hglS

id: Q88CC1
gene_symbol: hglS
aliases:
- ydcJ
- PP_5260
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida KT2440
description: 'HglS is a 2-oxoadipate dioxygenase/decarboxylase that catalyzes the final step in D-lysine catabolism by converting 2-oxoadipate to D-2-hydroxyglutarate through an Fe(II)- and O2-dependent mechanism involving successive decarboxylation and intramolecular hydroxylation. The enzyme shows high specificity for 2-oxoadipate (KM ~0.01-0.06 mM) and is essential for growth on both L-lysine and D-lysine. HglS belongs to the DUF1338 family and represents the last missing enzymatic step in plant lysine catabolism that was identified through high-resolution crystal structures (PDB: 6W1G, 6W1H) which revealed the molecular basis for substrate specificity mediated by a conserved arginine residue (Arg74).'
existing_annotations:
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Accurate but general - HglS is specifically a dioxygenase/decarboxylase
    action: KEEP_AS_NON_CORE
    reason: While correct, this term is too general. The more specific dioxygenase activity term better captures HglS function.
- term:
    id: GO:0051213
    label: dioxygenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Correct and specific - HglS performs dioxygenase activity on 2-oxoadipate
    action: ACCEPT
    reason: Accurately describes the core molecular function. HglS is a Fe(II)-dependent dioxygenase that incorporates O2 during the oxidative decarboxylation of 2-oxoadipate.
- term:
    id: GO:0019477
    label: L-lysine catabolic process
  evidence_type: IMP
  original_reference_id: PMID:31064836
  review:
    summary: Core biological process - HglS is essential for lysine catabolism. Term updated from obsolete GO:0006554 to GO:0019477.
    action: NEW
    reason: HglS catalyzes a key step in lysine breakdown and deletion mutants cannot grow on lysine. Original term GO:0006554 was obsoleted in favor of more specific terms.
    supported_by:
    - reference_id: PMID:31064836
      supporting_text: Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.
- term:
    id: GO:0042180
    label: ketone metabolic process
  evidence_type: IDA
  original_reference_id: PMID:31064836
  review:
    summary: Specific metabolic process - HglS processes 2-oxoadipate (a ketone derivative)
    action: NEW
    reason: The substrate 2-oxoadipate is a ketone derivative and the reaction involves ketone metabolism.
    supported_by:
    - reference_id: PMID:31064836
      supporting_text: Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.
- term:
    id: GO:0006520
    label: amino acid metabolic process
  evidence_type: IMP
  original_reference_id: PMID:31064836
  review:
    summary: Broad metabolic process - HglS functions in amino acid catabolism
    action: NEW
    reason: As part of lysine catabolism, HglS participates in amino acid metabolic processes.
    supported_by:
    - reference_id: PMID:31064836
      supporting_text: Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.
references:
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods.
  findings: []
- id: PMID:31064836
  title: Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism.
  findings:
  - statement: HglS catalyzes conversion of 2-oxoadipate to D-2-hydroxyglutarate
    supporting_text: involves the direct conversion of 2OA to d-2HG
  - statement: HglS is essential for growth on lysine isomers
    supporting_text: A ΔPP_5260 strain was unable to grow on either isomer of lysine
  - statement: HglS is involved in D-lysine catabolic pathway
    supporting_text: PP_5260, showed a significant fitness defect...near other d-lysine catabolic genes in the P. putida genome
  - statement: HglS shows high substrate specificity and kinetic parameters
    supporting_text: Kcat values for their given substrates (330 m−1 for PP_5260
  - statement: HglS expression is induced by lysine derivatives
    supporting_text: All five d-lysine pathway proteins examined (AmaA [PP_5257], AmaB [PP_5258], PP_4108, YdcJ [PP_5260], and YdiJ [PP_4493[) were upregulated when grown on l-lysine, d-lysine, or 2AA compared to the glucose control
- id: PMID:32523014
  title: An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.
