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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.
Data background
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 | |||
| 2K9I | Entity 1 containing Chain A, B | NMR structure of plasmid copy control protein ORF56 from sulfolobus islandicus | Weininger, U., Zeeb, M., Neumann, P., Low, C., Stubbs, M.T., Lipps, G., Balbach, J. | 10/20/2009 | Solution NMR | 110 | Uncharacterized protein ORF56 | |||
| 3FT7 | Entity 1 containing Chain A, B | Crystal structure of an extremely stable dimeric protein from sulfolobus islandicus | Weininger, U., Zeeb, M., Neumann, P., Low, C., Stubbs, M.T., Lipps, G., Balbach, J. | 10/20/2009 | X-ray Diffraction | 110 | Uncharacterized protein ORF56 | |||
| 1RNI | Entity 1 containing Chain A | Bifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1 | Lipps, G., Weinzierl, A.O., Von Scheven, G., Buchen, C., Cramer, P. | 1/27/2004 | X-ray Diffraction | 216 | ORF904 | |||
| 1RO0 | Entity 1 containing Chain A | Bifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1- Triple mutant F50M/L107M/L110M SeMet remote | Lipps, G., Weinzierl, A.O., Von Scheven, G., Buchen, C., Cramer, P. | 1/27/2004 | X-ray Diffraction | 216 | ORF904 | |||
| 1RO2 | Entity 1 containing Chain A | Bifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1- Triple mutant F50M/L107M/L110M manganese soak | Lipps, G., Weinzierl, A.O., Von Scheven, G., Buchen, C., Cramer, P. | 1/27/2004 | X-ray Diffraction | 216 | hypothetical protein ORF904 | |||
Methylated peptide
Data from:
- mcp.M115.057778-3.xlsx
- mcp.M115.057778-4.xlsx
| PDB id | NCBI - Accession Number | 'Methylated peptides' 'Sequence' in -3.xlsx | 'Methylated peptides' ' Modification' in -3.xlsx s | 'Methylated peptides' 'Sequence' in -4.xlsx | 'Methylated peptides' ' Modification' in -4.xlsx s |
|---|---|---|---|---|---|
| 4G2D | ADX84410 Sequence | SIDEIADLFIHDIkEGIQATSNK kIADKGSFIGLDR ILmEEGVDPGkILIGHLGDTDNTDYIK kNGmSEEVIDIIFK SIDEIADLFIHDIkEGIQATSNK SIDEIADLFIHDIkEGIQATSNK |
K14(Methyl) K1(Methyl) M3(Oxidation); K11(Trimethyl) K1(Methyl); M4(Oxidation) K14(Dimethyl) K14(Trimethyl) |
mRIPLVGkEPIEAEDmGFTLIHEHLR | M1(Oxidation); K8(Trimethyl); M16(Oxidation) |
Example
reinitialize
viewport 1100,700
# Imports
import aKMT_Lys_pred
# Load
fetch 4g2d, async=0
remove hydrogens
remove solvent
# Display
preset.publication(selection='4g2d')
center 4g2d
# Get the residues with lysine
return_list_resn_resi, return_list_resn_resi_sel = aKMT_Lys_pred.get_resis_from_resn("4g2d", "LYS")
print(return_list_resn_resi)
# Match resi with peptide sequence
python
peptides = [
["SIDEIADLFIHDIkEGIQATSNK", "K14"],
["kIADKGSFIGLDR", "K1"],
["ILmEEGVDPGkILIGHLGDTDNTDYIK", "K11"],
["kNGmSEEVIDIIFK", "K1"],
["mRIPLVGkEPIEAEDmGFTLIHEHLR", "K8"],
]
python end
# Find peptides
return_list_resn_match, return_list_resn_match_sel = aKMT_Lys_pred.match_peptides(target_sel="4g2d", peptides=peptides)
print(return_list_resn_match)
# Make list of lysines not methylated
lys_not_meth = [x for x in return_list_resn_resi if x not in return_list_resn_match]
print(lys_not_meth)
# Make stats
aKMT_Lys_pred.get_resi_stats(target_sel="4g2d", residues=lys_not_meth, group_id="not_meth", verb=True)
aKMT_Lys_pred.get_resi_stats(target_sel="4g2d", residues=return_list_resn_match, group_id="methylated", verb=True)
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