: 3.4.17.2
Find proteins for P09955 (Sus scrofa)
Go to Gene View: CPB1
Go to UniProtKB:  P09955
Small Molecules
Ligands 2 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
0X9
Query on 0X9

Download SDF File 
Download CCD File 
A
N~2~-sulfamoyl-L-arginine
C6 H15 N5 O4 S
PBEOTCYEZLQJNW-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.380α = 90.00
b = 79.380β = 90.00
c = 100.370γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references