ampC

UniProt ID: Q88IX3
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

AmpC is a chromosomally encoded class C beta-lactamase (cephalosporinase) that hydrolyzes the beta-lactam ring of penicillins and cephalosporins. It is localized to the periplasm after signal peptide cleavage (~40 kDa mature form). AmpC expression is regulated by the LysR-type transcriptional regulator AmpR, which responds to muropeptide signals imported via AmpG permease. Environmental cues such as indole can induce ampC expression in P. putida KT2440, increasing beta-lactam resistance. The enzyme directly confers antibiotic resistance by hydrolyzing beta-lactam antibiotics before they reach their targets (penicillin-binding proteins).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0008800 beta-lactamase activity
IEA
GO_REF:0000120
ACCEPT
Summary: AmpC is definitively a class C beta-lactamase (EC 3.5.2.6) that catalyzes the hydrolysis of beta-lactam antibiotics. This is the core molecular function of the protein. UniProt confirms EC=3.5.2.6 and the catalytic activity. The deep research confirms AmpC belongs to Ambler class C beta-lactamases that hydrolyze penicillins and cephalosporins.
Reason: This is the primary enzymatic function of AmpC. UniProt annotation, InterPro domain analysis (IPR058136 AmpC, IPR001586 Beta-lactam_class-C_AS), and literature all confirm this enzyme catalyzes beta-lactam hydrolysis. This term correctly represents the core molecular function.
Supporting Evidence:
file:PSEPK/ampC/ampC-deep-research-falcon.md
AmpC belongs to Ambler class C beta-lactamases (EC 3.5.2.6) that hydrolyze the beta-lactam ring of penicillins and cephalosporins
GO:0016787 hydrolase activity
IEA
GO_REF:0000043
ACCEPT
Summary: This is a parent term of GO:0008800 (beta-lactamase activity). While technically correct that AmpC has hydrolase activity, this annotation is redundant given the more specific beta-lactamase activity annotation. UniProt keyword mapping correctly identifies the hydrolase nature, but the more specific child term provides greater biological insight.
Reason: This term is accurate but generic. AmpC is indeed a hydrolase - specifically hydrolyzing the amide bond in the beta-lactam ring. The UniProt entry includes the Hydrolase keyword. While GO:0008800 (beta-lactamase activity) is more informative, retaining this broader annotation provides correct categorization and is acceptable as a parent term annotation from IEA evidence.
GO:0017001 antibiotic catabolic process
IEA
GO_REF:0000002
MODIFY
Summary: This term captures the biological process of AmpC - catabolism of antibiotics. However, GO:0030655 (beta-lactam antibiotic catabolic process) is a more specific child term that accurately reflects AmpC's substrate specificity. AmpC specifically catabolizes beta-lactam antibiotics (penicillins, cephalosporins, monobactams), not antibiotics in general.
Reason: While AmpC does participate in antibiotic catabolism, it specifically catabolizes beta-lactam antibiotics. The more specific term GO:0030655 beta-lactam antibiotic catabolic process (defined as chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic) precisely describes AmpC's biological process. Literature confirms substrate specificity for penicillins and cephalosporins.
Supporting Evidence:
file:PSEPK/ampC/ampC-deep-research-falcon.md
Hydrolysis of beta-lactam bonds in penicillins, cephalosporins, and monobactams is the signature activity of class C enzymes, conferring resistance when produced at elevated levels
GO:0030288 outer membrane-bounded periplasmic space
IEA
GO_REF:0000002
ACCEPT
Summary: Periplasmic localization is well-supported for AmpC. UniProt shows a signal peptide (residues 1-24) indicating secretion across the inner membrane. Deep research confirms AmpC is synthesized with an N-terminal signal peptide and localizes to the periplasm where it intercepts incoming beta-lactams, with mature protein size ~40 kDa after signal peptide cleavage.
Reason: This cellular component annotation is correct. AmpC functions in the periplasm where it can hydrolyze beta-lactam antibiotics before they reach their targets (penicillin-binding proteins on the inner membrane). The signal peptide and periplasmic localization are essential for the resistance mechanism. This represents a core aspect of AmpC function.
Supporting Evidence:
file:PSEPK/ampC/ampC-deep-research-falcon.md
AmpC is synthesized with an N-terminal signal peptide, exported across the inner membrane, and localized to the periplasm where it can intercept incoming beta-lactams; maturation yields a protein of ~40 kDa after signal peptide cleavage
GO:0046677 response to antibiotic
IEA
GO_REF:0000120
ACCEPT
Summary: This annotation captures AmpC's role in the organism's response to antibiotics. AmpC expression is induced by beta-lactam antibiotics and environmental signals (like indole), and its activity directly confers resistance. This term captures the broader biological context of response to antibiotic stress, including the regulatory induction. While GO:0030655 more precisely describes the enzymatic function, this term appropriately captures the response/resistance phenotype.
Reason: This annotation is legitimate for a beta-lactamase. AmpC expression is induced by beta-lactam antibiotics through the AmpR-muropeptide signaling pathway, and indole also induces ampC expression in P. putida KT2440. The enzyme directly responds to antibiotic exposure by increasing expression and activity. Retaining both GO:0030655 and this term provides complementary perspectives - one on the catabolic process and one on the response/resistance phenotype.
Supporting Evidence:
file:PSEPK/ampC/ampC-deep-research-falcon.md
Exogenous indole elevates ampC expression and beta-lactamase activity and increases the proportion of ampicillin-resistant P. putida KT2440 cells

Core Functions

AmpC is the primary beta-lactamase in P. putida KT2440. It hydrolyzes the beta-lactam ring in penicillins and cephalosporins in the periplasm, converting these antibiotics to inactive substituted beta-amino acids. This activity is the mechanistic basis for intrinsic and inducible beta-lactam resistance in this organism.

References

Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Combined Automated Annotation using Multiple IEA Methods
file:PSEPK/ampC/ampC-deep-research-falcon.md
Deep research on ampC in Pseudomonas putida KT2440
  • AmpC is a class C beta-lactamase that hydrolyzes penicillins and cephalosporins
    "AmpC belongs to Ambler class C beta-lactamases (EC 3.5.2.6) that hydrolyze the beta-lactam ring of penicillins and cephalosporins"
  • AmpC is localized to the periplasm
    "AmpC is synthesized with an N-terminal signal peptide, exported across the inner membrane, and localized to the periplasm where it can intercept incoming beta-lactams"
  • AmpC expression is induced by indole in P. putida KT2440
    "Exogenous indole elevates ampC expression and beta-lactamase activity and increases the proportion of ampicillin-resistant P. putida KT2440 cells"
  • AmpC confers resistance to beta-lactam antibiotics
    "Hydrolysis of beta-lactam bonds in penicillins, cephalosporins, and monobactams is the signature activity of class C enzymes, conferring resistance when produced at elevated levels"

📚 Additional Documentation

Deep Research Falcon

(ampC-deep-research-falcon.md)

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gene_id: ampC
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protein_description: 'RecName: Full=Beta-lactamase {ECO:0000256|ARBA:ARBA00012865,
ECO:0000256|RuleBase:RU361140}; EC=3.5.2.6 {ECO:0000256|ARBA:ARBA00012865, ECO:0000256|RuleBase:RU361140};'
gene_info: Name=ampC {ECO:0000313|EMBL:AAN68484.1}; OrderedLocusNames=PP_2876 {ECO:0000313|EMBL:AAN68484.1};
organism_full: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB
11950 / KT2440).
protein_family: Belongs to the class-C beta-lactamase family.
protein_domains: AmpC. (IPR058136); AmpC-like. (IPR050491); Beta-lactam-related.
(IPR001466); Beta-lactam/transpept-like. (IPR012338); Beta-lactam_class-C_AS.
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q88IX3
  • Protein Description: RecName: Full=Beta-lactamase {ECO:0000256|ARBA:ARBA00012865, ECO:0000256|RuleBase:RU361140}; EC=3.5.2.6 {ECO:0000256|ARBA:ARBA00012865, ECO:0000256|RuleBase:RU361140};
  • Gene Information: Name=ampC {ECO:0000313|EMBL:AAN68484.1}; OrderedLocusNames=PP_2876 {ECO:0000313|EMBL:AAN68484.1};
  • Organism (full): Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440).
  • Protein Family: Belongs to the class-C beta-lactamase family.
  • Key Domains: AmpC. (IPR058136); AmpC-like. (IPR050491); Beta-lactam-related. (IPR001466); Beta-lactam/transpept-like. (IPR012338); Beta-lactam_class-C_AS. (IPR001586)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ampC" matches the protein description above
  2. Verify the organism is correct: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ampC' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ampC (gene ID: ampC, UniProt: Q88IX3) in PSEPK.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q88IX3
  • Protein Description: RecName: Full=Beta-lactamase {ECO:0000256|ARBA:ARBA00012865, ECO:0000256|RuleBase:RU361140}; EC=3.5.2.6 {ECO:0000256|ARBA:ARBA00012865, ECO:0000256|RuleBase:RU361140};
  • Gene Information: Name=ampC {ECO:0000313|EMBL:AAN68484.1}; OrderedLocusNames=PP_2876 {ECO:0000313|EMBL:AAN68484.1};
  • Organism (full): Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440).
  • Protein Family: Belongs to the class-C beta-lactamase family.
  • Key Domains: AmpC. (IPR058136); AmpC-like. (IPR050491); Beta-lactam-related. (IPR001466); Beta-lactam/transpept-like. (IPR012338); Beta-lactam_class-C_AS. (IPR001586)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ampC" matches the protein description above
  2. Verify the organism is correct: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ampC' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ampC (gene ID: ampC, UniProt: Q88IX3) in PSEPK.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Plan
We verified identity and organism context; collected primary and recent literature on ampC in Pseudomonas putida KT2440 and mechanistic studies from Pseudomonas that resolve regulation and localization; extracted quantitative and functional evidence; and synthesized applications and expert perspectives. We embed a compact evidence table to complement the narrative.

