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Difference between revisions of "AKMT Lys pred"

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This script should try to make an analysis this for 3D, with residues up and downstream in angstrom distance to the residue of interest.
 
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 ==
+
== Data background ==
 +
=== PDB structures in Sulfolobus Islandicus ===
 
Following structures was found June 2017
 
Following structures was found June 2017
 
* www.rcsb.org -> Search advanced
 
* www.rcsb.org -> Search advanced
 
* Biology -> Source organism -> Sulfolobus organism
 
* Biology -> Source organism -> Sulfolobus organism
  
−
{| class="wikitable" style="text-align: left;"
+
{| class="mw-collapsible mw-collapsed wikitable" style="text-align: left;"
−
! PDB id !! Info !! Text !! Authors !! Released !! Method !! Residue Count !! Macromolecule: !! Gene Name(s) !! UniProtKB AC !! NCBI - Accession Numbers
+
! PDB id !! Info !! Text !! Authors !! Released !! Method !! Residue Count !! Macromolecule !! Gene Name(s) !! UniProtKB AC !! NCBI - Accession Numbers
 
|-
 
|-
−
4G2D || test
+
| 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 ||  ||  ||
 +
|-
 +
|
 
|-
 
|-
 
|}
 
|}
  
−
{| class="wikitable" style="margin: auto;"
+
=== Methylated peptide ===
−
| Orange
+
Data from:
−
| Apple
+
* mcp.M115.057778-3.xlsx
 +
* mcp.M115.057778-4.xlsx
 +
 
 +
{| class="mw-collapsible mw-collapsed wikitable" style="text-align: left;"
 +
! 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
 
|-
 
|-
−
| Bread
+
| 4G2D || ADX84410 Sequence
−
| Pie
+
| SIDEIADLFIHDIkEGIQATSNK <br> kIADKGSFIGLDR <br> ILmEEGVDPGkILIGHLGDTDNTDYIK <br> kNGmSEEVIDIIFK <br> SIDEIADLFIHDIkEGIQATSNK <br> SIDEIADLFIHDIkEGIQATSNK
 +
| K14(Methyl) <br> K1(Methyl)  <br> M3(Oxidation); K11(Trimethyl) <br> K1(Methyl); M4(Oxidation) <br> K14(Dimethyl) <br> K14(Trimethyl)
 +
| mRIPLVGkEPIEAEDmGFTLIHEHLR
 +
| M1(Oxidation); K8(Trimethyl); M16(Oxidation)
 
|-
 
|-
−
| Butter
 
−
| Ice cream
 
 
|}
 
|}
  
 
== Example ==
 
== Example ==
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
−
test
+
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)
 +
 
 
</syntaxhighlight>
 
</syntaxhighlight>
−
 
  
 
== References ==
 
== References ==

Latest revision as of 02:39, 24 July 2017

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

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