User:Wayne Decatur/Sandbox 1 vs 21 vs 2 vs 12

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1 vs 21 vs 2 vs 12

The Alignment

Alignment of yeast Snm1p to portions of other yeast proteins and Pyrococcus horikoshii Rpp21p:


Snm1      MNKDQAEKYQERSLRQKYNLLHVLP-------TLNSRALSGLYYKNFHNS-VKRYQIMLP
1x0t.1.A  -----------ERIDTLFTLAERV--------ARYSPDLAKRYVELALEI-QKKAKVKIP
Rpr2      -------------LNYLYQISAYQTRARQKARTDAHTPLA-RNYIKSMDLISKKTKTSLL
Rpa12     ------------------------------------------------------------

Snm1      EQLKSGKFCSHCGCVYVPNFNASLQLTTNTEQGDSDELGGESMEGPKKCIQVNCLNCEKS
1x0t.1.A  RKWK-RRYCKRCHTFLIPGVNARVRLRTKR----------------MPHVVITCLECGYI
Rpr2      PTIK-RTICKKCHRLLWTPKKLEITSD--------------------GALSVMC-GCGTV
Rpa12     -----KEKCPQCGNEEM------NYHTLQ--LRSADE---------GATVFYTCTSCGYK

Snm1      KLFEWKSEFVVPTFGQDVSPMINSTSSGKVSYAVKKPQKSKTSTGKERSKKRKLNSLTNL
1x0t.1.A  MRYPYLREVK--------------------------------------------------
Rpr2      KRFNIGADPNYRTYSEREGNLLNS------------------------------------
Rpa12     FRTNN-------------------------------------------------------

Snm1      LSKRNQEKKMEKKKSSSLSLESFMKS
1x0t.1.A  --------------------------
Rpr2      --------------------------
Rpa12     --------------------------

(Specifically, QKRKKATREVKQKRKKAT is left off C-terminus of 1xOt chain A (Rpp21p); MGKKAHGGKMKPEIDENGTLLVPPPRTIANQDHFHR is left off N-terminus of Rpr2p; just C-terminus of Rpa12p is shown; all residues of Snm1 are represented. All sequences from S. cerevisiae except 1x0t, which is Pyrococcus horikoshii.)

Structures superposed

Rpr2p, Snm1p, archaeal Rpp21p, and Rpa12p superposed

Understanding Rpr2p in the Yeast RNase P structure

To learn more about Rpr2p in the yeast RNase P cryo-EM structure [4] go to here and take the tour in sections 'Rpr2p overview' and 'Rpr2p binds zinc'. (Note that it is a work-in-progress.)

For smaller screens, such as tablets, use here


References

  1. Fernandez-Tornero C, Moreno-Morcillo M, Rashid UJ, Taylor NM, Ruiz FM, Gruene T, Legrand P, Steuerwald U, Muller CW. Crystal structure of the 14-subunit RNA polymerase I. Nature. 2013 Oct 31;502(7473):644-9. doi: 10.1038/nature12636. Epub 2013 Oct 23. PMID:24153184 doi:http://dx.doi.org/10.1038/nature12636
  2. Krishna SS, Majumdar I, Grishin NV. Structural classification of zinc fingers: survey and summary. Nucleic Acids Res. 2003 Jan 15;31(2):532-50. doi: 10.1093/nar/gkg161. PMID:12527760 doi:http://dx.doi.org/10.1093/nar/gkg161
  3. Odile Filhol, Maria José Benitez, and Claude Cochet. 2013. A Zinc Ribbon Motif Is Essential for the Formation of Functional Tetrameric Protein Kinase CK2. Madame Curie Bioscience Database Austin (TX): Landes Bioscience; 2000-2013. https://www.ncbi.nlm.nih.gov/books/NBK6254/
  4. Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M. Structural insight into precursor tRNA processing by yeast ribonuclease P. Science. 2018 Sep 27. pii: science.aat6678. doi: 10.1126/science.aat6678. PMID:30262633 doi:http://dx.doi.org/10.1126/science.aat6678

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Wayne Decatur

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