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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0019344 L-cysteine biosynthetic process | IBA GO_REF:0000033 | REMOVE | 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. 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 Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000034104 · PANTHER PTHR10314 root node SUPPORTS SOURCE BUT NOT TARGET The root node mixes cysteine synthase sources with the divergent Cds1 desulfhydrase subfamily; biosynthesis support does not transfer to the catabolic target. UniProtKB:P0ABK5 · E. coli CysK SUPPORTS SOURCE BUT NOT TARGET CysK supports cysteine biosynthesis, while MYCTU Cds1 is reviewed as a cysteine desulfhydrase with the opposite reaction direction. Supporting Evidence: PMID:34439535 Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys. file:MYCTU/cds1/cds1-deep-research-falcon.md Cds1 is a PLP-dependent L-cysteine desulfhydrase that produces H2S, pyruvate, and ammonia from L-cysteine file:interpro/panther/PTHR10314/PTHR10314-notes.md 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 |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: PMID:15525680 We report the identifications of 1044 proteins and their corresponding localizations in these compartments |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | 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. Reason: Cytoplasmic localization is appropriate and consistent with experimental HDA evidence from subcellular proteomics. |
| GO:0016829 lyase activity | IEA GO_REF:0000043 | MODIFY | 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). 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 replacements: L-cysteine desulfhydrase activity Supporting Evidence: PMID:34439535 Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys. |
| GO:0019450 obsolete L-cysteine catabolic process to pyruvate | IEA GO_REF:0000120 | ACCEPT | 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). Reason: Experimentally validated by PMID:34439535. Products were identified by LC-MS/MS confirming pyruvate as a product of the cysteine desulfhydrase reaction. Supporting Evidence: PMID:34439535 Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys. |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000104 | ACCEPT | 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. 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. Supporting Evidence: PMID:34439535 We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source. |
| GO:1901605 alpha-amino acid metabolic process | IEA GO_REF:0000117 | ACCEPT | 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. 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. |
| GO:0019450 obsolete L-cysteine catabolic process to pyruvate | IDA PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | ACCEPT | 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. 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). Supporting Evidence: PMID:34439535 Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys. |
| GO:0030170 pyridoxal phosphate binding | IDA PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | ACCEPT | 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. 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. Supporting Evidence: PMID:34439535 We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source. |
| GO:0042762 regulation of sulfur metabolic process | IMP PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | ACCEPT | 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. 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. Supporting Evidence: PMID:34439535 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 |
| GO:0045454 cell redox homeostasis | IMP PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:34439535 Lastly, our data demonstrate that Cds1-generated H2S modulates the levels of the major redox couples, EGT and MSH. |
| GO:0070814 hydrogen sulfide biosynthetic process | IDA PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | ACCEPT | 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. 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. Supporting Evidence: PMID:34439535 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 PMID:34439535 maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd |
| GO:1901857 positive regulation of cellular respiration | IMP PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:34439535 maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd PMID:34439535 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 |
| GO:0005829 cytosol | HDA PMID:15525680 Mycobacterium tuberculosis functional network analysis by gl... | ACCEPT | 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. 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. Supporting Evidence: PMID:15525680 We report the identifications of 1044 proteins and their corresponding localizations in these compartments |
| GO:0005886 plasma membrane | HDA PMID:14532352 Comprehensive proteomic profiling of the membrane constituen... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:14532352 739 proteins have been identified by two or more distinct peptide sequences and have been characterized |
| GO:0080146 L-cysteine desulfhydrase activity | IDA PMID:34439535 Mycobacterium tuberculosis H(2)S Functions as a Sink to Modu... | NEW | 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). 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. Supporting Evidence: PMID:34439535 Identification of the enzymatic products indicates that Cds1 is a cysteine desulfhydrase that generates H2S and pyruvate from Cys. PMID:34439535 We showed that this activity is PLP-dependent, is inhibited by AOAA and not PAG, and uses Cys as a sulfur source. |
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Download this section (compressed HTML)Q: What other enzymes contribute to H2S production in Mtb (since delta-cds1 does not completely eliminate H2S)?
Q: Is Cds1 regulated at the transcriptional or post-translational level under different growth conditions?
Q: What is the functional significance of the strain variation in H2S production?
Experiment: Structural characterization of Cds1 to understand substrate binding and catalytic mechanism
Hypothesis: Crystal structure will reveal active site architecture and substrate binding mode
Experiment: Investigation of potential allosteric regulation of Cds1 activity
Hypothesis: Cds1 activity may be regulated by metabolites or redox state
Experiment: Identification of other H2S-producing enzymes through genetic screening
Hypothesis: Additional genes contribute to residual H2S production in delta-cds1
Experiment: In vivo studies to assess Cds1 contribution to virulence and drug susceptibility
Hypothesis: Cds1-mediated H2S production affects Mtb survival in host
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