AKMT Lys pred

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	ExpandNCBI - 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	Expand'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