id: O69652
gene_symbol: cds1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:83332
  label: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
description: >-
  Cds1 (Rv3684) is an L-cysteine desulfhydrase (EC 4.4.1.1) that catalyzes the
  PLP-dependent beta-elimination of L-cysteine to produce hydrogen sulfide (H2S),
  pyruvate, and ammonia. It is a major source of endogenous H2S in M. tuberculosis.
  The H2S produced stimulates respiration primarily via cytochrome bd, modulates
  the balance between oxidative phosphorylation and glycolysis, contributes to
  redox homeostasis by affecting ergothioneine (EGT) and mycothiol (MSH) levels,
  and influences drug susceptibility. The enzyme likely also functions to eliminate
  toxic levels of cysteine. Kinetic parameters: KM = 11.26 mM for cysteine,
  kcat = 78.71 sec(-1). Activity is inhibited by aminooxyacetic acid (AOAA),
  a PLP inhibitor, but NOT by DL-propargylglycine (PAG), a cystathionine gamma-lyase
  inhibitor, confirming its identity as a cysteine desulfhydrase rather than a
  cystathionine gamma-lyase. Part of the Rv3682-Rv3683-cds1 operon.
existing_annotations:
- term:
    id: GO:0019344
    label: L-cysteine biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      This annotation is INCORRECT. Cds1 is an L-cysteine desulfhydrase that
      catalyzes L-cysteine CATABOLISM, not biosynthesis. The enzyme degrades
      cysteine to produce H2S, pyruvate, and ammonia (PMID:34439535). The IBA
      annotation derives from GO:0019344 being annotated at the root node
      (PTN000034104) of PANTHER family PTHR10314 and propagated to all descendants,
      including subfamily SF135 (Cds1) which has the opposite function.
    action: REMOVE
    reason: >-
      IBA propagation error from PANTHER family PTHR10314. GO:0019344 is annotated
      at the root node but SF135 (Cds1 subfamily) underwent neo-functionalization:
      (1) Active site motif differs: SF135 has ASSGST vs PTSGNTG in synthases;
      (2) Only 24% sequence identity with cysteine synthases (vs 43% between CysK/CysM);
      (3) Longest branch length (0.528) from root indicates greatest divergence;
      (4) Different EC: 4.4.1.1 (desulfhydrase) vs 2.5.1.47 (synthase);
      (5) Opposite reaction: L-cysteine → H2S + pyruvate (catabolism), not biosynthesis.
      See family analysis: interpro/panther/PTHR10314/PTHR10314-notes.md
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
    - reference_id: file:MYCTU/cds1/cds1-deep-research-falcon.md
      supporting_text: "Cds1 is a PLP-dependent L-cysteine desulfhydrase that produces H2S, pyruvate, and ammonia from L-cysteine"
    - reference_id: file:interpro/panther/PTHR10314/PTHR10314-notes.md
      supporting_text: "SF135 (Cds1) has a distinct active site signature motif (ASSGST) vs synthases (PTSGNTG); SF135 shares only ~24% identity with synthases; longest branch length (0.528) indicates neo-functionalization"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Cytoplasmic localization is consistent with what is expected for this
      PLP-dependent metabolic enzyme. UniProt assigns cytoplasm localization
      based on sequence features and family membership. The more specific
      annotation to cytosol (GO:0005829) is also present with HDA evidence
      from PMID:15525680.
    action: ACCEPT
    reason: >-
      Cytoplasmic localization is appropriate for this soluble PLP-dependent
      enzyme. There is no signal peptide or transmembrane domain. Consistent
      with HDA evidence from subcellular proteomics (PMID:15525680) showing
      cytosolic localization.
    supported_by:
    - reference_id: PMID:15525680
      supporting_text: "We report the identifications of 1044 proteins and their corresponding localizations in these compartments"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      This IEA annotation is redundant with the IBA annotation above but is
      acceptable. Cytoplasmic localization is correct based on the protein's
      properties as a soluble metabolic enzyme.
    action: ACCEPT
    reason: >-
      Cytoplasmic localization is appropriate and consistent with experimental
      HDA evidence from subcellular proteomics.
- term:
    id: GO:0016829
    label: lyase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Lyase activity is correct but very general. Cds1 is indeed a lyase (carbon-sulfur
      lyase) that catalyzes a beta-elimination reaction. However, there is a much more
      specific and informative term available: GO:0080146 (L-cysteine desulfhydrase
      activity).
    action: MODIFY
    reason: >-
      While technically correct, this term is too general. The specific molecular
      function term GO:0080146 (L-cysteine desulfhydrase activity) should be used
      instead, which precisely describes the catalyzed reaction: L-cysteine + H2O =
      ammonia + pyruvate + hydrogen sulfide + H(+). This is experimentally demonstrated
      in PMID:34439535.
    proposed_replacement_terms:
    - id: GO:0080146
      label: L-cysteine desulfhydrase activity
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
- term:
    id: GO:0019450
    label: obsolete L-cysteine catabolic process to pyruvate
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      This annotation is correct and represents a core function of Cds1. The enzyme
      catalyzes the conversion of L-cysteine to pyruvate (plus H2S and ammonia).
      This is supported by IDA evidence from PMID:34439535 (see separate entry).
    action: ACCEPT
    reason: >-
      Experimentally validated by PMID:34439535. Products were identified by LC-MS/MS
      confirming pyruvate as a product of the cysteine desulfhydrase reaction.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
- term:
    id: GO:0030170
    label: pyridoxal phosphate binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: >-
      PLP binding is correct. Cds1 contains a PLP-binding site at Lys67 and belongs
      to the TrpB-like PALP fold family. PLP-dependence is experimentally confirmed
      in PMID:34439535 through inhibition by AOAA.
    action: ACCEPT
    reason: >-
      PLP-dependence is experimentally confirmed. PMID:34439535 shows that activity
      is inhibited by aminooxyacetic acid (AOAA), a PLP inhibitor. UniProt annotates
      the PLP-binding lysine at position 67.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source."
- term:
    id: GO:1901605
    label: alpha-amino acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      This annotation is correct but very general. Cds1 does participate in amino
      acid metabolism by catabolizing L-cysteine. The more specific term GO:0019450
      (L-cysteine catabolic process to pyruvate) is preferred and already annotated.
    action: ACCEPT
    reason: >-
      Technically correct as a parent term of the more specific cysteine catabolic
      process. Acceptable as a broader IEA annotation alongside the more specific terms.
- term:
    id: GO:0019450
    label: obsolete L-cysteine catabolic process to pyruvate
  evidence_type: IDA
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This IDA annotation is well-supported by experimental evidence. Kunota et al.
      (2021) used LC-MS/MS to identify the products of the Cds1-catalyzed reaction
      and confirmed pyruvate as a major product. This is a core function annotation.
    action: ACCEPT
    reason: >-
      Directly demonstrated by enzymatic product identification using LC-MS/MS
      in PMID:34439535. Pyruvate is one of the three products of the L-cysteine
      desulfhydrase reaction (along with H2S and ammonia).
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
- term:
    id: GO:0030170
    label: pyridoxal phosphate binding
  evidence_type: IDA
  original_reference_id: PMID:34439535
  review:
    summary: >-
      PLP binding is experimentally demonstrated through inhibitor studies.
      AOAA (aminooxyacetic acid), a PLP inhibitor, blocks activity, while PAG
      (DL-propargylglycine), which specifically inhibits cystathionine gamma-lyase,
      does not affect activity.
    action: ACCEPT
    reason: >-
      Inhibition by AOAA (a PLP-dependent enzyme inhibitor) but not PAG demonstrates
      PLP-dependence of the enzyme activity. This is supported by the presence of
      the PALP domain (PF00291) and TrpB-like PLP fold.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source."
- term:
    id: GO:0042762
    label: regulation of sulfur metabolic process
  evidence_type: IMP
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This annotation reflects the role of Cds1-generated H2S in recycling sulfur
      back to cysteine. The delta-cds1 mutant shows altered sulfur metabolism. H2S
      functions as a sink to recycle sulfur atoms back to cysteine to maintain
      sulfur homeostasis.
    action: ACCEPT
    reason: >-
      PMID:34439535 demonstrates that H2S produced by Cds1 functions as a sink
      to recycle sulfur atoms back to cysteine, thereby regulating sulfur
      homeostasis in Mtb.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Importantly, H2S plays a key role in central metabolism by modulating the balance between oxidative phosphorylation and glycolysis, and it functions as a sink to recycle sulfur atoms back to cysteine to maintain sulfur homeostasis"
- term:
    id: GO:0045454
    label: cell redox homeostasis
  evidence_type: IMP
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This annotation is supported by mutant phenotype data. The delta-cds1 mutant
      shows decreased levels of the redox couples ergothioneine (EGT) and mycothiol
      (MSH). H2S modulates redox homeostasis and can function as either a pro-oxidant
      or antioxidant depending on conditions.
    action: KEEP_AS_NON_CORE
    reason: >-
      While the role in redox homeostasis is experimentally demonstrated, this is
      a downstream physiological effect of H2S production rather than the primary
      enzymatic function. The core function is cysteine catabolism/H2S production;
      redox regulation is a consequence.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Lastly, our data demonstrate that Cds1-generated H2S modulates the levels of the major redox couples, EGT and MSH."
