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O67082

- RNC_AQUAE

UniProt

O67082 - RNC_AQUAE

Protein

Ribonuclease 3

Gene

rnc

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 106 (01 Oct 2014)
      Sequence version 1 (01 Aug 1998)
      Previous versions | rss
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    Functioni

    Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Probably processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism.2 Publications

    Catalytic activityi

    Endonucleolytic cleavage to 5'-phosphomonoester.

    Cofactori

    Binds 2 Mg2+ per subunit. Mn2+ also supports catalytic activity.5 Publications

    Kineticsi

    1. KM=98 nM for 16S-u-hp RNA1 Publication

    pH dependencei

    Optimum pH is 8-9.1 Publication

    Temperature dependencei

    Optimum temperature is 70-85 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi40 – 401Magnesium1 Publication
    Active sitei44 – 441Sequence Analysis
    Metal bindingi107 – 1071Magnesium1 Publication
    Active sitei110 – 1101Curated
    Metal bindingi110 – 1101Magnesium1 Publication

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. ribonuclease III activity Source: UniProtKB-HAMAP
    3. RNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. mRNA processing Source: UniProtKB-HAMAP
    2. rRNA catabolic process Source: InterPro
    3. rRNA processing Source: UniProtKB-HAMAP
    4. tRNA processing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    mRNA processing, rRNA processing, tRNA processing

    Keywords - Ligandi

    Magnesium, Metal-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciAAEO224324:GJBH-678-MONOMER.
    BRENDAi3.1.26.3. 396.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonuclease 3 (EC:3.1.26.3)
    Alternative name(s):
    Ribonuclease III
    Short name:
    RNase III
    Gene namesi
    Name:rnc
    Ordered Locus Names:aq_946
    OrganismiAquifex aeolicus (strain VF5)
    Taxonomic identifieri224324 [NCBI]
    Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
    ProteomesiUP000000798: Chromosome

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi44 – 441D → N: Very low catalytic activity, binds RNA normally. 1 Publication
    Mutagenesisi110 – 1101E → K: Loss of magnesium, alters ds-RNA binding, loss of activity. 2 Publications
    Mutagenesisi157 – 1571Q → A: No RNase activity, no RNA binding. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 221221Ribonuclease 3PRO_0000180371Add
    BLAST

    Proteomic databases

    PRIDEiO67082.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    Protein-protein interaction databases

    DIPiDIP-48455N.
    STRINGi224324.aq_946.

    Structurei

    Secondary structure

    221
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni1 – 33
    Helixi4 – 118
    Helixi18 – 258
    Turni28 – 303
    Beta strandi32 – 343
    Helixi37 – 5721
    Helixi64 – 7411
    Helixi77 – 859
    Turni86 – 883
    Helixi89 – 913
    Beta strandi96 – 983
    Helixi102 – 11918
    Helixi124 – 14421
    Helixi152 – 16413
    Beta strandi169 – 1779
    Helixi179 – 1813
    Beta strandi183 – 1908
    Beta strandi193 – 2019
    Helixi202 – 21716

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1I4SX-ray2.15A/B1-147[»]
    1JFZX-ray2.10A/B/C/D1-147[»]
    1RC5X-ray2.30A/B/C/D1-147[»]
    1RC7X-ray2.15A1-220[»]
    1YYKX-ray2.50A/B1-221[»]
    1YYOX-ray2.90A/B1-221[»]
    1YYWX-ray2.80A/B/C/D1-221[»]
    1YZ9X-ray2.10A/B1-221[»]
    2EZ6X-ray2.05A/B1-221[»]
    2NUEX-ray2.90A/B1-221[»]
    2NUFX-ray2.50A/B1-221[»]
    2NUGX-ray1.70A/B1-221[»]
    4M2ZX-ray2.85A/B1-221[»]
    4M30X-ray2.50A/B1-221[»]
    ProteinModelPortaliO67082.
    SMRiO67082. Positions 1-221.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO67082.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini4 – 121118RNase IIIAdd
    BLAST
    Domaini151 – 21969DRBMAdd
    BLAST

    Sequence similaritiesi

    Contains 1 RNase III domain.Curated

    Phylogenomic databases

    eggNOGiCOG0571.
    HOGENOMiHOG000246808.
    KOiK03685.
    OMAiAQKDPKT.
    OrthoDBiEOG6T1WVS.

    Family and domain databases

    Gene3Di1.10.1520.10. 1 hit.
    3.30.160.20. 1 hit.
    HAMAPiMF_00104. RNase_III.
    InterProiIPR014720. dsRNA-bd_dom.
    IPR011907. RNase_III.
    IPR000999. RNase_III_dom.
    [Graphical view]
    PANTHERiPTHR11207. PTHR11207. 1 hit.
    PfamiPF00035. dsrm. 1 hit.
    PF00636. Ribonuclease_3. 1 hit.
    [Graphical view]
    SMARTiSM00358. DSRM. 1 hit.
    SM00535. RIBOc. 1 hit.
    [Graphical view]
    SUPFAMiSSF69065. SSF69065. 1 hit.
    TIGRFAMsiTIGR02191. RNaseIII. 1 hit.
    PROSITEiPS50137. DS_RBD. 1 hit.
    PS00517. RNASE_3_1. 1 hit.
    PS50142. RNASE_3_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O67082-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKMLEQLEKK LGYTFKDKSL LEKALTHVSY SKKEHYETLE FLGDALVNFF    50
    IVDLLVQYSP NKREGFLSPL KAYLISEEFF NLLAQKLELH KFIRIKRGKI 100
    NETIIGDVFE ALWAAVYIDS GRDANFTREL FYKLFKEDIL SAIKEGRVKK 150
    DYKTILQEIT QKRWKERPEY RLISVEGPHH KKKFIVEAKI KEYRTLGEGK 200
    SKKEAEQRAA EELIKLLEES E 221
    Length:221
    Mass (Da):26,100
    Last modified:August 1, 1998 - v1
    Checksum:iACB69735DB49641D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000657 Genomic DNA. Translation: AAC07049.1.
    PIRiG70381.
    RefSeqiNP_213645.1. NC_000918.1.
    WP_010880583.1. NC_000918.1.

    Genome annotation databases

    EnsemblBacteriaiAAC07049; AAC07049; aq_946.
    GeneIDi1193624.
    KEGGiaae:aq_946.
    PATRICi20959242. VBIAquAeo85532_0743.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000657 Genomic DNA. Translation: AAC07049.1 .
    PIRi G70381.
    RefSeqi NP_213645.1. NC_000918.1.
    WP_010880583.1. NC_000918.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1I4S X-ray 2.15 A/B 1-147 [» ]
    1JFZ X-ray 2.10 A/B/C/D 1-147 [» ]
    1RC5 X-ray 2.30 A/B/C/D 1-147 [» ]
    1RC7 X-ray 2.15 A 1-220 [» ]
    1YYK X-ray 2.50 A/B 1-221 [» ]
    1YYO X-ray 2.90 A/B 1-221 [» ]
    1YYW X-ray 2.80 A/B/C/D 1-221 [» ]
    1YZ9 X-ray 2.10 A/B 1-221 [» ]
    2EZ6 X-ray 2.05 A/B 1-221 [» ]
    2NUE X-ray 2.90 A/B 1-221 [» ]
    2NUF X-ray 2.50 A/B 1-221 [» ]
    2NUG X-ray 1.70 A/B 1-221 [» ]
    4M2Z X-ray 2.85 A/B 1-221 [» ]
    4M30 X-ray 2.50 A/B 1-221 [» ]
    ProteinModelPortali O67082.
    SMRi O67082. Positions 1-221.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48455N.
    STRINGi 224324.aq_946.

    Proteomic databases

    PRIDEi O67082.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC07049 ; AAC07049 ; aq_946 .
    GeneIDi 1193624.
    KEGGi aae:aq_946.
    PATRICi 20959242. VBIAquAeo85532_0743.

    Phylogenomic databases

    eggNOGi COG0571.
    HOGENOMi HOG000246808.
    KOi K03685.
    OMAi AQKDPKT.
    OrthoDBi EOG6T1WVS.

    Enzyme and pathway databases

    BioCyci AAEO224324:GJBH-678-MONOMER.
    BRENDAi 3.1.26.3. 396.

    Miscellaneous databases

    EvolutionaryTracei O67082.

    Family and domain databases

    Gene3Di 1.10.1520.10. 1 hit.
    3.30.160.20. 1 hit.
    HAMAPi MF_00104. RNase_III.
    InterProi IPR014720. dsRNA-bd_dom.
    IPR011907. RNase_III.
    IPR000999. RNase_III_dom.
    [Graphical view ]
    PANTHERi PTHR11207. PTHR11207. 1 hit.
    Pfami PF00035. dsrm. 1 hit.
    PF00636. Ribonuclease_3. 1 hit.
    [Graphical view ]
    SMARTi SM00358. DSRM. 1 hit.
    SM00535. RIBOc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF69065. SSF69065. 1 hit.
    TIGRFAMsi TIGR02191. RNaseIII. 1 hit.
    PROSITEi PS50137. DS_RBD. 1 hit.
    PS00517. RNASE_3_1. 1 hit.
    PS50142. RNASE_3_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: VF5.
    2. "Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates."
      Shi Z., Nicholson R.H., Jaggi R., Nicholson A.W.
      Nucleic Acids Res. 39:2756-2768(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION AS AN ENDORIBONUCLEASE, FUNCTION IN RRNA PRECURSOR PROCESSING, COFACTOR, RNA-BINDING, MUTAGENESIS OF GLN-157.
    3. "Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage."
      Blaszczyk J., Tropea J.E., Bubunenko M., Routzahn K.M., Waugh D.S., Court D.L., Ji X.
      Structure 9:1225-1236(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-147 WITH AND WITHOUT MANGANESE, COFACTOR, SUBUNIT.
      Strain: VF5.
    4. "Noncatalytic assembly of ribonuclease III with double-stranded RNA."
      Blaszczyk J., Gan J., Tropea J.E., Court D.L., Waugh D.S., Ji X.
      Structure 12:457-466(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-147 WITH MAGNESIUM, X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 1-220 WITH DS-RNA, RNA-BINDING, COFACTOR, SUBUNIT, MUTAGENESIS OF GLU-110.
      Strain: VF5.
    5. "Intermediate states of ribonuclease III in complex with double-stranded RNA."
      Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., Ji X.
      Structure 13:1435-1442(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH DS-RNA.
    6. "Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III."
      Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., Ji X.
      Cell 124:355-366(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH PRODUCT, FUNCTION AS AN RNASE, COFACTOR, SUBUNIT, RNA-BINDING, MUTAGENESIS OF ASP-44.
    7. "A stepwise model for double-stranded RNA processing by ribonuclease III."
      Gan J., Shaw G., Tropea J.E., Waugh D.S., Court D.L., Ji X.
      Mol. Microbiol. 67:143-154(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PRODUCT AND MAGNESIUM, COFACTOR, MUTAGENESIS OF GLU-110.

    Entry informationi

    Entry nameiRNC_AQUAE
    AccessioniPrimary (citable) accession number: O67082
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: August 1, 1998
    Last modified: October 1, 2014
    This is version 106 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3