Family Search for PF12469 (Cmr2_N)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF12469 hits 23 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
sll7090 hypothetical protein from Synechocystis sp. PCC 6803
Aligns to 222:344 / 979 (12.6%), covers 99.1% of PF12469, 129.8 bits
- Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
Riediger, The Plant cell 2021 - “...Cmr5, Cmr4, Cmr3, and Cmr2/Cas10 encoded by the genes sll7085 to sll7087, sll7089 , and sll7090 ) fractionated together and with the CRISPR3-associated crRNAs, with a peak in Fraction 10. This cofractionation indicates that the interference complex remained largely intact during the preparation. However, these proteins...”
- “...peak in the lower Fractions F3F4 without associated cr3RNA or the Cas10 protein (encoded by sll7090 ), hence constituting a potentially nonfunctional subcomplex or resulting from partial disassembly of the complex during lysis preparation or centrifugation ( Figure4B ). Interestingly, the slr7080 gene product, a Csx3...”
- The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803
Srikumar, The Journal of biological chemistry 2017 - “...bold letters). These genes were sll7064, sll7067, sll7085, sll7090, slr7091, sll5097 and sll6010. In addition, we chose two chromosomelocated genes, slr0909 and...”
- “...expression 100 10 slr0909 1 sll7064 0.1 sll7067 sll7085 sll7090 sll1396 sll6010 slr7091 sll5097 sll1130 / WT (Microarray) sll1130 / WT (qRT-PCR) ssl2245 / WT...”
- Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium
Ge, Molecular & cellular proteomics : MCP 2017 - “...and only five proteins (Sll7085, Sll7086, Sll7087, Sll7089, and sll7090) encoded by an operon on the plasmid pSYSA were downregulated in the mutant (Fig. 5B)....”
- “...(Cas) proteins including Sll7085, Sll7087, Sll7089, and Sll7090. Deletion of sll7090 results in complete loss of the precursor and processed RNA...”
- Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803
Borirak, Biotechnology for biofuels 2015 - “...may be a consequence of this. Besides that, three distinct proteins, i.e. Sll7065, Sll7087, and Sll7090, were found to be >2-fold up-regulated. The expression of these proteins, and their probable function, has recently been characterized [ 42 ]. They have been described as CRISPR2- or CRISPR3-system...”
- “...show any up-regulation in that mutant. Sll7065 was even significantly down-regulated in the ethanol-producing strain. Sll7090 (CRISPR3-associated protein Cmr2, cas10) could only be quantified in SAW041. Little is known about the exact function of these two CRISPR systems in Synechocystis , except that the CRISPR3 system...”
- CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein
Scholz, PloS one 2013 - “...CRISPR1 and CRISPR2 transcripts depends on at least two different Cas6 proteins. Mutation of gene sll7090 , encoding a Cmr2 protein led to the disappearance of all CRISPR3-derived crRNAs, providing in vivo evidence for a function of Cmr2 in the maturation, regulation of expression, Cmr complex...”
- “...Mature crRNAs are indicated by asterisks. 10.1371/journal.pone.0056470.g006 Figure 6 The Cmr2 protein encoded by gene sll7090 is a major factor for the expression of CRISPR3. The effect of its knock-out mutation () on the accumulation of CRISPR3-derived crRNAs, compared to wildtype (WT), is shown, together with...”
- Adaptation and modification of three CRISPR loci in two closely related cyanobacteria
Hein, RNA biology 2013 - “...of the gene. This result suggested Cmr2 (Sll7090) as involved in the maturation, regulation of expression, Cmr complex formation or stabilization...”
TM1794 conserved hypothetical protein from Thermotoga maritima MSB8
Aligns to 192:309 / 815 (14.5%), covers 99.1% of PF12469, 120.0 bits
3x1lA / Q8U1S6 Crystal structure of the crispr-cas RNA silencing cmr complex bound to a target analog (see paper)
Aligns to 4:114 / 573 (19.4%), covers 97.3% of PF12469, 113.7 bits
- Ligands: dna; zinc ion (3x1lA)
4dozA / Q8U1S6 Crystal structure of pyrococcus furiosus cmr2 (cas10) (see paper)
Aligns to 17:127 / 557 (19.9%), covers 97.3% of PF12469, 113.4 bits
3w2wA / Q8U1S6 Crystal structure of the cmr2dhd-cmr3 subcomplex bound to atp (see paper)
Aligns to 6:116 / 618 (18.0%), covers 97.3% of PF12469, 113.2 bits
- Ligands: zinc ion; adenosine-5'-triphosphate; magnesium ion (3w2wA)
4w8yA / Q8U1S6 Structure of full length cmr2 from pyrococcus furiosus (manganese bound form) (see paper)
Aligns to 207:317 / 835 (13.3%), covers 97.3% of PF12469, 112.1 bits
- Ligands: zinc ion; manganese (ii) ion (4w8yA)
CMR2_PYRFU / Q8U1S6 CRISPR system Cmr subunit Cmr2; CRISPR-associated protein Cas10/Cmr2, subtype III-B from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (see 7 papers)
PF1129 hypothetical protein from Pyrococcus furiosus DSM 3638
Aligns to 221:331 / 871 (12.7%), covers 97.3% of PF12469, 111.9 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation- dependent endoribonuclease activity specific for ssRNA complementary to the crRNA (target RNA), generating 5' hydroxy- and 3' phosphate or 2'- 3' cyclic phosphate termini. Cmr4 is probably the subunit that cleaves target RNA (PubMed:25280103). Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of target RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not absolutely necessary for target cleavage (PubMed:19945378).
cofactor: Ca(2+) (Binds 2 Ca(2+) per subunit, this may not be the physiological cation.)
cofactor: Mn(2+) (Binds 4 Mn(2+) per subunit.)
cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
subunit: Part of the type III-B Cmr ribonucleoprotein (RNP) complex, an elongated RNP with Cmr2 and Cmr3 as the base, with Cmr4 and Cmr5 forming a helical core along the mature crRNA (39 or 45 nt in length), while the complex is capped by Cmr6 and Cmr1. The 5' end of the crRNA is bound to Cmr2 and Cmr3, while Cmr6 and a Cmr1 subunit (Cmr1-1 or Cmr1-2) cap the 3' end of the crRNA. The target RNA lies antiparallel to the crRNA, with its 5' end near Cmr1 and Cmr6 and its 3' end near Cmr2 and Cmr3; major target cleavage occurs nears the junction of Cmr1/Cmr6 and Cmr4/Cmr, with minor cleavage occurring at 6 nt intervals which coincide with the proposed spacing of Cmr4 subunits (PubMed:24119404, PubMed:25280103). Forms a 1:1 complex with Cmr3 (PubMed:23583914, PubMed:23395183). The Cmr2-Cmr3 complex non- specifically binds ss-target RNA and crRNA (PubMed:23583914). Interacts with Cmr3, Cmr4 and Cmr5 (PubMed:25280103). - Harnessing Type I and Type III CRISPR-Cas systems for genome editing
Li, Nucleic acids research 2016 - “...of the N-termini of S. islandicus Cmr-2 (SiRe-0894), Cmr-2 (SiRe-0598) and its Pyrococcus furiosus homolog PF1129. Four conserved amino acids were chosen for constructing substitution mutations (indicated with red asterisks). ( B ) Schematic of the mutagenic strategy. The I-A target site is underlined and bases...”
- Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex
Shao, Structure (London, England : 1993) 2013 - “...Pf Cmr3 (Pf1128) was co-purified as a 1:1 complex with an N-terminally tagged Pf Cmr2dHD (Pf1129) lacking the N-terminal HD domain (residues 1 - 212) ( Cocozaki et al., 2012 ). The Cmr2dHD-Cmr3 complex was crystallized in space group I222 with one protein complex in the...”
- RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex
Hale, Cell 2009 - “...above. Expression and purification of recombinant proteins The genes encoding P. furiosus Cmr1-1 (PF1130), Cmr2 (PF1129), Cmr3 (PF1128), Cmr4 (PF1126), Cmr5 (PF1125) and Cmr6 (PF1124) were amplified by PCR from genomic DNA or existing constructs and cloned into a modified version of pET24d (PF1124, PF1125 and...”
- Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
Schut, Journal of bacteriology 2003 - “...PF1056 PF1104 [Unknown] PF1109 PF1110 [Unknown] PF1129 PF1130 [Methionine biosynthesis] PF1266 PF1267 PF1268 PF1269 Ferredoxin:NADPH oxidoreductase I PF1327...”
6s6bK / F0NDX2 Type iii-b cmr-beta cryo-em structure of the apo state (see paper)
Aligns to 189:339 / 1024 (14.7%), covers 100.0% of PF12469, 103.9 bits
SIRE_RS04505, SiRe_0894 type III-B CRISPR-associated protein Cas10/Cmr2 from Sulfolobus islandicus REY15A
Aligns to 189:315 / 882 (14.4%), covers 99.1% of PF12469, 100.6 bits
CMR2_SACS2 / Q97WX0 CRISPR system CMR subunit Cmr2; CRISPR-associated protein Cas10/Cmr2, subtype III-B from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see paper)
SSO1991 Hypothetical protein from Sulfolobus solfataricus P2
Aligns to 204:354 / 1045 (14.4%), covers 100.0% of PF12469, 100.6 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 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 CMR complex degrades RNA complementary to the crRNA (target RNA) within UA dinucleotides, generating 3'-OH and 5'-phosphate ends. Activity is dependent on the 8 nt long 5' tag in the crRNA, an unpaired 3' flag on the target RNA, and is stimulated by ATP. Some cleavage of the guide crRNA can also be observed.
cofactor: Ca(2+) (Binds 2 Ca(2+) per subunit.)
cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
subunit: Part of the CMR ribonucleoprotein complex, consisting of crRNA plus Cmr1/Cmr2/Cmr3/Cmr4/Cmr5/Cmr6 at 1:1 and possibly 3 Cmr7 dimers. A Cmr2/Cmr3/Cmr7 subcomplex without crRNA can also be isolated. It does not cleave target RNA. - Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene
Yokobori, BMC evolutionary biology 2009 - “...tree. Click here for file Additional file 9 Alignment of COG1353 proteins . Sulfolobus solfataricus SSO1991, a representative of COG1353 which was predicted as a putative reverse transcriptase, and the homologs from Hyperthermus butylicus , and Ignicoccus hospitalis are included. Click here for file Additional file...”
Pcal_0272 CRISPR-associated protein, Crm2 family from Pyrobaculum calidifontis JCM 11548
Aligns to 180:324 / 935 (15.5%), covers 99.1% of PF12469, 85.5 bits
Tneu_0563 type III-B CRISPR-associated protein Cas10/Cmr2 from Pyrobaculum neutrophilum V24Sta
Tneu_0563 CRISPR-associated RAMP Crm2 family protein from Thermoproteus neutrophilus V24Sta
Aligns to 156:287 / 898 (14.7%), covers 95.5% of PF12469, 84.2 bits
SiL_0601 type III-B CRISPR-associated protein Cas10/Cmr2 from Sulfolobus islandicus LAL14/1
Aligns to 204:324 / 825 (14.7%), covers 99.1% of PF12469, 79.9 bits
Pars_1118 CRISPR-associated protein, Crm2 family from Pyrobaculum arsenaticum DSM 13514
Aligns to 193:324 / 878 (15.0%), covers 93.7% of PF12469, 77.4 bits
Pcal_1284 CRISPR-associated protein, Crm2 family from Pyrobaculum calidifontis JCM 11548
Aligns to 187:329 / 874 (16.4%), covers 94.6% of PF12469, 75.3 bits
TTHB160 hypothetical protein from Thermus thermophilus HB8
Aligns to 4:109 / 584 (18.2%), covers 98.2% of PF12469, 65.8 bits
TT_P0115 No description from Thermus thermophilus HB27
Aligns to 4:109 / 584 (18.2%), covers 98.2% of PF12469, 65.6 bits
- DNA-guided DNA interference by a prokaryotic Argonaute
Swarts, Nature 2014 - “...Csm3 0.54 (<0.01) TT_P0105 Csm4 0.64 (0.01) TT_P0106 Csm5 0.52 (<0.01) TT_P0107 Csx1 0.28 (0.07) TT_P0115 Cmr2 0.32 (0.06) TT_P0116 Cmr3 0.30 (0.16) TT_P0117 Cmr1 0.43 (0.01) TT_P0118 Cmr4 0.41 (<0.01) TT_P0119 Cmr5 0.48 (<0.01) TT_P0120 RAMP 0.38 (0.03) TT_P0132 Cas3 0.22 (0.20) TT_P0133 Cas4 1.14...”
WP_011986674 type III-B CRISPR-associated protein Cas10/Cmr2 from Clostridium botulinum A str. ATCC 19397
Aligns to 8:158 / 570 (26.5%), covers 98.2% of PF12469, 56.4 bits
MXAN_7281 CRISPR-associated protein Crm2 from Myxococcus xanthus DK 1622
Aligns to 4:101 / 596 (16.4%), covers 97.3% of PF12469, 51.8 bits
WP_260918755 type III-B CRISPR-associated protein Cas10/Cmr2 from Aliarcobacter butzleri
Aligns to 3:102 / 453 (22.1%), covers 83.8% of PF12469, 42.7 bits
WP_209731901 type III-B CRISPR-associated protein Cas10/Cmr2 from Methanococcus voltae
Aligns to 7:108 / 585 (17.4%), covers 97.3% of PF12469, 40.4 bits
PG1987 CRISPR-associated protein, TM1811 family from Porphyromonas gingivalis W83
PG_1987 type III-B CRISPR-associated protein Cas10/Cmr2 from Porphyromonas gingivalis W83
Aligns to 6:121 / 548 (21.2%), covers 96.4% of PF12469, 37.9 bits
- Porphyromonas gingivalis Sphingolipid Synthesis Limits the Host Inflammatory Response
Rocha, Journal of dental research 2020 (secret) - Galactose Impacts the Size and Intracellular Composition of the Asaccharolytic Oral Pathobiont Porphyromonas gingivalis
Moye, Applied and environmental microbiology 2019 - “...PG1537 PG1765 PG1829 PG1877 PG1893 PG1894 PG1963 PG1980 PG1987 PG1988 PG1989 PG2019 PG2036 PG2038 PG2040 PG2181 Common name hslR nusA etfA-1 etfB-1 menD acpP...”
- Role of extracytoplasmic function sigma factor PG1660 (RpoE) in the oxidative stress resistance regulatory network of Porphyromonas gingivalis
Dou, Molecular oral microbiology 2018 - “...module RAMP protein Cmr4 1.86 0.0021017 PG1986 Type III-B CRISPR module-associated protein Cmr3 2.09 0.000221 PG1987 Type III-B CRISPR-associated protein Cas10/Cmr2 1.90 0.000221 PG2013 CRISPR-associated endonuclease Cas2 1.95 0.0401059 PG2014 Subtype I-B CRISPR-associated endonuclease Cas1 2.31 0.000221 PG2015 CRISPR-associated protein Cas4 2.00 0.000221 PG2016 CRISPR-associated helicase/endonuclease...”
- Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray
Wang, BMC microbiology 2017 - “...after treated with Nal-P-113 at a low concentration. PG2016, encoding CRISPR-associated helicase, PG1985, PG1986 and PG1987 encoding other CRISPR-associated proteins, were shown to be up-regulated and may be related to the immune response due to foreign DNA. The down-regulation in integrase and the up-regulation of CRISPR-associated...”
- The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis
Brunner, BMC microbiology 2010 - “...RNA polymerase sigma-70 factor, ECF subfamily PG1742 hypothetical protein PG1866 hypothetical protein PG1869 hypothetical protein PG1987 CRISPR-associated protein, TM1794 family PG2019 hypothetical protein PG2087 conserved hypothetical protein In order to maximize the mining of the genomic information, we subjected the data to three complementary analyses: 1)...”
- The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase
Ximinies, Microbiology spectrum 2023 - “...in P. gingivalis . It is noteworthy that P. gingivalis W83 carries a similar protein (PG_1987) with 89% identity to PGN_1932, and is annotated as a CRISPR-associated Csm1 family protein. In this study, we have further characterized the hypothetical protein PG_0686 to elucidate its role in...”
- “...2-oxoglutarate oxidoreductase 2.33 5.27E-03 2.35 1.70E-02 PG_1844 Lysine-specific cysteine protease (Kgp) 7.19 1.90E-02 3.38 2.86E-03 PG_1987 Type III-B CRISPR-associated protein Cas10/Cmr2 3.73 2.55E-02 1.55 3.30E-02 PG_2024 Gingipain R2 (RgpA) 4.62 2.51E-02 2.84 2.56E-02 PG_2100 T9SS C-terminal target domain-containing protein 2.79 7.90E-03 3.98 1.13E-02 PG_2101 Hypothetical protein...”
- Identification of a diguanylate cyclase and its role in Porphyromonas gingivalis virulence
Chaudhuri, Infection and immunity 2014 - “...should be noted that a P. gingivalis 83 protein (PG_1987) having 89% identity with PGN_1932 is annotated as a CRISPR-associated Csm1 family protein. A recent...”
WP_013175521 type III-B CRISPR-associated protein Cas10/Cmr2 from Syntrophothermus lipocalidus DSM 12680
Aligns to 4:104 / 524 (19.3%), covers 51.4% of PF12469, 30.3 bits
Or search for genetic data about PF12469 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory