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
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
3D structure info
PDB id Info Text Authors Released: Method: Residue Count: Macromolecule: Gene Name(s) UniProtKB AC NCBI - Accession Numbers

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