get comprehensive enzyme information, including ec number, structure, catalytic mechanism, and catalytic residue analysis

/skills/EnzymeAnalysis.md

Workflow for Detailed Enzyme Analysis

When user asks "tell me more about enzyme X":

Step 1: Gather comprehensive data

1. Call get_ec_number(enzyme_name) to get EC classification
2. Call get_enzyme_structure(enzyme_name) to get PDB info
3. Call search_uniprot_proteins(enzyme_name) to find UniProt entries
4. For the best-matching UniProt entry, call get_uniprot_protein_details(uniprot_id) to retrieve all relevant details including function, sequence, etc

Step 2: Deep catalytic-residue analysis via literature

Search for papers that describe catalytic residues, active-site interactions, and mutagenesis studies:

1. Call search_arxiv_papers("{enzyme_name}") (max_results=5)
2. Call search_preprints("{enzyme_name}") (max_results=5)
3. From each returned paper abstract/excerpt, extract:
   • Residue numbers and identities (e.g. His57, Asp102, Ser195)
   • The role of each residue (nucleophile, general acid/base, oxyanion hole, transition-state stabilisation, etc.)
   • Known interactions (hydrogen bonds, salt bridges, covalent intermediates, metal coordination, substrate contacts)
   • Mutagenesis results if reported (e.g. "H57A → 10,000-fold loss of kcat")

Step 3: Structure the response

Format as follows:

## Enzyme: {name}


**Example**:
- **Uniprot ID**: {uniprot_id}
- **Sequence**: {Sequence}
- **Organism**: {organism}
- **Function**: {function}

**EC Number**: {ec_number}

**Structure**:
- PDB ID: {pdb_id}
- Resolution: {resolution}
- UniProt ID: {uniprot_id}

**Catalytic Mechanism**:
{mechanism_details}

**Catalytic Residues**:
| Residue | Position | Role | Key Interactions | Evidence |
|---------|----------|------|------------------|----------|
| {residue_name} | {position} | {role} | {interactions} | {source: UniProt / PDB / literature} |
| ... | ... | ... | ... | ... |

**Interaction Network**:
- List each pair of residues that interact and the type of interaction
  (e.g. "Asp102 ── H-bond ── His57", "His57 ── covalent intermediate ── substrate")
- Note any metal ions or cofactors coordinated by catalytic residues

**Mutagenesis Highlights** (if available):
- {mutation} → {effect on activity} (Source: {reference})

**3D Visualization**:
[Link to structure viewer]

Step 4: Quality checks

• Ensure all sections are populated
• If any API call fails, note it explicitly
• Cross-reference residue numbers between UniProt annotations and literature; flag any discrepancies
• Provide literature references (arXiv/bioRxiv URLs or DOIs) for every claim about residue roles