  findings:
  - statement: HglS crystal structure reveals molecular basis for substrate specificity
    supporting_text: Initially, Hg1S was crystallized without substrate, and the Hg1S structure was solved at 1.1 Å resolution
  - statement: Arg74 is critical for substrate specificity
    supporting_text: arginine 74 forms a salt bridge with the distal carboxylate of the 2OA substrate...an R74A mutation abolished enzymatic activity
  - statement: HglS is highly specific for 2-oxoadipate substrate
    supporting_text: HglS exhibited activity only with 2OA, and displayed no detectable and statistically significant activity above background
  - statement: HglS represents the missing step in plant lysine catabolism
    supporting_text: DUF1338 family proteins catalyze the last unknown step of plant lysine catabolism
core_functions:
- description: Fe(II)-dependent dioxygenase that catalyzes oxidative decarboxylation of 2-oxoadipate to D-2-hydroxyglutarate with high substrate specificity (KM ~0.01-0.06 mM)
  molecular_function:
    id: GO:0051213
    label: dioxygenase activity
  directly_involved_in:
  - id: GO:0019477
    label: L-lysine catabolic process
  - id: GO:0042180
    label: ketone metabolic process
  supported_by:
  - reference_id: PMID:31064836
    supporting_text: involves the direct conversion of 2OA to d-2HG
  - reference_id: PMID:32523014
    supporting_text: HglS exhibited activity only with 2OA, and displayed no detectable and statistically significant activity above background
- description: Essential metabolic enzyme for bacterial growth on both L-lysine and D-lysine as carbon sources
  molecular_function:
    id: GO:0051213
    label: dioxygenase activity
  directly_involved_in:
  - id: GO:0019477
    label: L-lysine catabolic process
  - id: GO:0006520
    label: amino acid metabolic process
  supported_by:
  - reference_id: PMID:31064836
    supporting_text: A ΔPP_5260 strain was unable to grow on either isomer of lysine
  - reference_id: PMID:31064836
    supporting_text: PP_5260, showed a significant fitness defect...near other d-lysine catabolic genes in the P. putida genome
proposed_new_terms:
- proposed_name: 2-oxoadipate dioxygenase activity
  proposed_definition: Catalysis of the oxidative decarboxylation of 2-oxoadipate to form D-2-hydroxyglutarate using Fe(II) and O2 as cofactors
  justification: HglS represents a specific type of dioxygenase activity with unique substrate specificity. A more specific term would better capture this distinct enzymatic function than the general dioxygenase activity term.
suggested_experiments:
- experiment_type: Comparative enzymatic analysis
  description: Systematic comparison of HglS substrate specificity across different 2-oxo acids to fully define the substrate scope and identify any secondary activities.
- experiment_type: Structural-functional analysis
  description: Site-directed mutagenesis of residues beyond Arg74 to understand the complete molecular basis for substrate specificity and catalytic mechanism.
- experiment_type: Phylogenetic analysis
  description: Comprehensive analysis of DUF1338 family members across bacteria and eukaryotes to understand evolutionary conservation and functional divergence.
- experiment_type: Metabolic pathway analysis
  description: Complete mapping of lysine catabolism pathway in P. putida to understand HglS integration with upstream and downstream enzymes.
suggested_questions:
- question: How does HglS coordinate with other enzymes in the lysine catabolic pathway?
  experts:
  - Bacterial metabolism specialists
  - Enzyme biochemists
  - Systems biologists
- question: What is the evolutionary origin of the DUF1338 family and how did substrate specificity evolve?
  experts:
  - Evolutionary biochemists
  - Comparative genomics researchers
  - Structural biologists
- question: Can HglS be engineered for biotechnological production of D-2-hydroxyglutarate or related compounds?
  experts:
  - Enzyme engineers
  - Synthetic biologists
  - Metabolic engineers
tags:
- lbnl-favorites
status: COMPLETE