Interaction information

Interaction summary

Short label: mRNA 3'-end-processing protein RNA15-5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
Full name: mRNA 3'-end-processing protein RNA15 interacts with 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
Source database: RCSB PDB
ID: 2KM8
Date modified: 2011-03-23 19:10:40 JST

Protein information

Short label

mRNA 3'-end-processing protein RNA15

Full name

Chain B of model 2KM8: mRNA 3'-end-processing protein RNA15

Gene

RNA15 (Cleavage and polyadenylation factor I (CF I) component involved in cleavage and polyadenylation of mRNA 3' ends; interacts with the A-rich polyadenylation signal in complex with Rna14p and Hrp1p)

GeneID

852838

Official symbol

RNA15

Description

Cleavage and polyadenylation factor I (CF I) component involved in cleavage and polyadenylation of mRNA 3' ends; interacts with the A-rich polyadenylation signal in complex with Rna14p and Hrp1p

Other names

1 designation(s)

Rna15p

Ontologies

10 ontology(s)

Functions

5 function(s)

GO:0000166

[IEA] nucleotide binding

Evidence

IEA

Term ID

GO:0000166

Name

nucleotide binding

Namespace

molecular_function

Definition

Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose moiety.

Is-a

1 item(s)

GO:0005488: binding

GO:0003676

[IEA] nucleic acid binding

Evidence

IEA

Term ID

GO:0003676

Name

nucleic acid binding

Namespace

molecular_function

Definition

Interacting selectively and non-covalently with any nucleic acid.

Is-a

1 item(s)

GO:0005488: binding

GO:0003723

[IEA] RNA binding

Evidence

IEA

Term ID

GO:0003723

Name

RNA binding

Namespace

molecular_function

Definition

Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

Is-a

1 item(s)

GO:0003676: nucleic acid binding

GO:0003729

[IDA] mRNA binding

Evidence

IDA

References

1 reference(s)

PubMed

BUCHELI, Miriam E, et al., RNA 2007 Oct;13(10):1756-64

PMID

17684230

Title

Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI.

Authors

BUCHELI, Miriam E, et al.

BUCHELI, Miriam E
HE, Xiaoyuan
KAPLAN, Craig D
MOORE, Claire L
BURATOWSKI, Stephen

Citation

RNA 2007 Oct;13(10):1756-64

Term ID

GO:0003729

Name

mRNA binding

Namespace

molecular_function

Definition

Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA) or messenger RNA (mRNA).

Is-a

1 item(s)

GO:0003723: RNA binding

GO:0046982

[IPI] protein heterodimerization activity

Evidence

IPI

References

1 reference(s)

PubMed

NOBLE, Christian G, et al., Nucleic Acids Res. 2004;32(11):3364-75

PMID

15215336

Title

Rna14-Rna15 assembly mediates the RNA-binding capability of Saccharomyces cerevisiae cleavage factor IA.

Authors

NOBLE, Christian G, et al.

NOBLE, Christian G
WALKER, Philip A
CALDER, Lesley J
TAYLOR, Ian A

Citation

Nucleic Acids Res. 2004;32(11):3364-75

Term ID

GO:0046982

Name

protein heterodimerization activity

Namespace

molecular_function

Definition

Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.

Is-a

1 item(s)

GO:0046983: protein dimerization activity

Processes

3 process(s)

GO:0006378

[IDA] mRNA polyadenylation

Evidence

IDA

References

1 reference(s)

PubMed

GROSS, S, et al., Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

PMID

11344258

Title

Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I.

Authors

GROSS, S, et al.

GROSS, S
MOORE, C

Citation

Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

Term ID

GO:0006378

Name

mRNA polyadenylation

Namespace

biological_process

Definition

The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology

Synonyms

2 synonym(s)

cleavage and polyadenylylation specificity factor activity
mRNA polyadenylylation

Is-a

2 item(s)

GO:0031124: mRNA 3'-end processing
GO:0043631: RNA polyadenylation

GO:0006379

[IDA] mRNA cleavage

Evidence

IDA

References

1 reference(s)

PubMed

GROSS, S, et al., Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

PMID

11344258

Title

Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I.

Authors

GROSS, S, et al.

GROSS, S
MOORE, C

Citation

Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

Term ID

GO:0006379

Name

mRNA cleavage

Namespace

biological_process

Definition

Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.

