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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 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)DescriptionActionsGraphical viewLength
    Metal bindingi40MagnesiumCombined sources1 Publication2 Publications1
    Active sitei44Sequence analysis1
    Metal bindingi107MagnesiumCombined sources1 Publication2 Publications1
    Active sitei110Curated1
    Metal bindingi110MagnesiumCombined sources1 Publication2 Publications1

    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

    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
    Proteomesi
    • UP000000798 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi44D → N: Very low catalytic activity, binds RNA normally. 1 Publication1
    Mutagenesisi110E → K: Loss of magnesium, alters ds-RNA binding, loss of activity. 2 Publications1
    Mutagenesisi157Q → A: No RNase activity, no RNA binding. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001803711 – 221Ribonuclease 3Add BLAST221

    Proteomic databases

    PRIDEiO67082.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    Protein-protein interaction databases

    DIPiDIP-48455N.
    STRINGi224324.aq_946.

    Structurei

    Secondary structure

    1221
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni1 – 3Combined sources3
    Helixi4 – 11Combined sources8
    Helixi18 – 25Combined sources8
    Turni28 – 30Combined sources3
    Beta strandi32 – 34Combined sources3
    Helixi37 – 57Combined sources21
    Helixi64 – 74Combined sources11
    Helixi77 – 85Combined sources9
    Turni86 – 88Combined sources3
    Helixi89 – 91Combined sources3
    Beta strandi96 – 98Combined sources3
    Helixi102 – 119Combined sources18
    Helixi124 – 144Combined sources21
    Helixi152 – 164Combined sources13
    Beta strandi169 – 177Combined sources9
    Helixi179 – 181Combined sources3
    Beta strandi183 – 190Combined sources8
    Beta strandi193 – 201Combined sources9
    Helixi202 – 217Combined sources16

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO67082.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini4 – 121RNase IIIAdd BLAST118
    Domaini151 – 219DRBMAdd BLAST69

    Sequence similaritiesi

    Contains 1 RNase III domain.Curated

    Phylogenomic databases

    eggNOGiENOG4108ZBM. Bacteria.
    COG0571. LUCA.
    HOGENOMiHOG000246808.
    InParanoidiO67082.
    KOiK03685.
    OMAiLTHKSCK.
    OrthoDBiPOG091H00R1.

    Family and domain databases

    CDDicd00593. RIBOc. 1 hit.
    Gene3Di1.10.1520.10. 1 hit.
    3.30.160.20. 1 hit.
    HAMAPiMF_00104. RNase_III. 1 hit.
    InterProiIPR014720. dsRBD_dom.
    IPR011907. RNase_III.
    IPR000999. RNase_III_dom.
    [Graphical view]
    PfamiPF00035. dsrm. 1 hit.
    PF14622. Ribonucleas_3_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
    PDB 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.
    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

    eggNOGiENOG4108ZBM. Bacteria.
    COG0571. LUCA.
    HOGENOMiHOG000246808.
    InParanoidiO67082.
    KOiK03685.
    OMAiLTHKSCK.
    OrthoDBiPOG091H00R1.

    Enzyme and pathway databases

    BRENDAi3.1.26.3. 396.

    Miscellaneous databases

    EvolutionaryTraceiO67082.

    Family and domain databases

    CDDicd00593. RIBOc. 1 hit.
    Gene3Di1.10.1520.10. 1 hit.
    3.30.160.20. 1 hit.
    HAMAPiMF_00104. RNase_III. 1 hit.
    InterProiIPR014720. dsRBD_dom.
    IPR011907. RNase_III.
    IPR000999. RNase_III_dom.
    [Graphical view]
    PfamiPF00035. dsrm. 1 hit.
    PF14622. Ribonucleas_3_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...

    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: November 2, 2016
    This is version 123 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

    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 one 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.