Sandbox UC 11

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<scene name='3gkl/Align/2'>Structural alignment</scene> of the immunity protein 9 (Im9, [[1bxi]], <span style="color:yellow;background-color:black;font-weight:bold;">colored yellow</span>), <span style="color:lime;background-color:black;font-weight:bold;">evolved variant R12-2 (lime)</span>, and <font color='blue'><b>immunity protein 7 (Im7, colored blue</b></font>, [[7cei]]) reveals their structural identity. However, when the immunity proteins-bound <scene name='3gkl/Align/3'>colicins within their complexes were aligned</scene>, they demonstrate somewhat different picture. The Im9 and Im7 are differ more in their binding configurations (19°, with Tyr54-Tyr55 as the pivot), while the variant R12-2 is in an intermediate configuration between Im9 and Im7. Of note, in the variant R12-2 (3gkl) and Im9 ([[1bxi]]) there are Tyr54 and Tyr55, while in the Im7 ([[7cei]]) Tyr55 and Tyr56 are homologous to them. The most <scene name='3gkl/Align/4'>prominent differences</scene> are in the loop between helices α1 and α2 in Im9 (yellow, labeled in black) and <span style="color:lime;background-color:black;font-weight:bold;">evolved variant R12-2 (lime, labeled in black)</span>. This loop consists of three mutations: N24D, T27A, and S28T in variant R12-2. We can see the deviations in the relative position of helices α1 and α2, in the loop's backbone and in the side chains of residues 24, 26 and 28.
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<scene name='3gkl/Align/2'>Structural alignment</scene> of the immunity protein 9 (Im9, [[1bxi]], <span style="color:yellow;background-color:black;font-weight:bold;">colored yellow</span>), <span style="color:lime;background-color:black;font-weight:bold;">evolved variant R12-2 (lime)</span>, and <font color='blue'><b>immunity protein 7 (Im7, colored blue</b></font>, [[7cei]]) reveals their structural identity. However, when the immunity proteins-bound <scene name='3gkl/Align/3'>colicins within their complexes were aligned</scene>, they demonstrate somewhat different picture.
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Revision as of 20:20, 19 December 2012

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1mnm, resolution 2.25Å ()
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE (PDB entry 1mnm)

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Directed evolution and Colicin7/Immunity-proteins complexes[1]

PDB ID 3gkl

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  1. ↑ Levin KB, Dym O, Albeck S, Magdassi S, Keeble AH, Kleanthous C, Tawfik DS. Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nat Struct Mol Biol. 2009 Oct;16(10):1049-55. Epub 2009 Sep 13. PMID:19749752 doi:10.1038/nsmb.1670

Additional Literature

  • Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM. Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol. 1999 Mar;6(3):243-52. PMID:10074943 doi:http://dx.doi.org/10.1038/6683
  • Levin KB, Dym O, Albeck S, Magdassi S, Keeble AH, Kleanthous C, Tawfik DS. Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nat Struct Mol Biol. 2009 Oct;16(10):1049-55. Epub 2009 Sep 13. PMID:19749752 doi:10.1038/nsmb.1670


External Resources

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