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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

  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
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

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
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[»]
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.

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.

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[»]
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(2010) [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(2000) [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(2003) [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(2004) [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(2005) [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(2007) [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: April 1, 2015
This is version 112 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.