Family Search for PF01930 (Cas_Cas4)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF01930 hits 66 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
MTH1085 conserved protein from Methanothermobacter thermautotrophicus str. Delta H
Aligns to 15:175 / 175 (92.0%), covers 99.4% of PF01930, 203.1 bits
Q8U1T6 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) (EC 3.1.12.1) from Pyrococcus furiosus (see 2 papers)
PF1119 hypothetical protein from Pyrococcus furiosus DSM 3638
Aligns to 12:169 / 169 (93.5%), covers 98.8% of PF01930, 200.0 bits
- Primed CRISPR DNA uptake in Pyrococcus furiosus
Garrett, Nucleic acids research 2020 - “...cassette: Tko csg promoter-Cas2 (PF1117), Tko gdh promoter-Cas4 - 2 (PF1793), slp promoter-Cas4 - 1 (PF1119), PRP synthetase promoter-Cas1 (PF1118)) or pJE64 (Cas3 overexpression cassette: Tko csg promoter-Cas3 (PF1120)), respectively. Overexpression cassettes were digested by NotI and EcoRV and ligated with pMS030 or pMS088 to yield...”
- “...I-U system ( 76 ). Pyrococcus furiosus has two Cas4 proteins, Cas-associated Cas4 - 1 (PF1119) and isolated Cas4 - 2 (PF1793) (Figure 2A ), and we recently reported that both forms are involved in spacer processing and integration ( 53 ). To test whether either...”
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...compared with the available Cas4 sequence of the Pyrobaculum calidifontis (PcaCas4; A3MTK6), Pyrococcus furiosus (PfuCas41; Q8U1T6 and PfuCas42; Q8U027), Sulfolobus islandicus (SisCas4; F0NH45), and Sulfolobus solfataricus (Sso0001; Q97TX9). The secondary structure elements represented at the top are inferred based on the known crystal structures of the...”
TK0458 predicted exonuclease, RecB family from Thermococcus kodakaraensis KOD1
Aligns to 13:170 / 170 (92.9%), covers 99.4% of PF01930, 198.8 bits
MJ0377 conserved hypothetical protein from Methanocaldococcus jannaschii DSM 2661
Aligns to 12:170 / 170 (93.5%), covers 99.4% of PF01930, 196.8 bits
- Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference
Beloglazova, The EMBO journal 2011 - “...(MJ0378), Cas2 (MJ0386), Cas3 (MJ0376, MJ0383, MJ0384), Cas4 (MJ0377), Cas5 (MJ0382), and Cas6 (MJ0375, MJ1234). The other 11 Cas proteins represent the CRISPR...”
TTE2659 RecB family exonuclease from Thermoanaerobacter tengcongensis MB4
Aligns to 11:170 / 170 (94.1%), covers 99.4% of PF01930, 192.6 bits
PG2015 CRISPR-associated protein Cas4 from Porphyromonas gingivalis W83
Aligns to 5:166 / 170 (95.3%), covers 98.8% of PF01930, 189.0 bits
CD2977 hypothetical protein from Clostridium difficile 630
Aligns to 11:169 / 172 (92.4%), covers 99.4% of PF01930, 188.8 bits
- Discovery of new type I toxin-antitoxin systems adjacent to CRISPR arrays in Clostridium difficile
Maikova, Nucleic acids research 2018 - “...family protein 0.26 CD2979 CRISPR-associated Cas5 family protein 0.25 CD2978 CRISPR-associated Cas3 family helicase 0.30 CD2977 CRISPR-associated Cas4 family protein 0.33 CD2976 CRISPR-associated Cas1 family protein 0.37 CD2975 CRISPR-associated Cas2 family protein 0.37 CD2455 c CRISPR-associated protein 0.55 0.61 9.4 CD2454 Conserved hypothetical protein 0.55 CD2453...”
- Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile
Boudry, mBio 2015 - “...CD2982-CD2975 ) were created. The first part of the C.difficile cas operon (from CD2982 to CD2977 encoding the interference components) was cloned into the pCDF-1b expression vector (pDIA6351), and the rest of the operon ( cas1 [ CD2976 ] and cas2 [ CD2975 ] genes) was...”
- “...allowing the expression of C.difficile cas gene set lacking cas1 and cas2 (from CD2982 to CD2977 ). The Cas protein production and crRNA expression were induced by the addition of 1mM l -arabinose and 1mM IPTG. The serial dilutions of transformation mixtures deposited on LB plates...”
- Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen
Hargreaves, mBio 2014 - “...Makarova et al. ( 35 ) and is composed of cas2 (CD2975), cas1 (CD2976), cas4 (CD2977), cas3 (CD2978), cas5 (CD2979), cas7 (or cst2 ) (CD2980), cas8b (or cst1 ) (CD2981), and cas6 (CD2982), as assigned by the Genome Properties Report from the JCVI Comprehensive Microbial Resource....”
CD630_29770, CDIF630erm_03261 CRISPR-associated protein Cas4 from Clostridioides difficile 630
Aligns to 22:180 / 183 (86.9%), covers 99.4% of PF01930, 188.5 bits
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...prophages CD630_29750 CDIF630erm_03259 CRISPR-associated endoribonuclease Cas2 -0.74 -2.13 CD630_29760 CDIF630erm_03260 CRISPR-associated endonuclease Cas1 -0.87 -1.67 CD630_29770 CDIF630erm_03261 CRISPR-associated Cas4 family protein -0.41 -2.72 CD630_29780 CDIF630erm_03262 CRISPR-associated Cas3 family helicase -0.26 -2.20 CD630_29790 CDIF630erm_03263 CRISPR-associated Cas5 family protein -1.30 -1.66 CD630_29800 CDIF630erm_03264 CRISPR-associated autoregulatorDevR family protein 0.20...”
- “...CD630_29750 CDIF630erm_03259 CRISPR-associated endoribonuclease Cas2 -0.74 -2.13 CD630_29760 CDIF630erm_03260 CRISPR-associated endonuclease Cas1 -0.87 -1.67 CD630_29770 CDIF630erm_03261 CRISPR-associated Cas4 family protein -0.41 -2.72 CD630_29780 CDIF630erm_03262 CRISPR-associated Cas3 family helicase -0.26 -2.20 CD630_29790 CDIF630erm_03263 CRISPR-associated Cas5 family protein -1.30 -1.66 CD630_29800 CDIF630erm_03264 CRISPR-associated autoregulatorDevR family protein 0.20 -0.55...”
