1EF0

CRYSTAL STRUCTURE OF PI-SCEI MINIPRECURSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the protein splicing mechanism of PI-SceI.

Poland, B.W.Xu, M.Q.Quiocho, F.A.

(2000) J.Biol.Chem. 275: 16408-16413


  • PubMed Abstract: 
  • PI-SceI is a member of a class of proteins (inteins) that excise themselves from a precursor protein and in the process ligate the flanking protein sequences (exteins). We report here the 2.1-A resolution crystal structure of a PI-SceI miniprecursor ...

    PI-SceI is a member of a class of proteins (inteins) that excise themselves from a precursor protein and in the process ligate the flanking protein sequences (exteins). We report here the 2.1-A resolution crystal structure of a PI-SceI miniprecursor (VMA29) containing 10 N-terminal extein residues and 4 C-terminal extein residues. Mutations at the N- and C-terminal splicing junctions, blocking in vivo protein splicing, allowed the miniprecursor to be purified and crystallized. The structure reveals both the N- and C-terminal scissile peptide bonds to be in distorted trans conformations (tau approximately 100 degrees ). Modeling of the wild-type PI-SceI based on the VMA29 structure indicates a large conformational change (movement of >9 A) must occur to allow transesterification to be completed. A zinc atom was discovered at the C-terminal splicing junction. Residues Cys(455), His(453), and Glu(80) along with a water molecule (Wat(53)) chelate the zinc atom. The crystal structure of VMA29 has captured the intein in its pre-spliced state.


    Related Citations: 
    • Protein Splicing Converts the Yeast TFP1 Gene Product to the 69-kD Subunit of the Vacuolar H+-Adenosine Triphosphatase
      Kane, P.M.,Yamashiro, C.T.,Wolczyk, D.F.,Neff, N.,Goebl, M.,Stevens, T.H.
      (1990) Science 250: 651
    • Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity
      Duan, X.,Gimble, F.S.,Quiocho, F.A.
      (1997) Cell 89: 555
    • The chemical basis of protein splicing.
      Paulus, H.
      (1998) Chem.Soc.Rev. 27: 375


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PI-SCEI ENDONUCLEASE
A, B
462Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: VMA1 (CLS8, TFP1)
EC: 3.1.-.-, 3.6.3.14
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17255
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.003α = 90.00
b = 101.683β = 93.51
c = 86.765γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
XTALVIEWrefinement
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance