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Protein

Ribonuclease 3

Gene

rnc

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Mg2+5 PublicationsNote: Binds 2 Mg(2+) 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

    GO - Biological processi

    Complete GO annotation...

    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 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    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 – 33Combined sources
    Helixi4 – 118Combined sources
    Helixi18 – 258Combined sources
    Turni28 – 303Combined sources
    Beta strandi32 – 343Combined sources
    Helixi37 – 5721Combined sources
    Helixi64 – 7411Combined sources
    Helixi77 – 859Combined sources
    Turni86 – 883Combined sources
    Helixi89 – 913Combined sources
    Beta strandi96 – 983Combined sources
    Helixi102 – 11918Combined sources
    Helixi124 – 14421Combined sources
    Helixi152 – 16413Combined sources
    Beta strandi169 – 1779Combined sources
    Helixi179 – 1813Combined sources
    Beta strandi183 – 1908Combined sources
    Beta strandi193 – 2019Combined sources
    Helixi202 – 21716Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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.
    InParanoidiO67082.
    KOiK03685.
    OMAiSADHNER.
    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

            10         20         30         40         50
    MKMLEQLEKK LGYTFKDKSL LEKALTHVSY SKKEHYETLE FLGDALVNFF
    60 70 80 90 100
    IVDLLVQYSP NKREGFLSPL KAYLISEEFF NLLAQKLELH KFIRIKRGKI
    110 120 130 140 150
    NETIIGDVFE ALWAAVYIDS GRDANFTREL FYKLFKEDIL SAIKEGRVKK
    160 170 180 190 200
    DYKTILQEIT QKRWKERPEY RLISVEGPHH KKKFIVEAKI KEYRTLGEGK
    210 220
    SKKEAEQRAA EELIKLLEES E
    Length:221
    Mass (Da):26,100
    Last modified:August 1, 1998 - v1
    Checksum:iACB69735DB49641D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000657 Genomic DNA. Translation: AAC07049.1.
    PIRiG70381.
    RefSeqiNP_213645.1. NC_000918.1.
    WP_010880583.1. NC_000918.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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...

    Protein-protein interaction databases

    DIPiDIP-48455N.
    STRINGi224324.aq_946.

    Proteomic databases

    PRIDEiO67082.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiCOG0571.
    HOGENOMiHOG000246808.
    InParanoidiO67082.
    KOiK03685.
    OMAiSADHNER.
    OrthoDBiEOG6T1WVS.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiO67082.

    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]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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: May 27, 2015
    This is version 113 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.