2SNI

STRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR COMPLEXES. EGLIN-C-SUBTILISIN CARLSBERG AND CI-2-SUBTILISIN NOVO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo.

McPhalen, C.A.James, M.N.

(1988) Biochemistry 27: 6582-6598

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of the molecular complexes between two serine proteinases and two of their protein inhibitors have been determined: subtilisin Carlsberg with the recombinant form of eglin-c from the leech Hirudo medicinalis and subtilisin Novo ...

    The crystal structures of the molecular complexes between two serine proteinases and two of their protein inhibitors have been determined: subtilisin Carlsberg with the recombinant form of eglin-c from the leech Hirudo medicinalis and subtilisin Novo with chymotrypsin inhibitor 2 from barley seeds. The structures have been fully refined by restrained-parameter least-squares methods to crystallographic R factors (sigma[[Fo[ - [Fc[[/sigma[Fo[) of 0.136 at 1.8-A resolution and 0.154 at 2.1-A resolution, respectively. The 274 equivalent alpha-carbon atoms of the enzymes superpose with an rms deviation of 0.53 A. Sequence changes between the enzymes result in localized structural adjustments. Functional groups in the active sites superpose with an rms deviation of 0.19 A for 161 equivalent atoms; this close similarity in the conformation of active-site residues provides no obvious reason for known differences in catalytic activity between Carlsberg and Novo. Conformational changes in the active-site region indicate a small induced fit of enzyme and inhibitor. Some conformational differences are observed between equivalent active-site residues of subtilisin Carlsberg and alpha-chymotrypsin. Despite differences in tertiary architecture, most enzyme-substrate (inhibitor) interactions are maintained. Subtilisin Carlsberg has a rare cis-peptide bond preceding Thr211 (Gly211 in Novo). Both enzymes contain tightly bound Ca2+ ions. Site 1 is heptacoordinate with the oxygen atoms at the vertices of a pentagonal bipyramid. Site 2 in Carlsberg is probably occupied by a K+ ion in Novo. Conserved water molecules appear to play important structural roles in the enzyme interior, in the inhibitor beta-sheet, and at the enzyme-inhibitor interface. The 62 equivalent alpha-carbon atoms of the inhibitors superpose with an rms deviation of 1.68 A. Sequence changes result in somewhat different packing of the alpha-helix, beta-sheet, and reactive-site loop relative to each other. Hydrogen bonds and electrostatic interactions supporting the conformation of the reactive-site loop are conserved. The 24 main-chain plus C beta atoms of P4 to P1' overlap with an rms deviation of 0.19 A. Features contributing to the inhibitory nature of eglin-c and CI-2 are discussed.


    Related Citations: 
    • Crystal and Molecular Structure of the Serine Proteinase Inhibitor Ci-2 from Barley Seeds
      Mcphalen, C.A.,James, M.N.G.
      (1987) Biochemistry 26: 261
    • Crystal and Molecular Structure of Chymotrypsin Inhibitor 2 from Barley Seeds in Complex with Subtilisin Novo
      Mcphalen, C.A.,Svendsen, I.,Jonassen, I.,James, M.N.G.
      (1985) Proc.Natl.Acad.Sci.USA 82: 7242


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUBTILISIN NOVO
E
275Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00782 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00782
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHYMOTRYPSIN INHIBITOR 2
I
83Hordeum vulgareMutation(s): 0 
Find proteins for P01053 (Hordeum vulgare)
Go to UniProtKB:  P01053
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.190α = 90.00
b = 56.830β = 127.47
c = 68.740γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-09-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other