A Python library for annotating McrA protein sequences with known post-translational modification (PTM) sites in the active site of methyl-coenzyme M reductase.
Built to support research from the Nayak lab:
Nayak, Metcalf et al. (2017). Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea. eLife 6:e29218.
Nayak, Mahanta et al. (2020). Post-translational thioamidation of methyl-coenzyme M reductase is required for its activity in Methanosarcina acetivorans. PLoS Biology 18:e3000507.
The α subunit of MCR (McrA) contains six experimentally characterised post-translational modifications. The first five were identified in the crystal structure of Methanothermobacter marburgensis MCR (PDB 1MRO, Ermler et al. 1997). A sixth (didehydroaspartate) was identified by mass spectrometry and high-resolution X-ray crystallography (PDB 5A0Y, Wagner et al. 2016):
| PTM name | Residue | Position (M. marburgensis) | PDB | Reference |
|---|---|---|---|---|
| Thioglycine | G | 445 | 1MRO (GL3) | Nayak 2017 eLife |
| Didehydroaspartate | D | 446 | 5A0Y | Wagner 2016 Angew Chem |
| 1-N-methylhistidine | H | 257 | 1MRO (MHS) | Ermler 1997 |
| 5-(S)-methylarginine | R | 271 | 1MRO (AGM) | Deobald 2018 Sci Rep |
| 2-(S)-methylglutamine | Q | 400 | 1MRO (MGN) | Ermler 1997 |
| S-methylcysteine | C | 452 | 1MRO (SMC) | Ermler 1997 |
Known variability across organisms (Kahnt 2007, Selmer 2000):
- Thioglycine and 1-N-methylhistidine: conserved in all methanogens examined
- 5-(S)-methylarginine: present in all methanogens examined, absent in ANME-1
- 2-(S)-methylglutamine: absent in M. barkeri
- S-methylcysteine: low abundance or absent in many methanogens including M. maripaludis
- Didehydroaspartate: present in M. marburgensis and M. barkeri, absent in M. wolfeii
⚠ Important limitations:
- This tool reports candidate sites only. PTM presence must be confirmed experimentally (mass spectrometry).
- Position mapping is a heuristic scaled from PDB 1MRO. For definitive mapping, align your sequence against PDB 1MRO chain A (see below).
- PTM patterns vary across archaeal lineages. ANME MCRs have a different modification pattern (Shima et al. 2012).
git clone https://github.com/CameronCat/mcr-ptm-annotator
cd mcr-ptm-annotator
pip install -e ".[dev]"from mcr_ptm_annotator import McrAPTMAnnotator, report
annotator = McrAPTMAnnotator(
position_window=30, # ±residues to search around expected position
require_residue_match=True # only report correct residue type
)
# Annotate a single sequence (McrA protein, single-letter amino acids)
hits = annotator.annotate_sequence(my_mcra_protein_sequence, seq_id="MA0528")
print(report.summary(hits, seq_id="MA0528"))
# Export
report.to_tsv(hits, seq_id="MA0528", path="ptm_hits.tsv")
report.to_json(hits, seq_id="MA0528", path="ptm_hits.json")results = annotator.annotate_fasta("my_mcrA_sequences.faa")
for seq_id, hits in results.items():
print(report.summary(hits, seq_id=seq_id))from mcr_ptm_annotator import KNOWN_PTMS
for ptm in KNOWN_PTMS:
print(ptm.name, ptm.position_marburgensis, ptm.references)Because McrA is highly conserved across methanogens, the known PTM residues fall in narrow, predictable regions relative to total sequence length. The tool scales each reference position linearly:
expected_pos = round(ref_pos × query_length / 553)
Then it searches ±30 residues around that expected position for the correct residue type.
This is a shortcut, not a substitute for alignment. Confidence levels reflect distance from the expected position:
| Confidence | Δ from expected |
|---|---|
high |
≤ 10 residues |
moderate |
11–20 residues |
low |
21–30 residues |
For publication-quality results, align your McrA sequence against PDB 1MRO chain A using MUSCLE or MAFFT:
# 1. Download PDB 1MRO chain A sequence
efetch -db protein -id 1MRO_A -format fasta > 1MRO_A.faa
# 2. Combine with your query sequence
cat 1MRO_A.faa my_mcrA.faa > combined.faa
# 3. Align
muscle -in combined.faa -out aligned.faa
# or
mafft --auto combined.faa > aligned.faa
# 4. Read off the alignment columns for positions 257, 271, 400, 445, 452The example FASTA contains a synthetic placeholder. Download real sequences from:
| Organism | Protein | Accession |
|---|---|---|
| M. acetivorans C2A | McrA | NP_618892.1 |
| M. marburgensis (reference) | McrA | UniProt P11558 |
| M. mazei | McrA | NP_632996.1 |
efetch -db protein -id NP_618892.1 -format fasta > McrA_acetivorans.faamcr-ptm-annotator/
├── mcr_ptm_annotator/
│ ├── __init__.py
│ ├── annotator.py ← McrAPTMAnnotator, PTMHit
│ ├── ptm_database.py ← KNOWN_PTMS (experimentally verified only)
│ ├── report.py ← TSV / JSON / text export
│ └── utils.py ← FASTA parser
├── tests/
│ └── test_annotator.py
├── examples/
│ ├── example_mcrA.fasta ← synthetic placeholder + NCBI links
│ └── basic_usage.py
├── .github/workflows/ci.yml
├── pyproject.toml
└── README.md
pytest
pytest --cov=mcr_ptm_annotator- Ermler et al. (1997) Crystal structure of methyl-coenzyme M reductase. Science 278:1457. PDB: 1MRO.
- Selmer et al. (2000) Biosynthesis of methylated amino acids in the active site region of MCR. J Biol Chem 275:3755.
- Kahnt et al. (2007) Post-translational modifications in the active site region of MCR from methanogenic and methanotrophic archaea. FEBS J 274:4913.
- Nayak et al. (2017) Post-translational thioamidation of MCR. eLife 6:e29218.
- Wagner et al. (2016) Didehydroaspartate modification in MCR. Angew Chem Int Ed Engl 55:10630. PDB: 5A0Y.
- Deobald et al. (2018) Radical SAM methyltransferase for sp3-C-methylation of arginine in MCR. Sci Rep 8:7404.
- Nayak et al. (2020) Thioamidation required for MCR activity. PLoS Biol 18:e3000507.
If you use this tool in published research, please cite:
@article{nayak2017,
title = {Post-translational thioamidation of methyl-coenzyme M
reductase, a key enzyme in methanogenic and methanotrophic Archaea},
author = {Nayak, Dipti D and Mahanta, Nilkamal and Mitchell, Douglas A
and Metcalf, William W},
journal = {eLife},
volume = {6},
pages = {e29218},
year = {2017}
}MIT © 2024. See LICENSE.