- term:
    id: GO:0070814
    label: hydrogen sulfide biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This is a core function annotation. Cds1 is identified as the major
      H2S-producing enzyme in Mtb. H2S production was measured using multiple
      methods (lead acetate assay, BiCl3 assay, amperometric microsensor) and
      delta-cds1 significantly reduces but does not eliminate H2S production.
    action: ACCEPT
    reason: >-
      Directly demonstrated by multiple assays. "We identified Rv3684 (Cds1) as
      an H2S-producing enzyme in Mtb and show that cds1 disruption reduces, but
      does not eliminate, H2S production." H2S production is a primary output
      of the cysteine desulfhydrase reaction.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "We identified Rv3684 (Cds1) as an H2S-producing enzyme in Mtb and show that cds1 disruption reduces, but does not eliminate, H2S production, suggesting the involvement of multiple genes in H2S production"
    - reference_id: PMID:34439535
      supporting_text: "maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd"
- term:
    id: GO:1901857
    label: positive regulation of cellular respiration
  evidence_type: IMP
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This annotation reflects the downstream physiological effect of H2S production.
      The delta-cds1 mutant shows 40% reduction in basal oxygen consumption rate. H2S
      stimulates respiration primarily via cytochrome bd.
    action: KEEP_AS_NON_CORE
    reason: >-
      While experimentally demonstrated, this represents a downstream effect of
      H2S production rather than the primary enzymatic function. The connection
      is: Cds1 -> H2S production -> stimulation of respiration via cytochrome bd.
      This is a physiological effect rather than core function.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd"
    - reference_id: PMID:34439535
      supporting_text: "Importantly, H2S plays a key role in central metabolism by modulating the balance between oxidative phosphorylation and glycolysis, and it functions as a sink to recycle sulfur atoms back to cysteine to maintain sulfur homeostasis"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: HDA
  original_reference_id: PMID:15525680
  review:
    summary: >-
      Cytosolic localization identified by global subcellular proteomics profiling
      of M. tuberculosis. This is more specific than cytoplasm and is appropriate
      for this soluble PLP-dependent enzyme.
    action: ACCEPT
    reason: >-
      High-throughput subcellular proteomics study identified Cds1 in the cytosol
      fraction. Consistent with the protein being a soluble metabolic enzyme
      without signal peptide or transmembrane domains.
    supported_by:
    - reference_id: PMID:15525680
      supporting_text: "We report the identifications of 1044 proteins and their corresponding localizations in these compartments"
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: HDA
  original_reference_id: PMID:14532352
  review:
    summary: >-
      Detected in membrane proteomics study. This may represent peripheral
      membrane association or contamination from the abundant cytosolic pool.
      The protein lacks transmembrane domains or known membrane-anchoring motifs.
    action: KEEP_AS_NON_CORE
    reason: >-
      While detected in membrane fraction by proteomics, this is likely peripheral
      association or contamination given the protein's characteristics. The
      primary localization is cytosolic. The HDA evidence from a membrane proteomics
      study should be retained but not considered as representing core localization.
    additional_reference_ids:
    - PMID:15525680
    supported_by:
    - reference_id: PMID:14532352
      supporting_text: "739 proteins have been identified by two or more distinct peptide sequences and have been characterized"
# NEW annotation - L-cysteine desulfhydrase activity
- term:
    id: GO:0080146
    label: L-cysteine desulfhydrase activity
  evidence_type: IDA
  original_reference_id: PMID:34439535
  review:
    summary: >-
      This is the primary molecular function of Cds1 and should be annotated.
      GO:0080146 describes the catalysis of: L-cysteine + H2O = ammonia + pyruvate +
      hydrogen sulfide + H(+). This is exactly the reaction catalyzed by Cds1 as
      demonstrated by product identification via LC-MS/MS. Kinetic parameters:
      KM = 11.26 mM for cysteine, kcat = 78.71 sec(-1).
    action: NEW
    reason: >-
      The existing annotations lack the specific molecular function term for this
      enzyme. GO:0080146 (L-cysteine desulfhydrase activity) precisely describes
      the catalyzed reaction. This is the most informative MF term for this enzyme
      and should be the primary molecular function annotation.
    supported_by:
    - reference_id: PMID:34439535
      supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
    - reference_id: PMID:34439535
      supporting_text: "We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source."
