6RPQ

Crystal structure of PhoCDC21-1 intein

• PDB DOI:  https://doi.org/10.2210/pdb6RPQ/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C, Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-14 Released: 2019-08-14 
• Deposition Author(s): Beyer, H.M., Mikula, K.M., Iwai, H.
• Funding Organization(s): Academy of Finland, Novo Nordisk Foundation, Sigrid Juselius Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

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

• PubMed: 31363851 
• DOI: https://doi.org/10.1007/s00792-019-01117-4
• Primary Citation of Related Structures:  
  6RPP, 6RPQ


• 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 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.

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Related Citations: 

• 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

• 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 D Biol Crystallogr 66: 213

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Organizational Affiliation: 

Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.26 kDa 
• Atom Count: 2,037 
• Modelled Residue Count: 249 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,1108aa long hypothetical cell division control protein	A	279	Saccharomyces cerevisiae S288C, Pyrococcus horikoshii OT3 This entity is chimeric	Mutation(s): 1  Gene Names: SMT3, YDR510W, D9719.15, PH0606
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.92	α = 90
b = 100.92	β = 90
c = 91.72	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Beyer, H.M., Mikula, K.M., Iwai, H.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	137995, 277335
Novo Nordisk Foundation	Finland	NNF17OC0025402
Sigrid Juselius Foundation	Finland	--

Revision History  

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