Table 1.
Cas proteins and complexes: predicted and experimentally determined biochemical activities and possible functions in CRISPR-mediated immunity
| Proteina | Representation in CRISPR-Casb | Domain organizationb | Predicted activity and functionb | Three-dimensional structurec | Experimentally demonstrated activity and/or function |
|---|---|---|---|---|---|
| Cas1 (COG1518) | Universal | Highly conserved domain without detectable similarity to other proteins | Nuclease, possibly integrase; role in adaptation (integration of invader DNA) | 3GOD: unique mostly α-helical fold [28] | Metal-dependent nuclease, cleaves both DNA and RNA [28] |
| Cas2 (COG1343, COG3512, and additional small families) | Universal (except for some probably non-functional CASS variants) | Small domain distantly related to VapD, an uncharacterized bacterial protein linked to toxin-antitoxin system; some fusions with Cas3 | Nuclease, possible role in adaptation | 2IVY, 2I8E: ferredoxin-like fold [29] | Sequence-specific endoribonuclease [29] |
| Cas3 (COG1203) | Present in a substantial majority of CASS, with the exception of several reduced though possibly functional systems | Superfamily 2 helicase, typically fused to HD nuclease; in some CASS variants, helicase and nuclease are encoded by adjacent genes | Helicase-nuclease, possible roles at all stages of CASS-mediated immunity | None | Interacts with CASCADE, contributes to CASS-mediated interference [30]; endonuclease activity demonstrated from a stand-alone HD-protein from Sulfolobus [33] |
| Cas4 (COG1468, COG4343) | Present in a substantial majority of CASS, with the exception of several reduced though possibly functional systems | RecB-like nuclease domain and an additional metal-binding module | Nuclease, implicated in adaptation | None | None |
| RAMPs (Cas5 [COG1688], Cas6 [COG1583], COGs 1769, 1567, 1336, 1367, 1604, 1337, 1332, 5551, and additional small families) | Diverse subsets of RAMPs present in all CASS | RAMP | RNA-binding proteins, probably sequence-structure-specific | 1WJ9, 3I4H Duplicated ferredoxin-fold domain | Cas5 in Escherichia coli is a CASCADE subunit and directly cleaves CRISPR transcripts generating guide RNAs [30]; Cas6 performs the same function in Pyrococcus [31] |
| CASCADE [CasABCDE(Cse1234-Cas5e) complex] | E. coli; different combinations of subunits in other prokaryotes | Cas5e (COG1688) is a RAMP; other domains uncharacterized | Cse4 (COG1857): predicted nuclease; Cas5e: predicted RNA-binding protein | See above for Cas5. | CasC is the principal structural subunit; Cas5e is the nuclease subunit [30] |
aThese are only the most widespread and experimentally characterized Cas proteins; there is no unified nomenclature of Cas proteins [3]; the Cas protein names are accompanied by the numbers of clusters of orthologous genes (COGs) [34] where available. bData are from references [3] and [12]. cStructures are identified by Protein Data Bank accession numbers. Cas, CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein; CASCADE, CRISPR (clustered regularly interspaced short palindromic repeats)-associated complex for antiviral defense; CASS, CRISPR (clustered regularly interspaced short palindromic repeats)-associated system; CRISPR, clustered regularly interspaced short palindromic repeats; HD, HD (histidine-aspartate)-family nuclease; RAMP, repeat-associated mysterious protein.