5O9I

Crystal structure of transcription factor IIB Mvu mini-intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins.

Iwai, H.Mikula, K.M.Oeemig, J.S.Zhou, D.Li, M.Wlodawer, A.

(2017) J Mol Biol 429: 3942-3956

  • DOI: 10.1016/j.jmb.2017.10.016
  • Primary Citation of Related Structures:  
    5O9I, 5O9J

  • PubMed Abstract: 
  • Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains ...

    Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights into the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: wlodawer@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIB,Transcription initiation factor IIBA, B195Methanocaldococcus vulcanius M7Mutation(s): 0 
Gene Names: tfbMetvu_0030
UniProt
Find proteins for C9REA0 (Methanocaldococcus vulcanius (strain ATCC 700851 / DSM 12094 / M7))
Explore C9REA0 
Go to UniProtKB:  C9REA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9REA0
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.183α = 90
b = 67.245β = 102.43
c = 51.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
MR-Rosettaphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland1131413
Academy of FinlandFinland137995
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references