Aspect Key points Species / context Notable data (figures or details) Source (URL, year)
Identity verification Gene symbol ampC corresponding to locus PP_2876; chromosomal AmpC family cephalosporinase Pseudomonas putida KT2440 (primary evidence); broader Pseudomonas spp. context ampC referenced as PP_2876 in KT2440 studies and manipulated by targeted mutagenesis https://doi.org/10.3389/fmicb.2017.00433 (2017) (kim2017indoleinducedactivitiesof pages 1-2)
Enzyme class & catalytic activity Ambler class C beta-lactamase (cephalosporinase) that hydrolyzes the β-lactam ring of penicillins/cephalosporins (group I class C) Mechanistic/functional description from Pseudomonas research Described as chromosomally encoded class C cephalosporinase responsible for hydrolysis of penicillins, cephalosporins, monobactams https://doi.org/10.1128/aac.01688-10 (2011) (zamorano2011ampginactivationrestores pages 1-2); https://doi.org/10.1128/spectrum.02700-22 (2022) (barcelo2022roleofenzymatic pages 11-13)
Substrate specificity Broad β-lactam substrates (penicillins, cephalosporins; inducible by certain cephalosporins like cefoxitin); can affect 3rd-generation cephalosporin susceptibility when overproduced Evidence mainly from P. aeruginosa mechanistic/phenotypic studies; P. putida functional induction shown for ampicillin AmpC hyperproduction confers resistance to penicillins, cephalosporins and monobactams; cefoxitin is a classical inducer in Pseudomonas models https://doi.org/10.1128/msystems.00524-19 (2019) (torrens2019regulationofampcdriven pages 1-2); https://doi.org/10.1128/aac.01688-10 (2011) (zamorano2011ampginactivationrestores pages 1-2)
Cellular localization Periplasmic enzyme encoded with N-terminal signal peptide; matures to ~40 kDa after signal peptide cleavage Demonstrated in Pseudomonas aeruginosa and inferred for P. putida AmpC family members Periplasm-enriched detection with AmpC antibody; size consistent with signal peptide cleavage (~40 kDa) https://doi.org/10.1128/spectrum.02700-22 (2022) (barcelo2022roleofenzymatic pages 11-13)
Regulation / induction mechanisms Regulated by AmpR transcriptional regulator responding to peptidoglycan-derived muropeptides; inner-membrane permease(s) AmpG/AmpP import muropeptides; NagZ and AmpD process signals; environmental cue indole induces ampC in KT2440 Core signaling characterized in P. aeruginosa (mechanistic), direct indole induction shown in P. putida KT2440 Muropeptide activators (e.g., 1,6-anhydro-MurNAc–pentapeptides) activate AmpR → ampC; indole exposure increases ampC expression and β-lactamase activity in KT2440 https://doi.org/10.1128/msystems.00524-19 (2019) (torrens2019regulationofampcdriven pages 1-2), https://doi.org/10.1186/1471-2180-10-328 (2010) (kong2010pseudomonasaeruginosaβlactamase pages 1-2), https://doi.org/10.3389/fmicb.2017.00433 (2017) (kim2017indoleinducedactivitiesof pages 1-2)
Pathway context (peptidoglycan recycling) AmpC induction is coupled to peptidoglycan turnover/recycling: lytic transglycosylases and PBPs (e.g., PBP4/dacB) alter muropeptide pools that control AmpR ligand state Mechanistic data from P. aeruginosa; pathway components conserved across Pseudomonas Changes in muropeptide composition (e.g., anhMurNAc–pentapeptides increase upon cefoxitin or dacB mutation) shift AmpR from repressor to activator state https://doi.org/10.1128/msystems.00524-19 (2019) (torrens2019regulationofampcdriven pages 1-2); mechanistic overview in peptidoglycan turnover (eggers2024insightsintothe pages 23-26)
Applications / real-world relevance Environmental signaling and intrinsic resistance in P. putida; broader clinical relevance in Pseudomonas (AmpC hyperproduction drives β-lactam resistance and is a target for adjuvant strategies) P. putida: indole-mediated inducible resistance relevant in mixed communities; P. aeruginosa: clinical resistance driver and target for intervention Indole in environments can elevate ampC expression in KT2440; in clinical Pseudomonas, targeting AmpC regulatory pathway (e.g., ampG) can restore susceptibility https://doi.org/10.3389/fmicb.2017.00433 (2017) (kim2017indoleinducedactivitiesof pages 1-2); https://doi.org/10.1128/aac.01688-10 (2011) (zamorano2011ampginactivationrestores pages 1-2)
Quantitative data / experimental readouts P. putida KT2440: microarray-based upregulation of ampC (≥2-fold threshold), nitrocefin β-lactamase activity assay, MIC determinations; P. aeruginosa: ampG inactivation produced large MIC reductions (example imipenem 2 → 0.38 µg/mL) P. putida primary assays (transcriptomics, nitrocefin, MIC); P. aeruginosa provides quantitative resistance impacts for regulatory perturbations Microarray threshold used >2-fold up/down; nitrocefin hydrolysis assay described; ampG inactivation in P. aeruginosa lowered imipenem MIC from 2 to 0.38 µg/mL (illustrative of regulatory impact) Methods/data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86617 (microarray, 2017) and https://doi.org/10.1128/aac.01688-10 (2011) (kim2017indoleinducedactivitiesof pages 2-3, zamorano2011ampginactivationrestores pages 1-2)

Table: Compact evidence table summarizing identity, function, localization, regulation, pathway context, applications, and key quantitative readouts for ampC (PP_2876) in Pseudomonas putida KT2440, using primary KT2440 data where available and Pseudomonas mechanistic literature for context.

