Inteins - the ultimate selfish gene?

Inteins are selfish genetic elements similar to introns; however they get translated in frame together with the host protein (=extein) and splice themselves out of the translated protein. All inteins have selfsplicing activity, the large inteins also have an endonuclease activity. Inteins were first discovered in the vacuolar ATPase A-subunit in Saccharomyces. It also is present in the A-subunit of closely related yeasts, but all other V-ATPases in eukaryotes were found to NOT contain an intein, suggesting that this intein jumped into the A-subunit sometime in the evolution of this group of Fungi. Surprisingly the related archaeal ATPase of some archaea has an intein (small type) in the same subunit in nearly the same location.

Large inteins contain an endonuclease domain that functions as a homing endonuclease. See here for a recent review. ;-)

• TASK1: Using the sequence from the Thermoplasma A-ATPase catalytic subunit, do a databank search using blast, repeat the exercise with PSI blast (if too slow get the last iteration here). Is there a common motif among the sequences with significant similarity?
  
  
• TASK2: The structure from the Intein from the yeast V-ATPase has been determined (1VDE.PDB). Using the following alignment between the VMA-1 inteins, determine which part of the structure in yeast vma-1 intein corresponds to Thermoplasma intein. Hints: 1VDE is a dimer, you first need to delete one of the chains. One possibility is to color the aligned residues in a different color. Based on the structure, which part of the following alignment is questionable?
  
  

  ThermopAi CVSGDTPVLLDAG-ER-----RIGDLFM-EAIRPKERGEIGQ--NE---EIVRLHDXWRIYSMVG------SEIVETVSHAIYHG-KSNA
  
  vma1SCE-I CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPR-GRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNATHELVVRTPRSV
  
  
  
  ThermopAi IVNVRTENGRE----VRVTPVHKL--------FVKIGNSV-I--ERPA---SEV-N--------------EGDEIAWP
  
  vma1SCE-I RRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPER-ANELVESYRKASN-KAYFEWTIEARDLS
  
  
  
  ThermopAi SVSENGDSQTVTTTLVLTFDRVVS-KEMHSGVFD--------------------------
  
  vma1SCE-I LLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRAT
  
  
  
  ThermopAi ------------------------------------------------------------
  
  vma1SCE-I FSVDSRD-TSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRG-----------
  
  
  
  ThermopAi ------------------------------------------------------------
  
  vma1SCE-I ---NG---IRNNLN-----TEN-PLWDAIVGLGFLK---DGVKNIPSFLSTDNIGTRETF
  
  
  
  ThermopAi ------------------------------------------------------------
  
  vma1SCE-I LAGLIDSDG-YVTDEHG-IKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTK
  
  
  
  ThermopAi --------------------------------------------------------VYDLMVP-DYGY
  
  vma1SCE-I HKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSD-H-
  
  
  
  ThermopAi NFIGGNGLIVLHN
  
  vma1SCE-I QFLLANQV-VVHN
                         

• TASK 3: A short intein structure has been determined from the gyrase of Mycobacterium xenopi (1am2.pdb). Load this structure onto the yeast structure, use magic fit followed by improve fit to align the two structures. How does this alignment correspond to an alignment calculated by clustal? (the sequences are here)

There are many beautiful web sites devoted to inteins:

    The intein databank InBase is maintained by Fran Perler at NEB.

    A beautiful description of intein structure and evolution is at http://blocks.fhcrc.org/~pietro/inteins/