6RPQ

Crystal structure of PhoCDC21-1 intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.654 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site.

Beyer, H.M.Mikula, K.M.Kudling, T.V.Iwai, H.

(2019) Extremophiles 23: 669-679

  • DOI: 10.1007/s00792-019-01117-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing t ...

    Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.


    Related Citations: 
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr.,Sect.D 66: 213
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V.,Grosse-Kunstleve, R.W.,Echols, N.,Headd, J.J.,Moriarty, N.W.,Mustyakimov, M.,Terwilliger, T.C.,Urzhumtsev, A.,Zwart, P.H.,Adams, P.D.
      (2012) Acta Crystallogr. D Biol. Crystallogr. 68: 352


    Organizational Affiliation

    Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland.,Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland. hideo.iwai@helsinki.fi.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein SMT3,1108aa long hypothetical cell division control protein
A
279Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
This entity is chimeric
Mutation(s): 1 
Gene Names: SMT3
Find proteins for O58310 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58310
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12306
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.654 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 100.920α = 90.00
b = 100.920β = 90.00
c = 91.720γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland137995, 277335
Novo Nordisk FoundationFinlandNNF17OC0025402
Sigrid Juselius FoundationFinland--

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references