Comprehensive research report

Key concepts and definitions
- Identity and organism context: The target gene is ampC, encoding a chromosomal class C beta-lactamase (cephalosporinase) in Pseudomonas putida strain KT2440; in KT2440 literature, ampC is annotated at locus PP_2876 and is experimentally manipulated via mutagenesis, confirming symbol–locus correspondence (Frontiers in Microbiology, 2017; URL: https://doi.org/10.3389/fmicb.2017.00433; published March 21, 2017) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- Enzyme class and catalytic activity: AmpC belongs to Ambler class C beta-lactamases (EC 3.5.2.6) that hydrolyze the beta-lactam ring of penicillins and cephalosporins; it is typically chromosomal and inducible in Pseudomonas spp. (Antimicrobial Agents and Chemotherapy, 2011; URL: https://doi.org/10.1128/AAC.01688-10; May 2011) (zamorano2011ampginactivationrestores pages 1-2). Mechanistic work further links AmpC activity to phenotypic costs when hyperproduced (Microbiology Spectrum, 2022; URL: https://doi.org/10.1128/spectrum.02700-22; October 2022) (barcelo2022roleofenzymatic pages 11-13).
- Pathway and regulation overview: AmpC expression is controlled by the LysR-type regulator AmpR sensing cytosolic muropeptides imported by inner-membrane permeases (AmpG and, in P. aeruginosa, AmpP). Muropeptide processing enzymes NagZ and AmpD shape the signal pool. Specific muropeptide ligands switch AmpR between repressor and activator states, mediating induction by beta-lactams (mSystems, 2019; URL: https://doi.org/10.1128/mSystems.00524-19; December 2019) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3). In Pseudomonas, two permeases contribute to maximal induction (BMC Microbiology, 2010; URL: https://doi.org/10.1186/1471-2180-10-328; December 2010) (kong2010pseudomonasaeruginosaβlactamase pages 1-2).

Recent developments and latest research (prioritizing 2023–2024 where available)
- Updated regulatory signaling by defined muropeptides: High-resolution analyses in P. aeruginosa resolved the identity and potency hierarchy of peptidoglycan-derived AmpR ligands, showing that 1,6-anhydro-MurNAc-pentapeptides strongly activate AmpR, whereas UDP-MurNAc-pentapeptide acts as a repressor. These signals explain transient (cefoxitin) versus stable (dacB/PBP4) AmpC hyperproduction and provide a quantitative framework for inducible resistance across Pseudomonas (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).
- Peptidoglycan turnover enablers of AmpC induction: Recent syntheses emphasize roles for periplasmic lytic transglycosylases and amidases in generating muropeptide pools that drive ampC expression, linking cell wall remodeling to resistance phenotypes (doctoral thesis, 2024; URL: https://doi.org/10.15496/publikation-99680; October 2024) (eggers2024insightsintothe pages 23-26).
- Fitness/virulence costs of AmpC activity: Experimental dissection in P. aeruginosa shows that the enzymatic activity of AmpC contributes directly to virulence attenuation under certain recycling defects, while overproduction imposes energy burdens; this informs the anticipated physiological impact of AmpC modulation in related Pseudomonas (Microbiology Spectrum, 2022; URL as above) (barcelo2022roleofenzymatic pages 11-13).

Primary function and substrate specificity
- Catalytic reaction: Hydrolysis of beta-lactam bonds in penicillins, cephalosporins, and monobactams is the signature activity of class C enzymes, conferring resistance when produced at elevated levels (AAC, 2011; URL as above) (zamorano2011ampginactivationrestores pages 1-2).
- Substrate and inducer profile in Pseudomonas: In P. aeruginosa models, AmpC hyperproduction reduces susceptibility to antipseudomonal penicillins (e.g., piperacillin), cephalosporins (ceftazidime, cefepime), and aztreonam; certain cephalosporins (e.g., cefoxitin) act as strong inducers via muropeptide signaling (AAC 2011; mSystems 2019; URLs above) (zamorano2011ampginactivationrestores pages 1-2, torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3). In P. putida KT2440 specifically, ampicillin resistance increases with indole via ampC induction, implicating AmpC in penicillin hydrolysis in this species (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).

Cellular localization
- AmpC is synthesized with an N-terminal signal peptide, exported across the inner membrane, and localized to the periplasm where it can intercept incoming beta-lactams; maturation yields a protein of ~40 kDa after signal peptide cleavage. Periplasmic localization has been demonstrated with AmpC-specific antibodies in Pseudomonas (Microbiology Spectrum, 2022; URL as above) (barcelo2022roleofenzymatic pages 11-13).

Regulation, induction, and environmental cues
- AmpR–muropeptide control: ampR and ampC form a divergent operon; cytosolic UDP-MurNAc-pentapeptide represses, while 1,6-anhydro-MurNAc–peptides (notably pentapeptides) activate AmpR, switching on ampC. Perturbations such as cefoxitin exposure or loss of PBP4 (dacB) increase activating ligand levels and drive hyperproduction (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).
- Transport and processing: Inner-membrane permease AmpG (and AmpP in P. aeruginosa) mediates import of GlcNAc-anhMurNAc–peptides; periplasmic/cytosolic processing by NagZ and AmpD tunes the ligand pool. Disruption of ampG abrogates induction and restores susceptibility in Pseudomonas models (BMC Microbiology, 2010; AAC, 2011; URLs above) (kong2010pseudomonasaeruginosaβlactamase pages 1-2, zamorano2011ampginactivationrestores pages 1-2).
- Environmental indole in KT2440: Exogenous indole elevates ampC expression and beta-lactamase activity and increases the proportion of ampicillin-resistant P. putida KT2440 cells; it also upregulates RND efflux operons. These effects were supported by transcriptomics, enzyme assays (nitrocefin hydrolysis), and mutant analyses (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).

