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O67082

- RNC_AQUAE

UniProt

O67082 - RNC_AQUAE

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Protein
Ribonuclease 3
Gene
rnc, aq_946
Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed - 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.UniRule annotation

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.

Temperature dependencei

Optimum temperature is 70-85 degrees Celsius.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi40 – 401Magnesium
Active sitei44 – 441 Reviewed prediction
Metal bindingi107 – 1071Magnesium
Active sitei110 – 1101 Inferred
Metal bindingi110 – 1101Magnesium

GO - Molecular functioni

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

Subcellular locationi

Cytoplasm By similarity UniRule annotation

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 3UniRule annotation
PRO_0000180371Add
BLAST

Proteomic databases

PRIDEiO67082.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

DIPiDIP-48455N.
STRINGi224324.aq_946.

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiO67082.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 121118RNase III
Add
BLAST
Domaini151 – 21969DRBM
Add
BLAST

Sequence similaritiesi

Contains 1 RNase III domain.

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

« 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: September 3, 2014
This is version 105 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

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