Table 1.
Families constituting the CDE superfamily (SCOPe 54909, Pfam clade CL0032) and their properties
| Descriptive name | SCOPe | Pfam | Description | Taxonomic distribution |
|---|---|---|---|---|
| Families interacting with heme | ||||
| 1. Chlorite dismutase, Cld | 110965 | PF06778 | Catalyze the disproportionation of chlorite into chloride and oxygen using heme as a cofactor; characterized by a conserved distal arginine | Diverse Bacteria and Archaea |
| 2. DyP-type-peroxidase, DyP | 143265 | PF04261 | Heme peroxidases with wide substrate specificity, distinct active site and domain structure, and the ability to function well under lower pH conditions relative to other peroxidases | Diverse Bacteria and Fungi; Platyhelminthes, Nematoda, Chordata |
| 3. EfeB† | 143265 | PF04261 | DyPs with heme peroxidase activity, a twin-arginine motif targeting them for extracytoplasmic transport in their heme-bound form, and a role in iron assimilation | Gram-negative Bacteria; potentially others |
| 4. Aldoxime dehydratase, OxdA, OxdRE | -- | PF13816 | Catalyze the dehydration of aldoximes to their corresponding nitriles using heme as a cofactor | Fungi, Proteobacteria, Actinobacteria, Firmicutes |
| 5. HemQ† | 110965 | PF06778 | Cld-family proteins that catalyze the oxidative decarboxylation of coproheme to form heme b; characterized by a neutral distal residue in place of Arg | Gram-positive Bacteria and some (aerobic) Archaea |
| 6. IsdG family† | 82666, 110970 | PF03992 | Cofactorless monooxygenases involved in the oxidative degradation of heme; part of the ABM family | Gram-positive Bacteria; potentially others |
| Functionally characterized; no direct association with heme | ||||
| 7. Antibiotic monooxygenase, ABM; also called PG130 | 82666, 110970 | PF03992 | Small (~120 amino acid) cofactorless monooxygenases involved in the oxidation or oxygenation of organic molecules, particularly in the biosynthesis of antibiotics; frequently found as homodimers or fusions with a variety of other domains | Representatives in phylogenetically broad Bacteria, and Archaea; Fungi and Chordata |
| 8. EthD | 143272 | PF07110 | Involved in the degradation of ethyl tert-butyl ether | Diverse Bacteria; Fungi; Viridiplantae; Euryarcheota |
| 9. Lpr/AsnC transcriptional regulators | 69733 | PF1037 | Transcriptional regulators of the lysine-responsive protein type, frequently fused to helix-turn-helix-containing domains | Diverse Gram-positive and –negative Bacteria; Archaea; Nematoda |
| 10. Methylmucono-lactone methyl-isomerase, Mml-I | 160292 | PF09448 | Involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria | Proteobacteria |
| 11. Mucolactone delta-isomerase, MIase | 54910 | PF02426 | Catalyze the third step of catechol catabolism to succinate- and acetyl-CoA | Diverse Bacteria; Crenarchaeota |
| 12. Sulfur oxygenase reductase, SOR | 143278 | PF07682 | A non-heme-iron-containing 24-mer that catalyses the reaction: 4S + O2 + 4H2O → 2HSO3− + 2H2S + 2 H+ | Aquificae, Proteobacteria, Firmicutes; Crenarchaeota, Euryarchaeota |
| 13. NapD | -- | PF03927 | Involved in the formation of periplasmic nitrate reductase | Gram-negative Bacteria |
| 14. Polyketide synthesis cyclase | 110959 | PF04673 | Cyclase involved in polyketide synthesis and sharing structural similarity with polyketide monooxygenase | Actinobateria |
| Functions not well characterized | ||||
| 15. Yci-I | 102965 | PF03795 | Unknown function; contain a highly conserved Asp and His, suggesting an enzymatic function | Diverse Bacteria and Fungi |
| 16. DGPF domain | 110962 | PF03795 | Unknown function but thought to have a role in transcription initiation; specified by Pfam as a Yci-I subfamily, but listed as a separate family by SCOPe | Same as Yci-I |
| 17. Dabb-stress responsive protein | 89927 | PF07876 | Unknown function | Diverse Bacteria, Protists, and single-celled Eukaryotes; Fungi; Viridiplantae; Euryarchaeota |
| 18. YdhR | 117940 | PF08803 | Unknown function; homodimeric structure | Diverse Bacteria, Protists, and single-celled Eukaryotes; Fungi; Viridiplantae; Euryarchaeota |
| 19. NIPSNAP | 117943 | PF07978 | Many hypothetical proteins along with members of the NIPSNAP family which have roles in vesicular transport | Diverse Bacteria, Protists, and single-celled Eukaryotes; Fungi; Viridiplantae; Euryarchaeota |
| 20. Atu0297 (DUF‡1330) | 143275 | PF07045 | Unknown function; hypothetical proteins of ~90 residues in length | Diverse Bacteria, Protists, and single-celled Eukaryotes; Fungi; Viridiplantae; Euryarchaeota |
| 21. YbaA (DUF‡1428) | 160289 | PF07237 | Unknown function | Diverse Bacteria; Crenarchaeota |
| 22. YiiL (DUF718) | 160298 | PF05336 | Unknown function | Diverse Bacteria; Fungi; Chlorophyta; Euryarchaeota; Chordata |
| 23. Unnamed DUFs‡: 3291, 4188, 881 | -- | PF11695, PF13826, PF05949 | Unknown function; listed by PFam but not SCOPe | -- |
| 24. Marine metagenome family DABB1/2/3 | 160301 160295 160306 |
-- | Unknown function; listed by SCOPe but not Pfam | -- |
†
Proteins designated as part of other families by Pfam and/or SCOPe but having significant functional distinctions from the larger family cohort;
‡
DUF = domain of unknown function