- CRISPR Diversity and Microevolution in Clostridium difficile
Andersen, Genome biology and evolution 2016 - “...cas3 , cas5 , cas7 , cas8 and cas6 encoded as locus tag: CD630_29750, CD630_29760, CD630_29770, CD630_29780, CD630_29790, CD630_29800, CD630_29810 and CD630_29820, respectively). Identification and Clustering of Ancestral CRISPR Spacers CRISPR arrays conserved among the tested strains were identified by annotating each ancestral spacer in the...”
NEQ021 NEQ021 from Nanoarchaeum equitans Kin4-M
Aligns to 5:166 / 168 (96.4%), covers 98.8% of PF01930, 183.7 bits
- RNA processing in the minimal organism Nanoarchaeum equitans
Randau, Genome biology 2012 - “...DNA [ 23 , 24 ]. All universal proteins Cas1 (NEQ017), Cas2 (NEQ016) and Cas4 (NEQ021) proposed to be involved in the integration of spacers are present. Finally, NEQ018, Cas7 (NEQ019) and Cas5 (NEQ020) are proposed to form the Cascade complex that delivers the crRNAs to...”
Dtur_0620 CRISPR-associated protein Cas4 from Dictyoglomus turgidum DSM 6724
Aligns to 8:168 / 168 (95.8%), covers 100.0% of PF01930, 179.2 bits
CG479_RS10980 CRISPR-associated protein Cas4 from Bacillus cytotoxicus
Aligns to 2:159 / 165 (95.8%), covers 98.8% of PF01930, 177.8 bits
HLASA_0865 CRISPR-associated protein Cas4 from Halanaeroarchaeum sulfurireducens
Aligns to 26:183 / 184 (85.9%), covers 100.0% of PF01930, 162.8 bits
CAS4_HALVD / D4GQN9 CRISPR-associated exonuclease Cas4; EC 3.1.12.1 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii) (see paper)
HVO_RS02780 CRISPR-associated protein Cas4 from Haloferax volcanii DS2
Aligns to 26:183 / 183 (86.3%), covers 100.0% of PF01930, 153.8 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). This protein may be a 5' to 3' ssDNA exonuclease. Plasmid targeted by CRISPR locus P1 transform wild-type cells very poorly (PubMed:22767603).
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: Mg(2+) Mn(2+) Cu(2+) (Mg(2+) or Mn(2+) required for ssDNA cleavage activity. Can also utilise Cu(2+).)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit.)
disruption phenotype: Loss of the 8 Cas genes in this locus (cas1, cas2, cas3, cas4, cas5, cas6, cas7 and cas8b) leads to loss of CRISPR interference against plasmid targeted by this CRISPR locus, i.e. plasmid is not destroyed by CRISPR. - Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Makkay, Scientific reports 2020 - “...in planktonic cells starting at the 2-h time point to 24-h and 8-h, respectively. cas4 (HVO_RS02780), also assumed to be a part of the spacer acquisition module, had a significant increase in expression immediately at 0-h turning to lower expression for the rest of the experiment....”
SSO1392 Hypothetical protein from Sulfolobus solfataricus P2
Aligns to 20:191 / 201 (85.6%), covers 98.8% of PF01930, 110.5 bits
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...different tasks ( Liuetal., 2017 ). The Sulfolobus solfataricus genome encodes five Cas4-like proteins (Sso0001, Sso1392, Sso1449, Sso1391, Sso1451), which stake low sequence similarity (15 to 30% sequence identity) ( Lemaketal., 2013 ). The crystal structures of the Cas4 proteins from S. solfataricus (Sso0001) and Pyrobaculum...”
- Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus
Lemak, Journal of the American Chemical Society 2013 - “...which share low sequence similarity (15 to 30% sequence identity) and belong to DUF83 (SSO0001, SSO1392, SSO1449) and DUF911 (SSO1391, SSO1451) ( Supplementary Fig. S1 ). Recently, the purified SSO0001 has been shown to possess a 5 to 3 exonuclease activity 20 . Here, we demonstrate...”
COI_0270 CRISPR-associated protein Cas4 from Mannheimia haemolytica serotype A2 str. OVINE
Aligns to 26:204 / 221 (81.0%), covers 98.1% of PF01930, 106.5 bits
- A three-way comparative genomic analysis of Mannheimia haemolytica isolates
Lawrence, BMC genomics 2010 - “...B and O consist of four genes, COK_0798, COK_0799, COK_0800, COK_0801 and COI_0267, COI_0268, COI_0269, COI_0270 respectively. The Cas family, which is represented by CT1134 and CT1133 from Chlorobium tepidum , is also found in the B and O genomes (COK_0798, COK_0799 and COI_0267, COI_0268). This...”
- “...[ 78 ]. The last gene in this cluster is a recB exonuclease (COK_0801 and COI_0270) which is 100% identical between these two isolates. Furthermore, we also identified CRISPR/Cas loci in the A1 genome (MHA_0343, MHA_0344, MHA_0345, and MHA_0346), previously reported as hypothetical proteins [ 14...”
Q72TS4 CRISPR-associated exonuclease Cas4 from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
Aligns to 8:188 / 209 (86.6%), covers 98.1% of PF01930, 104.5 bits
HMPREF0389_01167 CRISPR-associated protein Cas4 from Filifactor alocis ATCC 35896
Aligns to 9:199 / 217 (88.0%), covers 98.1% of PF01930, 102.2 bits
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...48/0.34 10 4.84 C 0.213 M Ferritin-like di iron binding domain 0.65 Nonsecretory protein 42. HMPREF0389_01167 CRISPR-associated protein 18./20.1 22/3.9 16 3.56 C 0.251 M CRISPR domain (clustered regularly interspaced short palindromic repeats) 0.36 Nonsecretory protein 43. HMPREF0389_01230 Hypothetical protein 22/22.02 123/1.06 13 0.447 CM No...”
MHA_0346 CRISPR-associated protein Cas4 from Mannheimia haemolytica PHL213
Aligns to 26:204 / 224 (79.9%), covers 98.1% of PF01930, 101.7 bits
COK_0801 CRISPR-associated protein Cas4 from Mannheimia haemolytica serotype A2 str. BOVINE
Aligns to 26:204 / 221 (81.0%), covers 98.1% of PF01930, 100.3 bits
- A three-way comparative genomic analysis of Mannheimia haemolytica isolates
Lawrence, BMC genomics 2010 - “...]. The CRISPR/Cas loci of B and O consist of four genes, COK_0798, COK_0799, COK_0800, COK_0801 and COI_0267, COI_0268, COI_0269, COI_0270 respectively. The Cas family, which is represented by CT1134 and CT1133 from Chlorobium tepidum , is also found in the B and O genomes (COK_0798,...”
- “...family, TM1801 [ 78 ]. The last gene in this cluster is a recB exonuclease (COK_0801 and COI_0270) which is 100% identical between these two isolates. Furthermore, we also identified CRISPR/Cas loci in the A1 genome (MHA_0343, MHA_0344, MHA_0345, and MHA_0346), previously reported as hypothetical proteins...”
XALc_2890 probable crispr-associated protein cas4 from Xanthomonas albilineans
Aligns to 8:189 / 210 (86.7%), covers 98.1% of PF01930, 96.1 bits
8d3lI / A0A4Y7WTW2 Type i-c cas4-cas1-cas2 complex bound to a pam/pam prespacer (see paper)
Aligns to 10:200 / 218 (87.6%), covers 98.1% of PF01930, 92.4 bits
- Ligands: dna; iron/sulfur cluster; manganese (ii) ion (8d3lI)
AL347_11870 CRISPR-associated protein Cas4 from Pseudomonas aeruginosa
Aligns to 8:188 / 210 (86.2%), covers 96.3% of PF01930, 85.2 bits
TT_P0197 No description from Thermus thermophilus HB27
Aligns to 11:183 / 194 (89.2%), covers 98.1% of PF01930, 83.6 bits
Q6ZEI3 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) (EC 3.1.12.1) from Synechocystis sp. PCC 6803 (see paper)
slr7015 hypothetical protein from Synechocystis sp. PCC 6803
Aligns to 7:182 / 190 (92.6%), covers 96.9% of PF01930, 76.0 bits
8d3qJ / A0A4Y7WTW2 Type i-c cas4-cas1-cas2 complex bound to a pam/nopam prespacer (see paper)
Aligns to 9:172 / 190 (86.3%), covers 98.1% of PF01930, 73.1 bits
- Ligands: dna; iron/sulfur cluster (8d3qJ)
PFREUD_03690 CRISPR-associated endonuclease Cas4/Cas1 from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
Aligns to 8:184 / 533 (33.2%), covers 98.1% of PF01930, 72.2 bits
GKIL_1964 CRISPR-associated protein Cas4 from Gloeobacter kilaueensis JS1
Aligns to 9:185 / 198 (89.4%), covers 96.9% of PF01930, 69.6 bits
GSU0057 CRISPR-associated protein Cas1/Cas4 from Geobacter sulfurreducens PCA
Aligns to 12:198 / 559 (33.5%), covers 97.5% of PF01930, 67.3 bits
- Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas
Hu, Nature 2021 - “...spacers were extracted and analyzed as described previously 17 . Cloning, expression and purification Gsu_cas4/1 (Gsu0057 in KEGG) gene was cloned into pET28a -His 6 -Twin-Strep-SUMO vector or pGEX-41-T-His 6 -Flag-GST, between BamHI and XhoI sites and expressed in E. coli BL21 (DE3) star cells. A...”
- Evolution and classification of the CRISPR-Cas systems
Makarova, Nature reviews. Microbiology 2011 - “...and cas3 (in subtype I-F systems), of cas1 and cas4 (such as is found in GSU0057 from G. sulfurreducens ), of cas1 and a DEDDh family exonuclease (for example, LBUL_0800 from Lactobacillus delbrueckii subsp. bulgaricus ) and of cas1 and a reverse transcriptase (for example, VVA1544...”
7mi4A / Q74H36 Symmetrical pam-pam prespacer bound cas4/cas1/cas2 complex (see paper)
Aligns to 8:194 / 554 (33.8%), covers 97.5% of PF01930, 67.3 bits
- Ligands: dna; iron/sulfur cluster; manganese (ii) ion (7mi4A)
Pisl_1722 CRISPR-associated protein Cas4 from Pyrobaculum islandicum DSM 4184
Aligns to 54:213 / 218 (73.4%), covers 96.9% of PF01930, 65.2 bits
- The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity
Lemak, Nucleic acids research 2014 - “...SSO1391 from S. solfataricus , Pcal_0546 from P. calidifontis , PAE1763 from P. aerophilum and Pisl_1722 from P. islandicum . Based on sequence, these proteins belong to either of two groups of Cas4 proteins (DUF83 and DUF911) and share low-to-medium sequence similarity to each other and...”
- “...(Figure 1A ). In contrast, the purified preparations of the Cas4 proteins Pcal_0546, PAE1763 and Pisl_1722 consistently showed a reddish or pink color in solution. Moreover, their absorption spectra were similar to that of plant-type ferredoxins or Rieske proteins containing a [2Fe-2S] cluster with a shoulder...”
Q9KFY0 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) (EC 3.1.12.1) from Alkalihalobacillus halodurans (see 2 papers)
Aligns to 6:156 / 174 (86.8%), covers 57.1% of PF01930, 64.8 bits
NGO1001 hypothetical protein, putative phage associated protein from Neisseria gonorrhoeae FA 1090
Aligns to 19:159 / 161 (87.6%), covers 72.7% of PF01930, 64.3 bits
- Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
Piekarowicz, BMC microbiology 2007 - “...presumptive proteins engaged in the recombination, control of transcription and integration of DNA. NGO1000 and NGO1001 contain motifs typically characteristic for the RecBC family exonuclease protein, while NGO1020 contains the core domain characteristic for pfam 00665, Rve integrase. This family of genes is responsible for integration...”
- “...BLASTP % identities over stated number of amino acid) NGO1000 982212984008 75 RecB family exonuclease NGO1001 973188973673 161 RecB family exonuclease NGO1002 973680974048 122 transcriptional factor [ Exiguobacterium sp . 255-15] antiterminator 27,53% on 77 (traA) [Lactococcus lactis] 20,46% on 100 NGO1003 977880978314 184 hypothetical protein...”
TTX_1548 CRISPR-associated protein Cas4 from Thermoproteus tenax Kra 1
Aligns to 52:213 / 215 (75.3%), covers 98.1% of PF01930, 63.3 bits
Tneu_0576 CRISPR-associated Cas4 family protein from Thermoproteus neutrophilus V24Sta
Tneu_0576 CRISPR-associated protein Cas4 from Pyrobaculum neutrophilum V24Sta
Aligns to 11:174 / 180 (91.1%), covers 95.7% of PF01930, 62.0 bits
Pars_0755 CRISPR-associated protein Cas4 from Pyrobaculum arsenaticum DSM 13514
Aligns to 19:177 / 178 (89.3%), covers 96.9% of PF01930, 61.4 bits
CS4F1_MYXXD / Q1CW50 CRISPR-associated exonuclease Cas4/endonuclease Cas1 fusion; EC 3.1.-.-; EC 3.1.12.1 from Myxococcus xanthus (strain DK1622) (see paper)
Aligns to 33:209 / 568 (31.2%), covers 96.9% of PF01930, 57.9 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) (By similarity). The Cas4 region acts as a ssDNA exonuclease, while the Cas1 region acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit.)
cofactor: Mg(2+) Mn(2+)
subunit: Homodimer, forms a heterotetramer with a Cas2 homodimer.
Francci3_3345 CRISPR-associated protein Cas4 from Frankia sp. CcI3
Aligns to 18:198 / 221 (81.9%), covers 98.1% of PF01930, 57.0 bits
- Transcriptomes of Frankia sp. strain CcI3 in growth transitions
Bickhart, BMC microbiology 2011 - “...CRISPR-associated protein Francci3_0020 869 transcriptional regulator, CarD Francci3_4255 1596 hypothetical protein Francci3_4114 821 CRISPR-associated protein Francci3_3345 863 alanine dehydrogenase/PNT-like Francci3_2946 1532 Alcohol dehydrogenase Francci3_2945 796 glycosyl transferase Francci3_3318 859 serine phosphatase Francci3_3249 1453 hypothetical protein Francci3_3791 782 metallophosphoesterase Francci3_1990 839 chaperonin GroEL Francci3_0633 1439 acyl-CoA dehydrogenase...”
- “...Francci3_3248 906 Recombinase Francci3_2373 607 major facilitator MFS_1 Francci3_2752 643 translationinitiationfactorIF-1 Francci3_0605 904 CRISPR-associated protein Francci3_3345 606 Inorganic diphosphatase Francci3_4310 636 electron transfer flavoprotein Francci3_3659 889 hypothetical protein Francci3_2219 606 hypothetical protein Francci3_1032 636 hypothetical protein Francci3_4326 884 hypothetical protein Francci3_3299 605 DNA-directed RNA polymerase Francci3_3194...”
PAE0079 conserved hypothetical protein from Pyrobaculum aerophilum str. IM2
Aligns to 7:170 / 171 (95.9%), covers 96.3% of PF01930, 56.7 bits
- Annotation and Classification of CRISPR-Cas Systems
Makarova, Methods in molecular biology (Clifton, N.J.) 2015 - “...enzyme. Cas4 proteins of two distinct families are often present in the same operon (e.g., PAE0079- PAE0082 in Pyrobaculum aerophilum str. IM2) suggestive of functional differentiation ( Fig. 4 ). A variety of other Cas proteins and proteins that are sporadically present within CRISPR-Cas loci are...”
- Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum
Bernick, Frontiers in microbiology 2012 - “...Strand Pyrobaculum aerophilum PAE0067 cas3 PAE0068 cas3 Crispr1 39812 40776 PAE0075 cas6 PAE0077 csx1 + PAE0079 cas4 PAE0080 cas2 PAE0081 cas1 PAE0082 cas4 Crispr2 + 45503 46687 PAE0109 cas10 PAE0111 csm5 PAE0112 csm4 PAE0114 csm3 PAE0115 csm2 PAE0117 csx1 PAE0119 csx1 + PAE0122 nura + PAE0124...”
SSO1449 Hypothetical protein from Sulfolobus solfataricus P2
Aligns to 3:171 / 175 (96.6%), covers 98.1% of PF01930, 54.9 bits
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...tasks ( Liuetal., 2017 ). The Sulfolobus solfataricus genome encodes five Cas4-like proteins (Sso0001, Sso1392, Sso1449, Sso1391, Sso1451), which stake low sequence similarity (15 to 30% sequence identity) ( Lemaketal., 2013 ). The crystal structures of the Cas4 proteins from S. solfataricus (Sso0001) and Pyrobaculum calidifontis...”
- Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus
Lemak, Journal of the American Chemical Society 2013 - “...share low sequence similarity (15 to 30% sequence identity) and belong to DUF83 (SSO0001, SSO1392, SSO1449) and DUF911 (SSO1391, SSO1451) ( Supplementary Fig. S1 ). Recently, the purified SSO0001 has been shown to possess a 5 to 3 exonuclease activity 20 . Here, we demonstrate that...”
PAE1763 conserved hypothetical protein from Pyrobaculum aerophilum str. IM2
Aligns to 54:212 / 214 (74.3%), covers 96.9% of PF01930, 54.9 bits
- The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity
Lemak, Nucleic acids research 2014 - “...proteins from different organisms including SSO1391 from S. solfataricus , Pcal_0546 from P. calidifontis , PAE1763 from P. aerophilum and Pisl_1722 from P. islandicum . Based on sequence, these proteins belong to either of two groups of Cas4 proteins (DUF83 and DUF911) and share low-to-medium sequence...”
- “...[4Fe-4S] cluster (Figure 1A ). In contrast, the purified preparations of the Cas4 proteins Pcal_0546, PAE1763 and Pisl_1722 consistently showed a reddish or pink color in solution. Moreover, their absorption spectra were similar to that of plant-type ferredoxins or Rieske proteins containing a [2Fe-2S] cluster with...”
F0NH45 CRISPR-associated exonuclease Cas4 from Sulfolobus islandicus (strain REY15A)
SiRe_0763 CRISPR-associated protein Cas4 from Sulfolobus islandicus REY15A
Aligns to 3:171 / 175 (96.6%), covers 95.7% of PF01930, 54.6 bits
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...the Pyrobaculum calidifontis (PcaCas4; A3MTK6), Pyrococcus furiosus (PfuCas41; Q8U1T6 and PfuCas42; Q8U027), Sulfolobus islandicus (SisCas4; F0NH45), and Sulfolobus solfataricus (Sso0001; Q97TX9). The secondary structure elements represented at the top are inferred based on the known crystal structures of the Sso0001 and at the bottom one of...”
