Enzymes with RuvC domains

1. An engineered nuclease composition comprising:

(a) an endonuclease comprising a RuvC_III domain comprising a sequence having at least 90% sequence identity to SEQ ID NO2242; and

(b) an engineered guide ribonucleic acid structure configured to form a complex with said endonuclease comprising:

(i) a guide ribonucleic acid sequence configured to hybridize to a target deoxyribonucleic acid sequence; and

(ii) a tracr ribonucleic acid sequence configured to bind to said endonuclease

wherein said endonuclease comprises a sequence having at least 90% sequence identity to SEQ ID NO 421.

2. The engineered nuclease composition of claim 1 , wherein said endonuclease further comprises an HNH domain.

3. The engineered nuclease composition of claim 1 , wherein said tracr ribonucleic acid sequence comprises a sequence with at least 80% sequence identity to about 60 to 90 consecutive nucleotides from SEQ ID NO 5495.

4. The engineered nuclease composition of claim 1 , wherein said endonuclease is configured to bind to a protospacer adjacent motif (PAM) sequence of SEQ ID NO 5517.

5. The engineered nuclease composition of claim 1 , wherein said engineered guide ribonucleic acid structure comprises at least two ribonucleic acid polynucleotides.

6. The engineered nuclease composition of claim 1 , wherein said engineered guide ribonucleic acid structure comprises one ribonucleic acid polynucleotide comprising said guide ribonucleic acid sequence and said tracr ribonucleic acid sequence.

7. The engineered nuclease composition of claim 1 , wherein said guide ribonucleic acid sequence is complementary to a prokaryotic, bacterial, archaeal, eukaryotic, fungal, plant, mammalian, or human genomic sequence.

8. The engineered nuclease composition of claim 1 , wherein said endonuclease comprises one or more nuclear localization sequences (NLSs) proximal to an Nor C-terminus of said endonuclease.

9. The engineered nuclease composition of claim 8 , wherein said one or more NLSs comprises the sequence of SEQ ID NO 5597.

10. The engineered nuclease composition of claim 1 , further comprising

a single- or double-stranded DNA repair template comprising from 5′ to 3′: a first homology arm comprising a sequence of at least 20 nucleotides 5′ to said target deoxyribonucleic acid sequence, a synthetic DNA sequence of at least 10 nucleotides, and a second homology arm comprising a sequence of at least 20 nucleotides 3′ to said target deoxyribonucleic acid sequence.

11. The engineered nuclease composition of claim 1 , wherein said engineered nuclease system further comprises a source of Mg 2+ .

12. The engineered nuclease composition of claim 1 , wherein said endonuclease and said tracr ribonucleic acid sequence are derived from distinct bacterial species within a same phylum.

13. The engineered nuclease composition of claim 1 , wherein said guide RNA structure comprises an RNA sequence predicted to comprise a hairpin consisting of a stem and a loop, wherein the stem comprises at least 10 base-paired ribonucleotides, and an asymmetric bulge within 4 base pairs of the loop.

14. The engineered nuclease composition of claim 1 , wherein said tracr ribonucleic acid sequence of said engineered guide ribonucleic acid structure comprises a hairpin comprising at least 8 base-paired ribonucleotides.

15. The engineered nuclease composition of claim 1 , wherein said guide ribonucleic acid sequence of said engineered guide ribonucleic acid structure is predicted to comprise a hairpin with an uninterrupted base-paired region comprising at least 8 nucleotides of a guide ribonucleic acid sequence and at least 8 nucleotides of a tracr ribonucleic acid sequence, and wherein said tracr ribonucleic acid sequence comprises, from 5′ to 3′, a first hairpin and a second hairpin, wherein said first hairpin has a longer stem than said second hairpin.

16. The engineered nuclease composition of claim 1 , wherein said endonuclease comprises SEQ ID NO 421 or a conservatively substituted sequence having at least 90% identity thereto.