Biochemical pathway context
- AmpC induction is mechanistically tied to peptidoglycan recycling: periplasmic lytic enzymes generate muropeptides; transporters import them; cytosolic hydrolases process them; and AmpR senses them to regulate ampC. Quantitative analyses show that activator muropeptides increase with inducer beta-lactams or PBP4 loss, explaining stable versus transient hyperproduction (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3). Additional mechanistic synthesis highlights that multiple lytic transglycosylases and amidases modulate the muropeptide pool and thus ampC expression (2024 thesis; URL as above) (eggers2024insightsintothe pages 23-26).

Current applications and real-world implementations
- Environmental biotechnology and mixed communities: In KT2440, indole—a common microbial community metabolite—induces ampC and efflux, elevating ampicillin resistance. This has practical implications for community-based bioprocesses using P. putida, where environmental signals may transiently modulate beta-lactam susceptibility and selection dynamics (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- Therapeutic context from Pseudomonas: In P. aeruginosa, genetic inactivation of ampG restored susceptibility of pan–beta-lactam-resistant clinical strains, pointing to the AmpC regulatory pathway (transport and recycling) as a target for adjuvant strategies to resensitize bacteria (AAC, 2011; URL as above) (zamorano2011ampginactivationrestores pages 1-2). Understanding muropeptide signaling has guided expert models for predicting and preventing AmpC hyperproduction during therapy (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).

Expert opinions and analysis from authoritative sources
- Mechanistic framework: Oliver, Juan, and colleagues provide an authoritative, experimentally grounded model in Pseudomonas that AmpC-driven resistance is dominated by muropeptide activators with a clear potency hierarchy, offering actionable regulatory nodes (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).
- Regulatory transporters as intervention points: Mathee and co-workers demonstrate the requirement of two permeases for maximal induction in P. aeruginosa, underscoring transporter-mediated control as a strategic lever (BMC Microbiology, 2010; URL as above) (kong2010pseudomonasaeruginosaβlactamase pages 1-2). Oliver’s group further shows that targeting AmpG restores susceptibility in resistant strains (AAC, 2011; URL as above) (zamorano2011ampginactivationrestores pages 1-2).
- Physiological tradeoffs: Recent experimental work indicates that AmpC enzymatic activity per se contributes to virulence attenuation in Pseudomonas, suggesting antivirulence angles but also warning that variant selection may not be constrained by high biological cost (Microbiology Spectrum, 2022; URL as above) (barcelo2022roleofenzymatic pages 11-13).

Relevant statistics and quantitative data
- In KT2440, indole exposure increased ampC transcript levels by microarray threshold (>2-fold) and raised beta-lactamase activity measured by nitrocefin hydrolysis; indole also increased the proportion of ampicillin-resistant cells (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- In Pseudomonas aeruginosa clinical contexts, inactivation of ampG yielded large MIC reductions across multiple beta-lactams; for example, imipenem MIC decreased from 2 to 0.38 µg/mL in a representative background and from >32 to 0.5 µg/mL in an OprD-deficient mutant, with concomitant improvements for ceftazidime, piperacillin-tazobactam, meropenem, cefepime, and aztreonam (AAC, 2011; URL as above) (zamorano2011ampginactivationrestores pages 1-2).
- Muropeptide profiling shows that anhMurNAc-pentapeptide, normally ~1% of cytosolic muropeptides, increases by ~10-fold upon cefoxitin induction or dacB mutation, correlating with AmpC hyperexpression (mSystems, 2019; URL as above) (torrens2019regulationofampcdriven pages 2-3).

Conclusions
- Verification: The gene symbol ampC aligns with P. putida KT2440 locus PP_2876 and with UniProt Q88IX3; studies in KT2440 explicitly reference ampC (PP_2876), validating identity and organism (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- Function: AmpC is a periplasmic class C beta-lactamase that hydrolyzes penicillins and cephalosporins and is inducible via AmpR–muropeptide signaling, with transport and processing (AmpG/AmpP/NagZ/AmpD) coupling induction to peptidoglycan recycling (AAC 2011; BMC Microbiology 2010; mSystems 2019; URLs above) (zamorano2011ampginactivationrestores pages 1-2, kong2010pseudomonasaeruginosaβlactamase pages 1-2, torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).
- KT2440-specific regulation: Indole acts as an environmental cue in KT2440 that increases ampC expression and beta-lactamase activity while boosting efflux, yielding higher ampicillin resistance—direct primary evidence for this strain (Frontiers in Microbiology, 2017; URL as above) (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- Applications: In environmental and biotechnological settings employing KT2440, extracellular metabolites like indole may transiently elevate beta-lactam resistance via ampC and efflux; in medical contexts (extrapolating from Pseudomonas), targeting peptidoglycan recycling and transport can resensitize to beta-lactams (AAC 2011; mSystems 2019; URLs above) (zamorano2011ampginactivationrestores pages 1-2, torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).

References (with URLs and publication dates)
- Kim J, et al. Indole-Induced Activities of β-Lactamase and Efflux Pump Confer Ampicillin Resistance in Pseudomonas putida KT2440. Frontiers in Microbiology. Published March 21, 2017. URL: https://doi.org/10.3389/fmicb.2017.00433 (kim2017indoleinducedactivitiesof pages 1-2, kim2017indoleinducedactivitiesof pages 2-3).
- Zamorano L, et al. AmpG Inactivation Restores Susceptibility of Pan-β-Lactam-Resistant Pseudomonas aeruginosa Clinical Strains. Antimicrobial Agents and Chemotherapy. Published May 2011. URL: https://doi.org/10.1128/AAC.01688-10 (zamorano2011ampginactivationrestores pages 1-2).
- Torrens G, et al. Regulation of AmpC-Driven β-Lactam Resistance in Pseudomonas aeruginosa: Different Pathways, Different Signaling. mSystems. Published December 2019. URL: https://doi.org/10.1128/mSystems.00524-19 (torrens2019regulationofampcdriven pages 1-2, torrens2019regulationofampcdriven pages 2-3).
- Kong K-F, et al. Pseudomonas aeruginosa β-lactamase induction requires two permeases, AmpG and AmpP. BMC Microbiology. Published December 2010. URL: https://doi.org/10.1186/1471-2180-10-328 (kong2010pseudomonasaeruginosaβlactamase pages 1-2).
- Barceló IM, et al. Role of Enzymatic Activity in the Biological Cost Associated with the Production of AmpC β-Lactamases in Pseudomonas aeruginosa. Microbiology Spectrum. Published October 2022. URL: https://doi.org/10.1128/spectrum.02700-22 (barcelo2022roleofenzymatic pages 11-13).
- Eggers OHH. Insights into the Role of YgfB in β-Lactam Resistance and Beyond. Doctoral thesis, Universität Tübingen. Published October 2024. URL: https://doi.org/10.15496/publikation-99680 (eggers2024insightsintothe pages 23-26).

References

  1. (kim2017indoleinducedactivitiesof pages 1-2): Jisun Kim, Bora Shin, Chulwoo Park, and Woojun Park. Indole-induced activities of β-lactamase and efflux pump confer ampicillin resistance in pseudomonas putida kt2440. Frontiers in Microbiology, Mar 2017. URL: https://doi.org/10.3389/fmicb.2017.00433, doi:10.3389/fmicb.2017.00433. This article has 35 citations and is from a poor quality or predatory journal.

  2. (zamorano2011ampginactivationrestores pages 1-2): Laura Zamorano, Thomas M. Reeve, Carlos Juan, Bartolomé Moyá, Gabriel Cabot, David J. Vocadlo, Brian L. Mark, and Antonio Oliver. Ampg inactivation restores susceptibility of pan-β-lactam-resistant pseudomonas aeruginosa clinical strains. Antimicrobial Agents and Chemotherapy, 55:1990-1996, May 2011. URL: https://doi.org/10.1128/aac.01688-10, doi:10.1128/aac.01688-10. This article has 85 citations and is from a highest quality peer-reviewed journal.

  3. (barcelo2022roleofenzymatic pages 11-13): Isabel M. Barceló, Elena Jordana-Lluch, María Escobar-Salom, Gabriel Torrens, Pablo A. Fraile-Ribot, Gabriel Cabot, Xavier Mulet, Laura Zamorano, Carlos Juan, and Antonio Oliver. Role of enzymatic activity in the biological cost associated with the production of ampc β-lactamases in pseudomonas aeruginosa. Microbiology Spectrum, Oct 2022. URL: https://doi.org/10.1128/spectrum.02700-22, doi:10.1128/spectrum.02700-22. This article has 20 citations and is from a domain leading peer-reviewed journal.

  4. (torrens2019regulationofampcdriven pages 1-2): Gabriel Torrens, Sara Belén Hernández, Juan Alfonso Ayala, Bartolome Moya, Carlos Juan, Felipe Cava, and Antonio Oliver. Regulation of ampc-driven β-lactam resistance in pseudomonas aeruginosa: different pathways, different signaling. mSystems, Dec 2019. URL: https://doi.org/10.1128/msystems.00524-19, doi:10.1128/msystems.00524-19. This article has 94 citations and is from a peer-reviewed journal.

  5. (kong2010pseudomonasaeruginosaβlactamase pages 1-2): Kok-Fai Kong, Alian Aguila, Lisa Schneper, and Kalai Mathee. Pseudomonas aeruginosa β-lactamase induction requires two permeases, ampg and ampp. BMC Microbiology, 10:328-328, Dec 2010. URL: https://doi.org/10.1186/1471-2180-10-328, doi:10.1186/1471-2180-10-328. This article has 66 citations and is from a peer-reviewed journal.

  6. (eggers2024insightsintothe pages 23-26): Ole Hans Heiner Eggers. Insights into the role of ygfb in β-lactam resistance and beyond. Unknown, Oct 2024. URL: https://doi.org/10.15496/publikation-99680, doi:10.15496/publikation-99680. This article has 0 citations.