- A CRISPR-associated factor Csa3a regulates DNA damage repair in Crenarchaeon Sulfolobus islandicus
Liu, Nucleic acids research 2020 - “...subtype I-A adaptation module consisting of the csa1 (SiRe_0760), cas1 (SiRe_0761), cas2 (SiRe_0762) and cas4 (SiRe_0763) genes, which are regulated by a factor encoded by the CRISPR-associated csa3a gene (Figure 1A ) ( 7 ). Besides, this strain carries an ups operon and a ced cluster...”
- Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers
Zhang, Journal of bacteriology 2019 - “...Asp residue in S. islandicus Cas4 (D60 in SiRe_0763) and the CRISPR-linked Csa1 proteins and two conserved Trp/Leu residues in the CRISPR-linked Cas4 proteins...”
- “...C169 Cas4 SiRe_0763 IR.SELVTVKTI SSEEN..FYEGIVDLFDKVIYRILKFKEQDNEVYINATPGLKPESIFLTLAGLLAGADLI FY.VEF.PVDG....”
- Coupling transcriptional activation of CRISPR-Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus
Liu, Nucleic acids research 2017 - “...REY15A ( 42 ) was employed to delete the cas1 (SiRe_0761), cas2 (SiRe_0762) and cas4 (SiRe_0763) genes, and to prepare the cas3/cmr2/cmr2 (SiRe_0769/SiRe_0894/SiRe_0598) triple deletion mutant. The left sequence arm (L-arm), right sequence arm (R-arm), and target gene arm (G-arm) were amplified from S. islandicus REY15A...”
- “...10.10 SiRe_0761 Cas1 7.12 2.65 / / 6.80 SiRe_0762 Cas2 6.75 2.19 11.49 1.56 8.87 SiRe_0763 Cas4 7.74 1.52 9.81 3.24 7.57 SiRe_0764 Csa3a 8.05 3.15 10.15 2.67 8.58 SiRe_1994 Cas4 1.45 DNA repair and replication SiRe_0014 NurA 1.70 1.08 SiRe_0016 chromosome segregation protein (SMC)-like protein...”
- Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition
Liu, Nucleic acids research 2015 - “...encodes a single gene cassette containing the csa1 (SiRe_0760), cas1 (SiRe_0761), cas2 (SiRe_0762) and cas4 (SiRe_0763) genes, in which cas1 and cas2 have been implicated in spacer acquisition in this archaeon (Figure 1A ). To investigate the function of these cas genes and the regulation of...”
CAS4_FRATN / A0Q5Y6 CRISPR-associated exonuclease Cas4; EC 3.1.12.1 from Francisella tularensis subsp. novicida (strain U112) (see paper)
FTN_0760 hypothetical protein from Francisella tularensis subsp. novicida U112
Aligns to 13:195 / 196 (93.4%), covers 96.9% of PF01930, 54.0 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). This may be a 5' to 3' ssDNA exonuclease (By similarity).
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: Mg(2+) (Mg(2+) or Mn(2+) required for ssDNA cleavage activity.)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit. It may be important for protein stability, since mutation of the Cys that binds the cofactor leads to a colorless, insoluble protein.)
disruption phenotype: No effect on expression of bacterial lipoprotein FTN_1103. Bacteria are as virulent in mice as wild-type bacteria. - Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
Akimana, Frontiers in microbiology 2011 - “...protein, di- or tripeptide:H+ symporter FTN_0750 l -Serine dehydratase 1 sdaA FTN_0759 Conserved hypothetical protein FTN_0760 Conserved hypothetical protein FTN_0768 Tryptophan-rich sensory protein tspO FTN_0770 Major facilitator superfamily (MFS) transport protein, pseudogene bcr1 FTN_0772 Conserved protein of unknown function FTN_0773 4Fe4S ferredoxin (electron transport) family protein,...”
CAS4_PYRCJ / A3MTK6 CRISPR-associated exonuclease Cas4; EC 3.1.12.1 from Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1) (see 2 papers)
A3MTK6 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) (EC 3.1.12.1) from Pyrobaculum calidifontis (see paper)
Pcal_0546 CRISPR-associated protein Cas4 from Pyrobaculum calidifontis JCM 11548
Aligns to 54:211 / 213 (74.2%), covers 97.5% of PF01930, 53.4 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). A ssDNA exonuclease that has 5' to 3' activity, yielding 5'-OH and 3'-phosphate groups. Has Mn(2+)-dependent endonuclease activity on circular ssDNA. Can unwind dsDNA; unwinding does not require ATP.
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit. Not required for nuclease activity, since mutation of the Cys residues leads to a colorless but active protein.)
cofactor: Mn(2+) Co(2+) (Mn(2+) required for ssDNA cleavage activity. Can also utilize Co(2+) and to a lesser extent Mg(2+).)
subunit: Monomer. - Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays
Lee, Molecular cell 2018 - “...four distinct subunits ( Figure 1C ). Notably, the crystal structure of the Cas4 protein Pcal_0546 from Pyrobaculum calidifontis (PDB ID: 4R5Q) ( Lemak et al., 2014 ) fits perfectly into the two small subunits at the top of the claw, while the crystal structure of...”
- “...in Chimera ( Pettersen et al., 2004 ). The crystal structures of the Cas4 protein Pcal_0546 from Pyrobaculum calidifontis (PDB ID: 4R5Q) ( Lemak et al., 2014 ), Cas1 from Archaeoglobus fulgidus (PDB ID: 4N06) ( Kim et al., 2013 ), and the Cas1 dimers in...”
- Phylogenomics of Cas4 family nucleases
Hudaiberdiev, BMC evolutionary biology 2017 - “...16 ]. In the structures that have been solved for Cas4 proteins from Pyrobaculum calidifontis (Pcal_0546; pdb: 4R5Q) [ 15 ] and Sulfolobus solfataricus (SSO0001, pdb: 4IC1) [ 2 ], Pcal_0546 is a monomer, whereas SSO0001 forms a toroidal decamer composed of 5 tightly packed dimers....”
- “...T Flick R Brown G Joachimiak A Savchenko A Yakunin AF The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity Nucleic Acids Res 2014 42 17 11144 11155 10.1093/nar/gku797 25200083 16. Zhang J Kasciukovic T White MF The...”
- The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity
Lemak, Nucleic acids research 2014 - “...0305-1048 1362-4962 Oxford University Press 4176176 25200083 10.1093/nar/gku797 Nucleic Acid Enzymes The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity Lemak Sofia 1 Nocek Boguslaw 2 Beloglazova Natalia 1 Skarina Tatiana 1 Flick Robert 1 Brown Greg 1...”
- “...about their structure and activity. Here we report the crystal structure of the Cas4 protein Pcal_0546 from Pyrobaculum calidifontis , which revealed a monomeric protein with a RecB-like fold and one [2Fe-2S] cluster coordinated by four conserved Cys residues. Pcal_0546 exhibits metal-dependent 5 to 3 exonuclease...”
- Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus
Lemak, Journal of the American Chemical Society 2013 - “...activity of Cas4 proteins The purified Cas4 proteins SSO0001 and SSO1391 from S. solfataricus and Pcal_0546 from Pyrobaculum calidifontis exhibited a brown color indicating the presence of functional Fe-S clusters ( Fig. 1a ). Their absorption spectra showed the presence of a broad shoulder at 380420...”
- “...i ). The 5' to 3' exonuclease activity was also observed in the Cas4 protein Pcal_0546 (also DUF83), whereas SSO1391 (DUF911) produced a range of cleavage products with both substrates indicating that it cleaves ssDNA in both directions (5' 3' and 3' 5') ( Fig. 1c...”
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...the CRISPR-Cas I-B is compared with the available Cas4 sequence of the Pyrobaculum calidifontis (PcaCas4; A3MTK6), Pyrococcus furiosus (PfuCas41; Q8U1T6 and PfuCas42; Q8U027), Sulfolobus islandicus (SisCas4; F0NH45), and Sulfolobus solfataricus (Sso0001; Q97TX9). The secondary structure elements represented at the top are inferred based on the known...”
- Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China.
Xu, Journal of virology 2020
PAE0198 conserved hypothetical protein from Pyrobaculum aerophilum str. IM2
Aligns to 6:182 / 190 (93.2%), covers 97.5% of PF01930, 53.3 bits
4r5qA / A3MTK6 Crystal structure and nuclease activity of the crispr-associated cas4 protein pcal_0546 from pyrobaculum calidifontis containing a [2fe-2s] cluster
Aligns to 57:214 / 215 (73.5%), covers 97.5% of PF01930, 53.3 bits
- Ligands: magnesium ion; fe2/s2 (inorganic) cluster (4r5qA)
Pcal_1277 CRISPR-associated protein Cas4 from Pyrobaculum calidifontis JCM 11548
Aligns to 6:181 / 189 (93.1%), covers 97.5% of PF01930, 52.8 bits
CAS4_THETK / G4RJY5 CRISPR-associated exonuclease Cas4; EC 3.1.12.1 from Thermoproteus tenax (strain ATCC 35583 / DSM 2078 / JCM 9277 / NBRC 100435 / Kra 1) (see paper)
Aligns to 6:182 / 190 (93.2%), covers 97.5% of PF01930, 51.7 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). This may be a 5' to 3' ssDNA exonuclease (By similarity).
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: Mg(2+) Mn(2+) Cu(2+) (Mg(2+) or Mn(2+) required for ssDNA cleavage activity. Can also utilise Cu(2+).)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit. It may be important for protein stability, since mutation of the Cys that bind the cofactor leads to a colorless, insoluble protein.)
subunit: Can form a Cascis complex with Cas1/2 and Csa1.
MM_0557 hypothetical protein from Methanosarcina mazei Goe1
Aligns to 12:199 / 199 (94.5%), covers 98.8% of PF01930, 50.9 bits
MM_RS02925 CRISPR-associated protein Cas4 from Methanosarcina mazei Go1
Aligns to 37:224 / 224 (83.9%), covers 98.8% of PF01930, 50.3 bits
Tneu_1142 CRISPR-associated protein Cas4 from Pyrobaculum neutrophilum V24Sta
Tneu_1142 CRISPR-associated Cas4 family protein from Thermoproteus neutrophilus V24Sta
Aligns to 6:182 / 190 (93.2%), covers 97.5% of PF01930, 49.1 bits
FTL_1320 hypothetical protein from Francisella tularensis subsp. holarctica
Aligns to 11:189 / 190 (94.2%), covers 96.9% of PF01930, 44.9 bits
- Identification of small RNAs in Francisella tularensis
Postic, BMC genomics 2010 - “...a gene encoded on the non-coding strand. The ftrA gene is located between FTL_1319 and FTL_1320 (Table 1 and Figure 3 ) and is encoded on the coding strand. The flanking genes encode a transposase and a conserved hypothetical protein. FtrB is encoded on the coding...”
Pars_1121 CRISPR-associated protein Cas4 from Pyrobaculum arsenaticum DSM 13514
Aligns to 7:182 / 190 (92.6%), covers 96.9% of PF01930, 44.3 bits
FN0524 DNA helicase II from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Aligns to 758:917 / 919 (17.4%), covers 70.8% of PF01930, 41.8 bits
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...8 5 1 Covers: FN0019, FN0047, FN0065, FN0117, FN0157, FN0158, FN0224, FN0268, FN0297, FN0374, FN0462, FN0524, FN0547, FN0592, FN0622, FN0693, FN0705, FN0962, FN1103, FN1149, FN1217, FN1226, FN1304, FN1581, FN1660, FN1717, FN1864, FN2018. 2 Covers: FN1088, FN1123, FN1163, FN1983, FN1984, FN2007, FN2067. 3 Covers: FN0113, FN0114, FN0116,...”
- Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics
Mira, BMC evolutionary biology 2004 - “...402 and 618 bp 2137 FN0515 to FN0519 Vibrio cholerae 22 Mixed functions cluster 3044 FN0524 to FN0527 23 LPS synthesis and/or decoration and outer membarne stabilization Includes recA and recX proteins with best match to Caulobacter and Vibrio 29100 FN0538 to FN0548 Haemophilus ducreyi 24...”
CIMG_13558 DNA replication helicase Dna2 from Coccidioides immitis RS
Aligns to 760:880 / 1659 (7.3%), covers 62.7% of PF01930, 35.4 bits
lpp0163 hypothetical protein from Legionella pneumophila str. Paris
Aligns to 9:195 / 197 (94.9%), covers 97.5% of PF01930, 34.0 bits
FACI_IFERC00001G0010 ATP-dependent DNA helicase from Ferroplasma acidarmanus Fer1
Aligns to 735:886 / 889 (17.1%), covers 67.1% of PF01930, 32.2 bits
NP_666553 hypothetical protein from Sulfolobus islandicus rod-shaped virus 2
Aligns to 26:204 / 207 (86.5%), covers 94.4% of PF01930, 31.5 bits
SiRe_1994 CRISPR-associated protein Cas4 from Sulfolobus islandicus REY15A
Aligns to 22:199 / 202 (88.1%), covers 96.9% of PF01930, 31.4 bits
CAS4_SACS2 / Q97TX9 CRISPR-associated exonuclease Cas4; EC 3.1.12.1 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see 2 papers)
Q97TX9 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) (EC 3.1.12.1) from Saccharolobus solfataricus (see 3 papers)
SSO0001 Hypothetical protein from Sulfolobus solfataricus P2
Aligns to 22:199 / 202 (88.1%), covers 96.3% of PF01930, 30.6 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (By similarity). This protein is a 5' to 3' partially processive exonuclease that cleaves off single mononucleotides. Has a marked preference for ssDNA, although in vitro it also acts on dsDNA and ssRNA. Has low endonuclease activity with circular ssDNA. Binds ssDNA and can unwind dsDNA; unwinding does not require ATP.
catalytic activity: exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.
cofactor: Mg(2+) Mn(2+) Cu(2+) (Mg(2+) or Mn(2+) required for ssDNA cleavage activity. Can also utilise Cu(2+).)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit (PubMed:24171432). It may be important for protein stability, since mutation of the Cys that bind the cofactor leads to a colorless, insoluble protein.)
subunit: Homodecamer, formed by the assembly of dimers into a decameric toroid, with the active sites oriented towards the central tunnel. - The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity.
Dixit, Current research in microbial sciences 2021 - “...Pyrococcus furiosus (PfuCas41; Q8U1T6 and PfuCas42; Q8U027), Sulfolobus islandicus (SisCas4; F0NH45), and Sulfolobus solfataricus (Sso0001; Q97TX9). The secondary structure elements represented at the top are inferred based on the known crystal structures of the Sso0001 and at the bottom one of PcaCas4 . Four conserved cysteine...”
- The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity
Dixit, Current research in microbial sciences 2021 - “...execute different tasks ( Liuetal., 2017 ). The Sulfolobus solfataricus genome encodes five Cas4-like proteins (Sso0001, Sso1392, Sso1449, Sso1391, Sso1451), which stake low sequence similarity (15 to 30% sequence identity) ( Lemaketal., 2013 ). The crystal structures of the Cas4 proteins from S. solfataricus (Sso0001) and...”
- “...cluster coordinated by four conserved cysteine residues ( Zhangetal., 2012 ; Lemaketal., 2014 ). The Sso0001 possesses a 4Fe-4S cluster coordinated by four cysteine residues (Cys32, 188, 191, and 197) ( Lemaketal., 2013 ). Mutation of one of the cysteine residues of Sso0001 results in the...”
- Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers
Zhang, Journal of bacteriology 2019 - “...motif (Fig. 8B). D70, corresponding to S. solfataricus Sso0001, is essential to its in vitro nuclease activity (34), and D70 corresponds to the residue...”
- “...CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. J Am Chem Soc 135: 17476 -17487....”
- Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen
Goethe, Entropy (Basel, Switzerland) 2018 - “...Entropy (Basel) entropy Entropy 1099-4300 MDPI 7513108 10.3390/e20080580 entropy-20-00580 Article Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen https://orcid.org/0000-0002-5826-2180 Goethe Martin 1 2 * Fita Ignacio 3 Rubi J. Miguel 1 1 Department of Condensed Matter Physics, University of Barcelona, Carrer Mart i Franqus 1,...”
- “...entropy for performance reasons. Here, we apply Popcoen to various conformations of the Cas4 protein SSO0001 of Sulfolobus solfataricus , a protein that assembles to a decamer of known toroidal shape. We provide numerical evidence that the native state (NAT) of a SSO0001 monomer has a...”
- Comparative genetic and genomic analysis of the novel fusellovirus Sulfolobus spindle-shaped virus 10
Goodman, Virus evolution 2018 - “...Transcriptional regulator C102 (T6) Transmembrane protein Replication complex (2 TMH) B205 (T6) S. solfataricus Cas4 SSO0001 (PDB: 4IC1) 95%@100 Anti-CRISPR/DNA repair C127 (T6) SSV1 ORF B129 C2H2 Zinc Finger (PDB: 2WBT) 99%@100 Transcriptional regulator A110 (T6) Transmembrane protein Virion assembly/egress (3 TMH) B298 (T3) Transmembrane protein...”
- “...directly ( Plagens etal. 2012 ). In S. solfataricus , monomers of the Cas4 protein SSO0001 come together to form a decameric toroidal quaternary structure thought to be part of the CRISPR/Cas spacer acquisition complex along with Cas1 and Cas2 ( Zhang etal. 2012 ; Lemak...”
- Functional divergence and comparative in-silico study of Cas4 proteins of DUF83 class
Kaushik, Journal of molecular recognition : JMR 2018 (PubMed)- “...ORDS Cas4, divergence, DUF83, Pyrobaculum calidifontis (P.cali_0546), Sulfolobus solfatricus (SSO0001) 1 | I N T RO D U CT I O N interference step. In this...”
- “...structures of 2 Cas4 protein from Sulfolobus solfatricus (SSO0001) and mentary file) of DUF83 class were retrieved from Uniprot and Both European Nucleotide...”
- Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation
Kieper, Cell reports 2018 - “...substituting a divalent metal-ion binding aspartic acid for alanine (i.e., D76 corresponding to D99 in Sso0001) ( Zhang etal., 2012 ). When this mutant was introduced in strains containing pCas1-2, the same spacer length mode was observed as when cas4 was absent, showing that the catalytic...”
- “...Yakunin A.F. Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus J.Am. Chem. Soc. 135 2013 17476 17487 24171432 Lemak S. Nocek B. Beloglazova N. Skarina T. Flick R. Brown G. Joachimiak A. Savchenko A. Yakunin A.F. The...”
- Structural insights into DNA degradation by human mitochondrial nuclease MGME1
Yang, Nucleic acids research 2018 - “...similar to that of Ec RecE (PDB_ID: 3H4R) ( 42 ), followed by Cas4 nuclease SSO0001 from Sulfolobus solfataricus (PDB_ID: 4IC1) ( 43 ) and an uncharacterized exonuclease from Eubacterium rectale (PDB_ID: 3L0A). MGME1 also shares structural similarity with the structure of phage-related exonuclease (PDB_ID: 3K93)...”
- “...DNA from the 5-end similar to the phage lambda exonuclease. Unlike Ec RecE, Cas4 nuclease SSO0001, the uncharacterized E.rectale exonuclease, phage-related exonuclease, and phage lambda exonuclease, which all function as oligomers, Hs MGME1 functions as a monomer. This unique feature sets Hs MGME1 apart from other...”
- Phylogenomics of Cas4 family nucleases
Hudaiberdiev, BMC evolutionary biology 2017 - “...for Cas4 proteins from Pyrobaculum calidifontis (Pcal_0546; pdb: 4R5Q) [ 15 ] and Sulfolobus solfataricus (SSO0001, pdb: 4IC1) [ 2 ], Pcal_0546 is a monomer, whereas SSO0001 forms a toroidal decamer composed of 5 tightly packed dimers. The Pcal_0546 protein has been shown to exhibit a...”
- “...Yakunin AF Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus J Am Chem Soc 2013 135 46 17476 17487 10.1021/ja408729b 24171432 3. Li M Wang R Zhao D Xiang H Adaptation of the Haloarcula hispanica CRISPR-Cas system...”
- More
4ic1D / Q97TX9 Crystal structure of sso0001 (see paper)
Aligns to 26:203 / 206 (86.4%), covers 96.3% of PF01930, 30.5 bits
- Ligands: manganese (ii) ion; iron/sulfur cluster (4ic1D)
BTH_I1443 Superfamily I DNA and RNA helicases from Burkholderia thailandensis E264
Aligns to 773:915 / 920 (15.5%), covers 70.8% of PF01930, 29.1 bits
NP_001184943 DNA replication helicase from Arabidopsis thaliana
Aligns to 482:661 / 1315 (13.7%), covers 90.1% of PF01930, 28.6 bits
JHS1_ARATH / A0A1P8ASY1 DNA replication ATP-dependent helicase/nuclease JHS1; Protein EMBRYO DEFECTIVE 2411; Protein JING HE SHENG 1; EC 3.1.-.-; EC 3.6.4.12 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Aligns to 498:677 / 1331 (13.5%), covers 90.1% of PF01930, 28.6 bits
- function: Essential protein required during embryogenesis (PubMed:15266054). Key enzyme involved in DNA replication and damage repair, shoot apical meristem (SAM) maintenance, and development (PubMed:26951435). Involved in Okazaki fragments processing. Possesses different enzymatic activities, such as single-stranded DNA (ssDNA)- dependent ATPase, 5'-3' helicase and endonuclease activities. While the ATPase and endonuclease activities are well-defined and play a key role in Okazaki fragments processing and DSB repair, the 5'-3' DNA helicase activity is atypical: it cannot load onto its tracking strand internally and has an absolute free 5'-end requirement (By similarity).
catalytic activity: ATP + H2O = ADP + H(+) + phosphate (RHEA:13065)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
disruption phenotype: Defective embryo arrested at preglobular/early globular stage with the formation of giant endosperm nuclei (PubMed:15266054). In jhs1, retarded growth, abnormal pattern of shoot apical meristem (SAM) cell division and differentiation, and morphological defects such as fasciation, irregular arrangement of siliques and phyllotaxy, and short roots (PubMed:26951435). Increased sensitivity to DNA damage stress (PubMed:26951435). Increased DNA damage response, including increased expression of genes involved in DNA damage repair and cell cycle regulation, and a higher frequency of homologous recombination (PubMed:26951435). Meristems exhibit a delayed cell cycle progression at the G2 or late S phase, and a misregulation of genes essential for meristem maintenance (PubMed:26951435).
SJAG_04183 DNA replication endonuclease-helicase Dna2 from Schizosaccharomyces japonicus yFS275
Aligns to 317:442 / 1133 (11.1%), covers 59.0% of PF01930, 28.2 bits
NGO1000 hypothetical protein, putative phage associated protein from Neisseria gonorrhoeae FA 1090
Aligns to 14:56 / 75 (57.3%), covers 24.2% of PF01930, 25.1 bits
- Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
Piekarowicz, BMC microbiology 2007 - “...only the presumptive proteins engaged in the recombination, control of transcription and integration of DNA. NGO1000 and NGO1001 contain motifs typically characteristic for the RecBC family exonuclease protein, while NGO1020 contains the core domain characteristic for pfam 00665, Rve integrase. This family of genes is responsible...”
- “...proteins in GeneBank (Scores represent filtered BLASTP % identities over stated number of amino acid) NGO1000 982212984008 75 RecB family exonuclease NGO1001 973188973673 161 RecB family exonuclease NGO1002 973680974048 122 transcriptional factor [ Exiguobacterium sp . 255-15] antiterminator 27,53% on 77 (traA) [Lactococcus lactis] 20,46% on...”
TT_P0136 No description from Thermus thermophilus HB27
Aligns to 7:108 / 116 (87.9%), covers 47.8% of PF01930, 23.7 bits
- DNA-guided DNA interference by a prokaryotic Argonaute
Swarts, Nature 2014 - “...Cas3 0.22 (0.20) TT_P0133 Cas4 1.14 (<0.01) TT_P0134 Cas8C 0.80 (<0.01) TT_P0135 Cas7 0.50 (<0.01) TT_P0136 Cas4 0.48 (0.01) TT_P0195 Cas2 1.42 (0.15) TT_P0196 Cas1 0.52 (0.20) TT_P0197 Cas4 0.34 (0.44) TT_P0204 Cas6 0.73 (0.01) TT_P0215 Cas1 0.16 (0.42) Expression values are given as log 2...”
Or search for genetic data about PF01930 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory