AKMT Lys pred

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Type Python Script
Download aKMT_Lys_pred.py
Author(s) Troels Schwarz-Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Overview

Chu et al. has compiled a large information of peptides which are methylated in Sulfolobus Islandicus. The mass-spec data is available at: http://www.mcponline.org/content/15/9/2908/suppl/DC1 in

  • Supplemental Table S2a revisied (.xlsx, 6.5 MB) - Supplemental Table S2a revisied : mcp.M115.057778-3.xlsx
  • Supplemental Table S2a revisied (.xlsx, 4.8 MB) - Supplemental Table S2a revisied : mcp.M115.057778-4.xlsx

The authors has tried to find correlation with amino acids in 1D, with 7 residues up and downstream to the lysines. The authors also tried to first predict secondary structure in the chain, and then find correlation. They made a weblogo figure http://weblogo.threeplusone.com with their findings. There seems to be a preference for helical structure and Glutamic acid (E), Isoleucin (I), Leucin (L) and Valine (V) seems to be dominant with 7 residues up/downstream to the methylated lysines.

This script should try to make an analysis this for 3D, with residues up and downstream in angstrom distance to the residue of interest.

PDB structures in Sulfolobus Islandicus

Following structures was found June 2017

  • www.rcsb.org -> Search advanced
  • Biology -> Source organism -> Sulfolobus organism
PDB id Info Text Authors Released Method Residue Count Macromolecule Gene Name(s) UniProtKB AC NCBI - Accession Numbers
 4G2D Entity 1 containing Chain A Crystal structure of the hyperthermophilic Sulfolobus islandicus PLL SisLac Hiblot, J., Gotthard, G., Chabriere, E., Elias, M. 10/24/2012 X-ray Diffraction 315 Aryldialkylphosphatase M164_0332 C4KKZ9 ADX84410
5EWT Entity 1 containing Chain A Crystal structure of ExoIII endonuclease from Sulfolobus islandicus Yan, Z., Yuan, Z.L., Gu, L.C., Shen, Y.L. 11/23/2016 X-ray Diffraction 247 Exodeoxyribonuclease III Xth SiRe_0100 F0NG49  ADX84195
5JWJ Entity 1 containing Chain A NMR solution structure of a thermophilic lysine methyl transferase from Sulfolobus islandicus de Lichtenberg, C., Stiefler-Jensen, D., Schwarz-Linnet, T., She, Q., Teilum, K.  5/24/2017 Solution NMR 172 Protein-lysine N-methyltransferase
5F4H Entity 1 containing Chain A, B, C, D, E, F Archael RuvB-like Holiday junction helicase Zhai, B., DuPrez, K.T., Doukov, T.I., Shen, Y., Fan, L. 12/21/2016 X-ray Diffraction 505/3030 Nucleotide binding protein PINc LS215_1665 C3MQK6 ADX85498
5FA8 Entity 1 containing Chain A SAM complex with aKMT from the hyperthermophilic archaeon Sulfolobus islandicu Chu, Y., Zhu, Y., Chen, Y., Li, W., Zhang, Z., Liu, D., Wang, T., Ma, J., Deng, H., Liu, Z.J., Ouyang, S., Huang, L. 6/29/2016 X-ray Diffraction 161 Ribosomal protein L11 methyltransf
5FAD Entity 1 containing Chain A SAH complex with aKMT from the hyperthermophilic archaeon Sulfolobus islandicus Chu, Y., Zhu, Y., Chen, Y., Li, W., Zhang, Z., Liu, D., Wang, T., Ma, J., Deng, H., Liu, Z.J., Ouyang, S., Huang, L.  6/29/2016 X-ray Diffraction 161 Ribosomal protein L11 methyltransf
3O27 Entity 1 containing Chain A, B The crystal structure of C68 from the hybrid virus-plasmid pSSVx Contursi, P., D'Ambrosio, K., Pirone, L., Pedone, E.M., Aucelli, T., She, Q., De Simone, G., Bartolucci, S. 1/19/2011 X-ray Diffraction 136 Putative uncharacterized protein
3M1M Entity 1 containing Chain A Crystal structure of the primase-polymerase from Sulfolobus islandicus Beck, K., Vannini, A., Cramer, P., Lipps, G. 6/16/2010 X-ray Diffraction 335 ORF904

Example

test


References

For Mass-Spec data
aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism'
Chu, Yindi; Zhu, Yanping; Chen, Yuling; Li, Wei; Zhang, Zhenfeng; Liu, Di; Wang, Tongkun; Ma, Juncai; Deng, Haiteng; Liu, Zhi-Jie; Ouyang, SongyingHuang, Li
Molecular & Cellular Proteomics 2016, Vol 15, Issue 9, 2908-2923, DOI: 10.1074/mcp.M115.057778