Family Search for PF20247 (DUF6602)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF20247 hits 9 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
Marme_0670 DUF6602 domain-containing protein from Marinomonas mediterranea MMB-1
Aligns to 33:137 / 256 (41.0%), covers 97.1% of PF20247, 116.8 bits
- A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition
Mohr, Molecular cell 2018 - “...MMB-1 chromosome (III-B Operon) and expressed the pre-crRNA processing and CRISPR adaptation factors (Cas6-RT-Cas1, Cas2, Marme_0670, and the CRISPR03 array) from a plasmid ( Figure 5A ). Pre-crRNA processing was assayed by RNA-seq, using a protocol that preserves strand information and faithfully reports the 3 end...”
- “...and RNA Constructs Plasmids for the expression of WT M. mediterranea type III-B adaptation components (Marme_0670, Cas6-RT-Cas1, Cas2, and CRISPR03) and empty-vector controls supplying only CRISPR03 for in vivo assays were described previously ( Silas et al., 2017a ; 2016 ). Additional Cas6-RT-Cas1 mutants used in...”
- Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems
Silas, eLife 2017 - “...complex, the 58-spacer CRISPR02 array, the 8-spacer CRISPR03 array, and two genes of unknown function (Marme_0670, 0671). The Cas10 HD nuclease domain, required for DNA interference in some type III-B systems ( Elmore et al., 2016 ), is not evident in the M. mediterranea Cas10 (Cmr2)....”
- “...newly acquired spacers. ( A ) Arrangement of the type III-B CRISPR adaptation genes encoding Marme_0670, RT-Cas1, and Cas2 on a pKT230 broad-host-range vector under control of the putative 16S rRNA promoter (Adapted from [ Silas et al., 2016 ]). ( B ) Proportion of newly...”
- Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein
Silas, Science (New York, N.Y.) 2016 - “...CRISPR03 array ( 35 ), the genes encoding RT-Cas1 and Cas2, and an adjacent gene (Marme_0670) with limited homology to the NERD family ( 36 ), or together with a second cassette additionally encoding the remaining CRISPR-associated factors, Cmr1-Cmr6 and Marme_0671) ( Fig. 2A,B ). Acquisition...”
- “...complement of Cas genes, or the subset containing only the potential adaptation genes (RT-Cas1, Cas2, Marme_0670). Bona fide spacer acquisition is evidenced by the precise junctions between the inserted spacer DNA and CRISPR repeats ( Fig. S1A ), and by the diversity of acquired spacers (...”
NUCC_VIBMT / P0DUD6 CRISPR-associated endodeoxyribonuclease NucC; EC 3.1.-.- from Vibrio metoecus (see paper)
Aligns to 23:128 / 245 (43.3%), covers 98.1% of PF20247, 112.4 bits
- function: CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
function: A cyclic nucleotide-activated dsDNase. In the presence of 3',3',3'-cyclic AMP-AMP-AMP (cAAA), and to a much lesser extent 3',3',3'-cyclic AMP-AMP-GMP (cAAG) and cyclic-di-AMP (c-di-AMP), endonucleolytically degrades dsDNA. The nuclease digests dsDNA to about 50 bp lengths. Not stimulated by cGAMP or linear di-AMP (PubMed:31932164). DNA has been modeled to contact a pair of juxtaposed active sites (one from each layer of the hexamer), accounting for cleavage on both strands (By similarity).
cofactor: Mg(2+)
subunit: Forms homotrimers and homohexamers; in the presence of cAAA only the homohexamers of face-to-face associated trimers are formed (PubMed:31932164). The 2 cAAA-binding sites are on the exterior of the hexamer at the three-way junction, there are maximally 2 cyclic nucleotides per hexamer (Probable).
7zgvA / A0A2I5TBB8 Serratia nucc bound to ca3 (see paper)
Aligns to 28:133 / 246 (43.1%), covers 98.1% of PF20247, 111.3 bits
- Ligands: rna; calcium ion (7zgvA)
NUCC_PSEAI / P0DTF8 Endodeoxyribonuclease NucC; NucC nuclease; EC 3.1.-.- from Pseudomonas aeruginosa (see 2 papers)
ACG06_12960, WP_003050273 CBASS effector endonuclease NucC from Pseudomonas aeruginosa
Aligns to 22:127 / 241 (44.0%), covers 97.1% of PF20247, 106.6 bits
- function: Effector DNase of a CBASS antivirus system (PubMed:31932165, PubMed:31932164) (Probable). CBASS (cyclic oligonucleotide-based antiphage signaling system) provides immunity against bacteriophage. The CD-NTase protein synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection. A type III-C(AAA) CBASS system (PubMed:32839535).
function: A cyclic nucleotide-activated dsDNase. In the presence of 3',3',3'-cyclic AMP-AMP-AMP (cAAA) and to a lesser extent cyclic-di-AMP (c-di-AMP), endonucleolytically degrades dsDNA (Probable). Binds one cAAA in a pocket on one surface of the trimer; cAAA binding promotes hexamerization which is probably necessary for nuclease activation (PubMed:31932164). The nuclease digests dsDNA to about 50 bp lengths. DNA has been modeled to contact a pair of juxtaposed active sites (one from each layer of the hexamer), accounting for cleavage on both strands (By similarity).
cofactor: Mg(2+)
subunit: Self-oligomerizes (PubMed:31932165). Forms homotrimers; in the presence of cAAA the trimers associate face-to-face to form homohexamers. The 2 cAAA-binding sites are on the exterior of the hexamer at the three-way junction, there are maximally 2 cyclic nucleotides per hexamer (PubMed:31932164). - Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity
Lau, Molecular cell 2020 - “...coli MS1151 (Genbank ID EFJ98159 ; synthesized by Invitrogen/Geneart), P. aeruginosa ATCC 27853 (Genbank ID WP_003050273 ; amplified from genomic DNA), Vibrio metoecus sp. RC341 (IMG ID 647193063; synthesized by Invitrogen/Geneart), and Gynuella sunshinyii YC6258 (IMG ID 2632356247; synthesized by Invitrogen/Geneart) were cloned into UC Berkeley...”
- Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853
Cao, BMC genomics 2017 - “...Heavy metal, cooper response 2,668,513 2,677,091 8578 ACG06_12800- ACG06_12845 Mercuric resistance 2,690,535 2,695,956 5421 ACG06_12920- ACG06_12960 - 2,736,058 2,742,733 6675 ACG06_13180- ACG06_13200 Virulence 3,210,856 3,216,077 5221 ACG06_14975- ACG06_15000 Hydrolase 3,217,225 3,221,802 4577 ACG06_15010- ACG06_15040 Hypothetical protein 3,260,302 3,265,059 4757 ACG06_15285- ACG06_15305 Antibiotics biosynthesis 3,271,888 3,278,016 6128...”
NUCC_ECOM1 / D7Y2H5 Endodeoxyribonuclease NucC; NucC nuclease; EC 3.1.-.- from Escherichia coli (strain MS 115-1) (see 2 papers)
Aligns to 22:127 / 241 (44.0%), covers 98.1% of PF20247, 104.5 bits
- function: Effector DNase of a CBASS antivirus system (PubMed:31932165, PubMed:31932164). CBASS (cyclic oligonucleotide-based antiphage signaling system) provides immunity against bacteriophage. The CD-NTase protein synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection. A type III-C(AAA) CBASS system (PubMed:32839535).
function: A cyclic nucleotide-activated dsDNase. In the presence of 3',3',3'-cyclic AMP-AMP-AMP (cAAA), and to a lesser extent 3',3',3'- cyclic AMP-AMP-GMP (cAAG) and cyclic-di-AMP (c-di-AMP), endonucleolytically degrades dsDNA (PubMed:31932165, PubMed:31932164). Binds one cAAA in a pocket on one surface of the trimer; cAAA binding promotes hexamerization, which is necessary for nuclease activation. Also binds c-diAMP or linear di-AMP with lower affinity. The nuclease digests dsDNA to about 50 bp lengths with a 2-base 3' overhang and a consensus recognition site of 5'-Axx|T-3'. DNA has been modeled to contact a pair of juxtaposed active sites (one from each layer of the hexamer), accounting for cleavage on both strands and the 2-base overhang (PubMed:31932164).
function: Protects E.coli strain JP313 against bacteriophage lambda cI- infection. When the cdnC-cap7-cap6-nucC operon is transformed into a susceptible strain it confers bacteriophage immunity. Mutations in the sensor (Cap7 also called HORMA) or effector proteins (CdnC, NucC) but not the disassembly protein (Cap6 also called Trip13) no longer confer immunity. The presence of the intact operon leads to culture collapse and cell death which occurs before the phage has finished its replication cycle, thus protecting non-infected bacteria by aborting the phage infection and preventing its propagation.
cofactor: Mg(2+)
subunit: Self-oligomerizes (PubMed:31932165). Forms homotrimers; in the presence of cAAA the trimers associate face-to-face to form homohexamers. The 2 cAAA-binding sites are on the exterior of the hexamer at the three-way junction, there are maximally 2 cyclic nucleotides per hexamer (PubMed:31932164).
6q1hA / P0DTF8 Structure of p. Aeruginosa atcc27853 nucc, caaa-bound form (see paper)
Aligns to 21:126 / 240 (44.2%), covers 97.1% of PF20247, 102.2 bits
6p7pC / D7Y2H5 Structure of e. Coli ms115-1 nucc, caaa-bound form (see paper)
Aligns to 24:129 / 242 (43.8%), covers 98.1% of PF20247, 100.1 bits
VCA0399 hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 57:163 / 291 (36.8%), covers 93.3% of PF20247, 86.1 bits
- Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
Pombo, Frontiers in microbiology 2022 - “...HigA-1 1 VCA0395 Hypothetical protein 1 VCA0396-397 VCA0396 Hypothetical protein 2 VCA0397 Hypothetical protein 1 VCA0399 Hypothetical protein 2 VCA0407 Hypothetical protein 1 VCA0422-423 VCA0423 Hypothetical protein 2 VCA0435 Hypothetical protein 1 VCA0463 Biphenyl-2,3-diol 1,2-dioxygenase 1 VCA0464 Hypothetical protein 3 VCA0466 Hypothetical protein 1 VCA0467 Hypothetical...”
SEV_RS01820 DUF6602 domain-containing protein from Salmonella enterica subsp. enterica serovar Virchow str. SL491
Aligns to 17:124 / 263 (41.1%), covers 96.2% of PF20247, 82.0 bits
- In silico Identification of Serovar-Specific Genes for Salmonella Serotyping
Zhang, Frontiers in microbiology 2019 - “...Gene 2 = SEN1384 (Enteritidis-clade B); Gene 3 = R561_RS18155 (Enteritidis-clade A/C); Gene 4 = SEV_RS01820 (Virchow); Gene 5 = SESPA_RS08460 (Saintpaul-I); Gene 6 = SeSPB_A1749 (Saintpaul-II); Gene 7 = Saintpaul-III; Gene 8 = L287_RS37190 (Infantis); Gene 9 = SPAB_01124 (Paratyphi B-I&II); Gene 10 = SPAB_01338...”
Or search for genetic data about PF20247 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory