1SRP

STRUCTURAL ANALYSIS OF SERRATIA PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution.

Hamada, K.Hata, Y.Katsuya, Y.Hiramatsu, H.Fujiwara, T.Katsube, Y.

(1996) J.Biochem.(Tokyo) 119: 844-851


  • PubMed Abstract: 
  • The crystal structure of Serratia protease from Serratia sp. E-15 was solved by the single isomorphous replacement method supplemented with anomalous scattering effects from both the Zn atom in the native crystal and the Sm atom in the derivative cry ...

    The crystal structure of Serratia protease from Serratia sp. E-15 was solved by the single isomorphous replacement method supplemented with anomalous scattering effects from both the Zn atom in the native crystal and the Sm atom in the derivative crystal, and refined at 2.0 A resolution to a crystallographic R-factor of 0.194. The enzyme consists of N-terminal catalytic and C-terminal beta-sandwich domains, as observed in alkaline protease from Pseudomonas aeruginosa IFO3080. The catalytic domain with a five-stranded antiparallel beta-sheet and five alpha-helices shares a basically common folding topology with those of other zinc metalloendoproteases. The catalytic zinc ion at the bottom of the active site cleft is ligated by His176, His180, His186, Tyr216, and a water molecule in a distorted trigonalbipyramidal manner. The C-terminal domain is a beta-strand-rich domain containing eighteen beta-strands and a short alpha-helix, and has seven Ca2+ ions bound to calcium binding loops. An unusual beta-sheet coil motif is observed in this domain, where the beta-strands and calcium binding loops are alternately incorporated into an elliptical right-handed spiral so as to form a two-layer untwisted beta-sandwich structure. The Ca2+ ions in the C-terminal domain seem to be very important for the folding and stability of the beta-sheet coil structure.


    Related Citations: 
    • Preliminary X-Ray Studies on Serratia Protease
      Katsuya, Y.,Hamada, K.,Hata, Y.,Tanaka, N.,Sato, M.,Katsube, Y.,Katiuchi, K.,Miyata, K.
      (1985) J.Biochem.(Tokyo) 98: 1139
    • Structural Studies of Serratia Protease by X-Ray Analysis
      Hamada, K.,Hiramatsu, H.,Fujiwara, T.,Katsuya, Y.,Hata, Y.,Katsube, Y.
      (1992) Photon Factory Activity Report 10: 125


    Organizational Affiliation

    Faculty of Science, Shimane University. hamadak@cis.shimane.u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERRALYSIN
A
471Serratia marcescens (strain ATCC 21074 / E-15)Mutation(s): 0 
EC: 3.4.24.40
Find proteins for P07268 (Serratia marcescens (strain ATCC 21074 / E-15))
Go to UniProtKB:  P07268
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
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.140α = 90.00
b = 150.890β = 90.00
c = 42.640γ = 90.00
Software Package:
Software NamePurpose
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance