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PMID:15236960

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Citation

Callaghan, AJ, Aurikko, JP, Ilag, LL, Günter Grossmann, J, Chandran, V, Kühnel, K, Poljak, L, Carpousis, AJ, Robinson, CV, Symmons, MF and Luisi, BF (2004) Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340:965-79

Abstract

The hydrolytic endoribonuclease RNase E, which is widely distributed in bacteria and plants, plays key roles in mRNA degradation and RNA processing in Escherichia coli. The enzymatic activity of RNase E is contained within the conserved amino-terminal half of the 118 kDa protein, and the carboxy-terminal half organizes the RNA degradosome, a multi-enzyme complex that degrades mRNA co-operatively and processes ribosomal and other RNA. The study described herein demonstrates that the carboxy-terminal domain of RNase E has little structure under native conditions and is unlikely to be extensively folded within the degradosome. However, three isolated segments of 10-40 residues, and a larger fourth segment of 80 residues, are predicted to be regions of increased structural propensity. The larger of these segments appears to be a protein-RNA interaction site while the other segments possibly correspond to sites of self-recognition and interaction with the other degradosome proteins. The carboxy-terminal domain of RNase E may thus act as a flexible tether of the degradosome components. The implications of these and other observations for the organization of the RNA degradosome are discussed.

Links

PubMed Online version:10.1016/j.jmb.2004.05.046

Keywords

Amino Acid Sequence; Binding Sites; Circular Dichroism; Endoribonucleases/chemistry; Endoribonucleases/genetics; Endoribonucleases/isolation & purification; Endoribonucleases/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Molecular Sequence Data; Multienzyme Complexes/chemistry; Multienzyme Complexes/metabolism; Phosphopyruvate Hydratase/isolation & purification; Phosphopyruvate Hydratase/metabolism; Polyribonucleotide Nucleotidyltransferase/chemistry; Polyribonucleotide Nucleotidyltransferase/metabolism; Protein Binding; Protein Structure, Tertiary; RNA Helicases/chemistry; RNA Helicases/metabolism; RNA, Bacterial/chemistry; RNA, Bacterial/metabolism; RNA-Binding Proteins/metabolism; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

ECOLI:PNP

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P21513

F

Seeded From UniProt

complete

ECOLI:ENO

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P21513

F

Seeded From UniProt

complete

ECOLI:RHLB

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P21513

F

Seeded From UniProt

complete

ECOLI:RHLB

enables

GO:0003724: RNA helicase activity

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

ECOLI:RHLB

enables

GO:0097718: disordered domain specific binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P21513

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P05055

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P0A6P9

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P0A8J8

F

Seeded From UniProt

complete

ECOLI:RNE

involved_in

GO:1902280: regulation of RNA helicase activity

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ECOLI:ENO

part_of

GO:0000015: phosphopyruvate hydratase complex

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

ECOLI:ENO

enables

GO:0042802: identical protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P0A6P9

F

Seeded From UniProt

complete

ECOLI:ENO

enables

GO:0004634: phosphopyruvate hydratase activity

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

ECOLI:PNP

enables

GO:0042802: identical protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P05055

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0042802: identical protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P21513

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0008312: 7S RNA binding

ECO:0000315: mutant phenotype evidence used in manual assertion

F

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0003723: RNA binding

ECO:0000315: mutant phenotype evidence used in manual assertion

F

Seeded From UniProt

complete

ECOLI:RNE

involved_in

GO:1902280: regulation of ATP-dependent RNA helicase activity

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ECOLI:RNE

enables

GO:0017151: DEAD/H-box RNA helicase binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P0A8J8

F

Seeded From UniProt

complete


See also

References

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