  7. (kim2017indoleinducedactivitiesof pages 2-3): Jisun Kim, Bora Shin, Chulwoo Park, and Woojun Park. Indole-induced activities of β-lactamase and efflux pump confer ampicillin resistance in pseudomonas putida kt2440. Frontiers in Microbiology, Mar 2017. URL: https://doi.org/10.3389/fmicb.2017.00433, doi:10.3389/fmicb.2017.00433. This article has 35 citations and is from a poor quality or predatory journal.

  8. (torrens2019regulationofampcdriven pages 2-3): Gabriel Torrens, Sara Belén Hernández, Juan Alfonso Ayala, Bartolome Moya, Carlos Juan, Felipe Cava, and Antonio Oliver. Regulation of ampc-driven β-lactam resistance in pseudomonas aeruginosa: different pathways, different signaling. mSystems, Dec 2019. URL: https://doi.org/10.1128/msystems.00524-19, doi:10.1128/msystems.00524-19. This article has 94 citations and is from a peer-reviewed journal.

Citations

  1. kim2017indoleinducedactivitiesof pages 1-2
  2. zamorano2011ampginactivationrestores pages 1-2
  3. barcelo2022roleofenzymatic pages 11-13
  4. torrens2019regulationofampcdriven pages 1-2
  5. eggers2024insightsintothe pages 23-26
  6. torrens2019regulationofampcdriven pages 2-3
  7. kim2017indoleinducedactivitiesof pages 2-3
  8. https://doi.org/10.3389/fmicb.2017.00433
  9. https://doi.org/10.1128/aac.01688-10
  10. https://doi.org/10.1128/spectrum.02700-22
  11. https://doi.org/10.1128/msystems.00524-19
  12. https://doi.org/10.1186/1471-2180-10-328
  13. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86617
  14. https://doi.org/10.3389/fmicb.2017.00433;
  15. https://doi.org/10.1128/AAC.01688-10;
  16. https://doi.org/10.1128/spectrum.02700-22;
  17. https://doi.org/10.1128/mSystems.00524-19;
  18. https://doi.org/10.1186/1471-2180-10-328;
  19. https://doi.org/10.15496/publikation-99680;
  20. https://doi.org/10.1128/AAC.01688-10
  21. https://doi.org/10.1128/mSystems.00524-19
  22. https://doi.org/10.15496/publikation-99680
  23. https://doi.org/10.3389/fmicb.2017.00433,
  24. https://doi.org/10.1128/aac.01688-10,
  25. https://doi.org/10.1128/spectrum.02700-22,
  26. https://doi.org/10.1128/msystems.00524-19,
  27. https://doi.org/10.1186/1471-2180-10-328,
  28. https://doi.org/10.15496/publikation-99680,

📄 View Raw YAML

id: Q88IX3
gene_symbol: ampC
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
    / KT2440)
description: >-
  AmpC is a chromosomally encoded class C beta-lactamase (cephalosporinase) that
  hydrolyzes the beta-lactam ring of penicillins and cephalosporins. It is localized
  to the periplasm after signal peptide cleavage (~40 kDa mature form). AmpC expression
  is regulated by the LysR-type transcriptional regulator AmpR, which responds to
  muropeptide signals imported via AmpG permease. Environmental cues such as indole
  can induce ampC expression in P. putida KT2440, increasing beta-lactam resistance.
  The enzyme directly confers antibiotic resistance by hydrolyzing beta-lactam antibiotics
  before they reach their targets (penicillin-binding proteins).
existing_annotations:
- term:
    id: GO:0008800
    label: beta-lactamase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      AmpC is definitively a class C beta-lactamase (EC 3.5.2.6) that catalyzes
      the hydrolysis of beta-lactam antibiotics. This is the core molecular function
      of the protein. UniProt confirms EC=3.5.2.6 and the catalytic activity. The deep
      research confirms AmpC belongs to Ambler class C beta-lactamases that hydrolyze
      penicillins and cephalosporins.
    action: ACCEPT
    reason: >-
      This is the primary enzymatic function of AmpC. UniProt annotation, InterPro
      domain analysis (IPR058136 AmpC, IPR001586 Beta-lactam_class-C_AS), and
      literature all confirm this enzyme catalyzes beta-lactam hydrolysis. This term
      correctly represents the core molecular function.
    supported_by:
      - reference_id: file:PSEPK/ampC/ampC-deep-research-falcon.md
        supporting_text: "AmpC belongs to Ambler class C beta-lactamases (EC 3.5.2.6) that hydrolyze the beta-lactam ring of penicillins and cephalosporins"

- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      This is a parent term of GO:0008800 (beta-lactamase activity). While technically
      correct that AmpC has hydrolase activity, this annotation is redundant given
      the more specific beta-lactamase activity annotation. UniProt keyword mapping
      correctly identifies the hydrolase nature, but the more specific child term
      provides greater biological insight.
    action: ACCEPT
    reason: >-
      This term is accurate but generic. AmpC is indeed a hydrolase - specifically
      hydrolyzing the amide bond in the beta-lactam ring. The UniProt entry includes
      the Hydrolase keyword. While GO:0008800 (beta-lactamase activity) is more
      informative, retaining this broader annotation provides correct categorization
      and is acceptable as a parent term annotation from IEA evidence.

- term:
    id: GO:0017001
    label: antibiotic catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      This term captures the biological process of AmpC - catabolism of antibiotics.
      However, GO:0030655 (beta-lactam antibiotic catabolic process) is a more specific
      child term that accurately reflects AmpC's substrate specificity. AmpC specifically
      catabolizes beta-lactam antibiotics (penicillins, cephalosporins, monobactams),
      not antibiotics in general.
    action: MODIFY
    reason: >-
      While AmpC does participate in antibiotic catabolism, it specifically catabolizes
      beta-lactam antibiotics. The more specific term GO:0030655 beta-lactam antibiotic
      catabolic process (defined as chemical reactions and pathways resulting in
      the breakdown of a beta-lactam antibiotic) precisely describes AmpC's biological
      process. Literature confirms substrate specificity for penicillins and cephalosporins.
    proposed_replacement_terms:
      - id: GO:0030655
        label: beta-lactam antibiotic catabolic process
    supported_by:
      - reference_id: file:PSEPK/ampC/ampC-deep-research-falcon.md
        supporting_text: "Hydrolysis of beta-lactam bonds in penicillins, cephalosporins, and monobactams is the signature activity of class C enzymes, conferring resistance when produced at elevated levels"

- term:
    id: GO:0030288
    label: outer membrane-bounded periplasmic space
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Periplasmic localization is well-supported for AmpC. UniProt shows a signal
      peptide (residues 1-24) indicating secretion across the inner membrane.
      Deep research confirms AmpC is synthesized with an N-terminal signal peptide
      and localizes to the periplasm where it intercepts incoming beta-lactams,
      with mature protein size ~40 kDa after signal peptide cleavage.
    action: ACCEPT
    reason: >-
      This cellular component annotation is correct. AmpC functions in the periplasm
      where it can hydrolyze beta-lactam antibiotics before they reach their
      targets (penicillin-binding proteins on the inner membrane). The signal
      peptide and periplasmic localization are essential for the resistance
      mechanism. This represents a core aspect of AmpC function.
    supported_by:
      - reference_id: file:PSEPK/ampC/ampC-deep-research-falcon.md
        supporting_text: "AmpC is synthesized with an N-terminal signal peptide, exported across the inner membrane, and localized to the periplasm where it can intercept incoming beta-lactams; maturation yields a protein of ~40 kDa after signal peptide cleavage"

- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      This annotation captures AmpC's role in the organism's response to antibiotics.
      AmpC expression is induced by beta-lactam antibiotics and environmental signals
      (like indole), and its activity directly confers resistance. This term captures
      the broader biological context of response to antibiotic stress, including the
      regulatory induction. While GO:0030655 more precisely describes the enzymatic
      function, this term appropriately captures the response/resistance phenotype.
    action: ACCEPT
    reason: >-
      This annotation is legitimate for a beta-lactamase. AmpC expression is induced
      by beta-lactam antibiotics through the AmpR-muropeptide signaling pathway, and
      indole also induces ampC expression in P. putida KT2440. The enzyme directly
      responds to antibiotic exposure by increasing expression and activity. Retaining
      both GO:0030655 and this term provides complementary perspectives - one on the
      catabolic process and one on the response/resistance phenotype.
    supported_by:
      - reference_id: file:PSEPK/ampC/ampC-deep-research-falcon.md
        supporting_text: "Exogenous indole elevates ampC expression and beta-lactamase activity and increases the proportion of ampicillin-resistant P. putida KT2440 cells"

references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []

- 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: file:PSEPK/ampC/ampC-deep-research-falcon.md
  title: "Deep research on ampC in Pseudomonas putida KT2440"
  findings:
    - statement: AmpC is a class C beta-lactamase that hydrolyzes penicillins and cephalosporins
      supporting_text: "AmpC belongs to Ambler class C beta-lactamases (EC 3.5.2.6) that hydrolyze the beta-lactam ring of penicillins and cephalosporins"
    - statement: AmpC is localized to the periplasm
      supporting_text: "AmpC is synthesized with an N-terminal signal peptide, exported across the inner membrane, and localized to the periplasm where it can intercept incoming beta-lactams"
    - statement: AmpC expression is induced by indole in P. putida KT2440
      supporting_text: "Exogenous indole elevates ampC expression and beta-lactamase activity and increases the proportion of ampicillin-resistant P. putida KT2440 cells"
    - statement: AmpC confers resistance to beta-lactam antibiotics
      supporting_text: "Hydrolysis of beta-lactam bonds in penicillins, cephalosporins, and monobactams is the signature activity of class C enzymes, conferring resistance when produced at elevated levels"

core_functions:
  - molecular_function:
      id: GO:0008800
      label: beta-lactamase activity
    directly_involved_in:
      - id: GO:0030655
        label: beta-lactam antibiotic catabolic process
    locations:
      - id: GO:0030288
        label: outer membrane-bounded periplasmic space
    description: >-
      AmpC is the primary beta-lactamase in P. putida KT2440. It hydrolyzes the
      beta-lactam ring in penicillins and cephalosporins in the periplasm,
      converting these antibiotics to inactive substituted beta-amino acids.
      This activity is the mechanistic basis for intrinsic and inducible
      beta-lactam resistance in this organism.