Synonyms

3 synonym(s)

cleavage and polyadenylylation specificity factor activity
cleavage stimulation factor activity
pre-mRNA cleavage factor activity

Is-a

2 item(s)

GO:0006397: mRNA processing
GO:0090305: nucleic acid phosphodiester bond hydrolysis

GO:0006397

[IEA] mRNA processing

Evidence

IEA

Term ID

GO:0006397

Name

mRNA processing

Namespace

biological_process

Definition

Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

Synonyms

1 synonym(s)

mRNA maturation

Is-a

2 item(s)

GO:0006396: RNA processing
GO:0016071: mRNA metabolic process

Components

2 component(s)

GO:0005634

[IEA] nucleus

Evidence

IEA

Term ID

GO:0005634

Name

nucleus

Namespace

cellular_component

Definition

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Synonyms

1 synonym(s)

cell nucleus

Is-a

1 item(s)

GO:0043231: intracellular membrane-bounded organelle

GO:0005849

[IPI] mRNA cleavage factor complex

Evidence

IPI

References

1 reference(s)

PubMed

GROSS, S, et al., Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

PMID

11344258

Title

Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I.

Authors

GROSS, S, et al.

GROSS, S
MOORE, C

Citation

Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(11):6080-5

Term ID

GO:0005849

Name

mRNA cleavage factor complex

Namespace

cellular_component

Definition

Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.

Is-a

2 item(s)

GO:0043234: protein complex
GO:0044451: nucleoplasm part

Origin

Saccharomyces cerevisiae

NCBI Taxonomy ID

4932

Name

Saccharomyces cerevisiae

Synonyms

12 synonym(s).

Candida robusta
Saccaromyces cerevisiae
Saccharomyces capensis
Saccharomyces italicus
Saccharomyces oviformis
Saccharomyces uvarum var. melibiosus
Saccharomyes cerevisiae
Sccharomyces cerevisiae
baker's yeast
brewer's yeast
lager beer yeast
yeast

Cross references

1 item(s)

UniProt: P25299

Sequence

2KM8B:mRNA 3'-end-processing protein RNA15

RNA information

Short label: 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
Full name: Chain A of model 2KM8: 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
Sequence: 2KM8A:5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'

Experiments (1)

Experiment 1

leeper-2010

Full name

Solution NMR

Detection method

nuclear magnetic resonance (MI:0077)

Term ID

MI:0077

Name

nuclear magnetic resonance

Definition

NMR requires a small volume of concentrated compound solution that is placed in a strong magnetic field. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; that is, they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.

Synonyms

2 synonym(s)

NMR (PSI-MI-alternate)
nmr (PSI-MI-short)

Is-a

2 item(s)

MI:0013: biophysical
MI:0659: experimental feature detection

Host organisms

1 host organism(s)

Origin

Escherichia coli

NCBI Taxonomy ID

562

Name

Escherichia coli

Synonyms

16 synonym(s).

"Bacillus coli" Migula 1895
"Bacterium coli commune" Escherich 1885
"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Escherichia coli (Migula 1895) Castellani and Chalmers 1919
Escherichia coli retron Ec107
Escherichia coli retron Ec67
Escherichia coli retron Ec79
Escherichia coli retron Ec86
Eschericia coli
bacterium 10a
bacterium E3

Reference

LEEPER, Thomas C, et al., J. Mol. Biol. 2010 Aug;401(3):334-49

PMID

20600122

Title

Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1.

Authors

LEEPER, Thomas C, et al.

LEEPER, Thomas C
QU, Xiangping
LU, Connie
MOORE, Claire
VARANI, Gabriele

Citation

J. Mol. Biol. 2010 Aug;401(3):334-49

References (1)

Reference 1

LEEPER, Thomas C, et al., J. Mol. Biol. 2010 Aug;401(3):334-49

PMID

20600122

Title

Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1.

Authors

LEEPER, Thomas C, et al.

LEEPER, Thomas C
QU, Xiangping
LU, Connie
MOORE, Claire
VARANI, Gabriele

Citation

J. Mol. Biol. 2010 Aug;401(3):334-49

Attributes (1)

Attributes

1 attribute(s)

3d-structure: Interdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex

Interaction information