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: Phylogenetic inference led to incorrect assignment of cysteine biosynthetic process
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings:
  - statement: Lyase keyword mapped to GO:0016829
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
  findings:
  - statement: PLP binding transferred based on PALP domain
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings:
  - statement: Alpha-amino acid metabolic process inferred
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: Cytoplasm and L-cysteine catabolic process annotations
- id: PMID:14532352
  title: Comprehensive proteomic profiling of the membrane constituents of a Mycobacterium tuberculosis strain.
  findings:
  - statement: Rv3684 detected in membrane fraction by mass spectrometry
    supporting_text: "739 proteins have been identified by two or more distinct peptide sequences and have been characterized"
- id: PMID:15525680
  title: Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling.
  findings:
  - statement: Rv3684 identified in cytosol fraction by subcellular proteomics
    supporting_text: "We report the identifications of 1044 proteins and their corresponding localizations in these compartments"
- id: PMID:34439535
  title: Mycobacterium tuberculosis H(2)S Functions as a Sink to Modulate Central Metabolism, Bioenergetics, and Drug Susceptibility.
  findings:
  - statement: Identified Rv3684 (Cds1) as an H2S-producing enzyme in Mtb
    supporting_text: "We identified Rv3684 (Cds1) as an H2S-producing enzyme in Mtb and show that cds1 disruption reduces, but does not eliminate, H2S production, suggesting the involvement of multiple genes in H2S production"
  - statement: Demonstrated cysteine desulfhydrase activity producing H2S and pyruvate
    supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
  - statement: Showed PLP-dependence through AOAA inhibition
    supporting_text: "We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source."
  - statement: Kinetic parameters KM = 11.26 mM, kcat = 78.71 sec(-1)
    supporting_text: "we determined the Km of Rv3684 to be 11.26 ± 0.75 mM with a kcat of 78.71 ± 12.72 S−1"
  - statement: Delta-cds1 reduces H2S production and basal oxygen consumption
    supporting_text: "cds1 disruption reduces, but does not eliminate, H2S production"
  - statement: H2S stimulates respiration via cytochrome bd
    supporting_text: "maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd"
  - statement: H2S modulates redox homeostasis (EGT, MSH levels)
    supporting_text: "Lastly, our data demonstrate that Cds1-generated H2S modulates the levels of the major redox couples, EGT and MSH."
  - statement: Cds1 likely eliminates toxic levels of cysteine
    supporting_text: "Cds1 can mitigate toxic levels of Cys by converting excess Cys into H2S"
  - statement: Part of Rv3682-Rv3683-cds1 operon
    supporting_text: "cds1 is in an operon with rv3682 (ponA2) and rv3683"
- id: file:MYCTU/cds1/cds1-deep-research-falcon.md
  title: Deep research for cds1 gene function
  findings:
  - statement: Cds1 is a PLP-dependent L-cysteine desulfhydrase that produces H2S, pyruvate, and ammonia from L-cysteine
    supporting_text: "Cds1 is a PLP-dependent L-cysteine desulfhydrase that produces H2S, pyruvate, and ammonia from L-cysteine"
core_functions:
- description: >-
    PLP-dependent L-cysteine desulfhydrase catalyzing beta-elimination of
    L-cysteine to produce hydrogen sulfide (H2S), pyruvate, and ammonia.
    This is the major H2S-producing enzyme in M. tuberculosis. The H2S
    produced serves as a sulfur recycling sink, returning sulfur atoms
    back to the cysteine biosynthetic pathway to maintain sulfur homeostasis.
    Kinetics: KM = 11.26 mM for cysteine, kcat = 78.71 sec(-1). Activity is
    inhibited by AOAA (PLP inhibitor) but NOT by PAG (cystathionine gamma-lyase
    inhibitor), confirming identity as a true cysteine desulfhydrase.
  supported_by:
  - reference_id: PMID:34439535
    supporting_text: "Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys."
  - reference_id: PMID:34439535
    supporting_text: "We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source."
  - reference_id: PMID:34439535
    supporting_text: "H2S...functions as a sink to recycle sulfur atoms back to cysteine to maintain sulfur homeostasis"
  molecular_function:
    id: GO:0080146
    label: L-cysteine desulfhydrase activity
  directly_involved_in:
  - id: GO:0019448
    label: L-cysteine catabolic process
  - id: GO:0070814
    label: hydrogen sulfide biosynthetic process
  - id: GO:0042762
    label: regulation of sulfur metabolic process
  locations:
  - id: GO:0005829
    label: cytosol
proposed_new_terms: []
suggested_questions:
- question: What other enzymes contribute to H2S production in Mtb (since delta-cds1 does not completely eliminate H2S)?
- question: Is Cds1 regulated at the transcriptional or post-translational level under different growth conditions?
- question: What is the functional significance of the strain variation in H2S production?
suggested_experiments:
- description: Structural characterization of Cds1 to understand substrate binding and catalytic mechanism
  hypothesis: Crystal structure will reveal active site architecture and substrate binding mode
- description: Investigation of potential allosteric regulation of Cds1 activity
  hypothesis: Cds1 activity may be regulated by metabolites or redox state
- description: Identification of other H2S-producing enzymes through genetic screening
  hypothesis: Additional genes contribute to residual H2S production in delta-cds1
- description: In vivo studies to assess Cds1 contribution to virulence and drug susceptibility
  hypothesis: Cds1-mediated H2S production affects Mtb survival in host