Enzyme Specificity Project

Warnings (1)

Enzyme Specificity Project

Overview

This project tracks genes where GO annotations fail to capture the correct enzyme specificity - either:
1. Too narrow: Annotation to one substrate when enzyme has broader specificity
2. Too broad: Generic enzyme class when specific activity is known
3. Wrong reaction: Incorrect reaction type based on domain classification

Enzyme specificity is crucial for accurate functional annotation. Misannotated specificity can:
- Mislead metabolic pathway reconstruction
- Cause errors in drug target identification
- Propagate incorrect annotations via IBA

Source: Presented at Gene Ontology Consortium Meeting, October 2025, Cambridge UK. See ai4curation/ai-gene-review.

Categories

1. Substrate Specificity Errors

The Problem: Enzyme annotated to specific substrate when it has broader or different specificity.

Example - LPL1 (C. albicans):
- Annotated: GO:0004622 (phosphatidylcholine lysophospholipase activity)
- Actual: Phospholipase B with three distinct activities:
1. sn-1/sn-2 fatty acid ester hydrolase
2. Lysophospholipase activity (on ALL glycerophospholipids, not just PC)
3. Transacylase activity
- Action: MODIFY → GO:0102545 (phospholipase B activity)

2. Reaction Mechanism Errors

The Problem: Wrong reaction type inferred from domain classification.

Example - PHYKPL (human):
- Domain: Aminotransferase III family
- Annotated: GO:0008483 (transaminase activity)
- Actual: Phospho-lyase (EC 4.2.3.134), NOT a transaminase
- Evidence: "Unlike AGXT2, AGXT2L1 and AGXT2L2 did not act as transaminases"
- Action: REMOVE transaminase; ADD GO:0016838 (carbon-oxygen lyase activity, acting on phosphates)

3. Cofactor Specificity Errors

The Problem: Enzyme annotated with wrong cofactor preference.

Examples:
- NAD+ vs NADP+ dependent dehydrogenases
- PLP-dependent enzymes with different reaction types

4. Non-Enzymatic Homologs

The Problem: Enzymatic activity annotated to proteins that have lost catalytic function.

Example - Epe1 (S. pombe) (see CONTESTED_FUNCTION.md):
- Annotated: Histone demethylase, oxidoreductase, dioxygenase
- Actual: Pseudo-enzyme with degenerate active site
- Action: REMOVE all enzymatic annotations

LPL1 (Candida albicans)

UniProt: Q5AMS2
Species: CANAL
Status: COMPLETE

Specificity Issue:
- GO:0004622 (phosphatidylcholine lysophospholipase) - too narrow
- Enzyme acts on ALL glycerophospholipids, not just PC
- Has three distinct activities (hydrolase, lysophospholipase, transacylase)

Also: GO:0047372 (monoacylglycerol lipase activity) marked KEEP_AS_NON_CORE
- Likely substrate promiscuity, not primary function

PHYKPL (Homo sapiens)

UniProt: Q8IUZ5
Species: human
Status: COMPLETE

Specificity Issue:
- Classified in aminotransferase family → annotated with transaminase activity
- Biochemically demonstrated to be a phospho-lyase
- Different reaction mechanism entirely

Proposed New Terms:
- 5-phosphooxy-L-lysine phospho-lyase activity - specific MF for PHYKPL
- 5-phosphohydroxy-L-lysine catabolic process - specific BP

GND1 (Candida albicans)

UniProt: A0A1D8PFS4
Species: CANAL
Status: INITIALIZED (annotations pending review)

Notes: 6-phosphogluconate dehydrogenase with interesting dual localization (cytosol and peroxisome via alternative splicing). Review needed for specificity annotations.

Genes for Review

Priority 1: Completed

Gene Species Issue Status
LPL1 CANAL Substrate specificity too narrow COMPLETE
PHYKPL human Wrong reaction mechanism COMPLETE

Priority 2: Pending

Gene Species Issue Status
GND1 CANAL Review pending INITIALIZED

Curation Principles

  1. Verify substrate range: Don't assume specificity from one characterized reaction
  2. Check reaction mechanism: Domain family doesn't guarantee mechanism
  3. Distinguish promiscuity from core function: Secondary activities → KEEP_AS_NON_CORE
  4. Propose specific terms: When existing terms are too broad or narrow

STATUS

Completed Reviews

Pending Reviews

Last updated: 2026-01-22

NOTES

2026-01-22

Project Creation

Created project to track enzyme specificity annotation issues.

LPL1 Key Points:
- Phospholipase B enzymes have three activities in one protein
- Current annotation (GO:0004622) captures only lysophospholipase on PC
- Better term: GO:0102545 (phospholipase B activity)
- Also: GO:0047372 (monoacylglycerol lipase) kept as non-core (likely promiscuous)

PHYKPL Key Points:
- Domain classification misleading (aminotransferase family)
- Biochemically: "did not act as transaminases"
- Functions as phospho-lyase (EC 4.2.3.134)
- Needs specific GO term for its reaction