Ribonuclease 3 - Aquifex aeolicus (strain VF5)

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O67082 (RNC_AQUAE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 97. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribonuclease 3
EC=3.1.26.3

Alternative name(s):
Ribonuclease III
Short name=RNase III

Gene names

Name:	rnc
Ordered Locus Names:	aq_946

Organism

Aquifex aeolicus (strain VF5) [Reference proteome] [HAMAP]

Taxonomic identifier

224324 [NCBI]

Taxonomic lineage

Bacteria › Aquificae › Aquificales › Aquificaceae › Aquifex ›

Protein attributes

Sequence length	221 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.2 Ref.6
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomonoester. HAMAP-Rule MF_00104
Cofactor	Binds 2 Mg²⁺ per subunit. Mn²⁺ also supports catalytic activity. Ref.2 Ref.3 Ref.4 Ref.6 Ref.7
Subunit structure	Homodimer. Ref.3 Ref.4 Ref.6
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Contains 1 DRBM (double-stranded RNA-binding) domain. Contains 1 RNase III domain.
Biophysicochemical properties	Kinetic parameters: K_M=98 nM for 16S-u-hp RNA Ref.2 pH dependence: Optimum pH is 8-9. Temperature dependence: Optimum temperature is 70-85 degrees Celsius.

Ontologies

Keywords
Biological process	mRNA processing rRNA processing tRNA processing
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding RNA-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA processing Inferred from electronic annotation. Source: HAMAP nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC rRNA catabolic process Inferred from electronic annotation. Source: InterPro rRNA processing Inferred from electronic annotation. Source: HAMAP tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	double-stranded RNA binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease III activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 221

221

Ribonuclease 3 HAMAP-Rule MF_00104

PRO_0000180371

Regions

Domain

4 – 121

118

RNase III

Domain

151 – 219

DRBM

Sites

Active site

Potential

Active site

110

Probable

Metal binding

Magnesium

Metal binding

107

Magnesium

Metal binding

110

Magnesium

Experimental info

Mutagenesis

D → N: Very low catalytic activity, binds RNA normally. Ref.6

Mutagenesis

110

E → K: Loss of magnesium, alters ds-RNA binding, loss of activity. Ref.4 Ref.7

Mutagenesis

157

Q → A: No RNase activity, no RNA binding. Ref.2

Secondary structure

221

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O67082 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: ACB69735DB49641D
Show »

FASTA

221

26,100

        10         20         30         40         50         60 
MKMLEQLEKK LGYTFKDKSL LEKALTHVSY SKKEHYETLE FLGDALVNFF IVDLLVQYSP 

        70         80         90        100        110        120 
NKREGFLSPL KAYLISEEFF NLLAQKLELH KFIRIKRGKI NETIIGDVFE ALWAAVYIDS 

       130        140        150        160        170        180 
GRDANFTREL FYKLFKEDIL SAIKEGRVKK DYKTILQEIT QKRWKERPEY RLISVEGPHH 

       190        200        210        220 
KKKFIVEAKI KEYRTLGEGK SKKEAEQRAA EELIKLLEES E

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome of the hyperthermophilic bacterium Aquifex aeolicus." Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R., Feldman R.A., Short J.M., Olsen G.J., Swanson R.V. Nature 392:353-358(1998) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000657 Genomic DNA. Translation: AAC07049.1.

PIR

G70381.

RefSeq

NP_213645.1. NC_000918.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

O67082.

SMR

O67082. Positions 1-221.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48455N.

STRING

224324.aq_946.

Proteomic databases

PRIDE

O67082.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC07049; AAC07049; aq_946.

GeneID

1193624.

KEGG

aae:aq_946.

PATRIC

20959242. VBIAquAeo85532_0743.

Phylogenomic databases

eggNOG

COG0571.

HOGENOM

HOG000246808.

K03685.

OMA

LTHKSCK.

ProtClustDB

CLSK2748388.

Enzyme and pathway databases

BioCyc

AAEO224324:GJBH-678-MONOMER.

BRENDA

3.1.26.3. 396.

Family and domain databases

Gene3D

1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.

HAMAP

MF_00104. RNase_III.

InterPro

IPR001159. Ds-RNA-bd.
IPR014720. dsRNA-bd-like_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]

PANTHER

PTHR11207. PTHR11207. 1 hit.

Pfam

PF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
[Graphical view]

SMART

SM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]

SUPFAM

SSF69065. RNase_III. 1 hit.

TIGRFAMs

TIGR02191. RNaseIII. 1 hit.

PROSITE

PS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O67082.

Entry information

Entry name

RNC_AQUAE

Accession

Primary (citable) accession number: O67082

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	August 1, 1998
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents