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PDBsum entry 2rok
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RNA binding protein
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PDB id
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2rok
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Contents |
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* Residue conservation analysis
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PDB id:
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RNA binding protein
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Title:
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Solution structure of the cap-binding domain of parn complexed with the cap analog
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Structure:
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Poly(a)-specific ribonuclease. Chain: a. Fragment: cap-binding domain. Synonym: polyadenylate-specific ribonuclease. Engineered: yes
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Source:
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Mus musculus. Mouse. Organism_taxid: 10090. Gene: parn
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NMR struc:
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20 models
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Authors:
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T.Nagata,S.Suzuki,R.Endo,M.Shirouzu,T.Terada,M.Inoue,T.Kigawa, P.Guntert,Y.Hayashizaki,Y.Muto,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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T.Nagata
et al.
(2008).
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
Nucleic Acids Res,
36,
4754-4767.
PubMed id:
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Date:
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28-Mar-08
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Release date:
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10-Feb-09
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PROCHECK
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Headers
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References
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Q8VDG3
(PARN_MOUSE) -
Poly(A)-specific ribonuclease PARN from Mus musculus
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Seq:
Struc:
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624 a.a.
100 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 14 residue positions (black
crosses)
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Enzyme class:
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E.C.3.1.13.4
- poly(A)-specific ribonuclease.
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Reaction:
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Exonucleolytic cleavage of poly(A) to 5'-AMP.
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Nucleic Acids Res
36:4754-4767
(2008)
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PubMed id:
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The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
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T.Nagata,
S.Suzuki,
R.Endo,
M.Shirouzu,
T.Terada,
M.Inoue,
T.Kigawa,
N.Kobayashi,
P.Güntert,
A.Tanaka,
Y.Hayashizaki,
Y.Muto,
S.Yokoyama.
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ABSTRACT
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The degradation of the poly(A) tail is crucial for posttranscriptional gene
regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN)
is one of the major mammalian 3' specific exo-ribonucleases involved in the
degradation of the mRNA poly(A) tail, and it is also involved in the regulation
of translation in early embryonic development. The interaction between PARN and
the m(7)GpppG cap of mRNA plays a key role in stimulating the rate of
deadenylation. Here we report the solution structures of the cap-binding domain
of mouse PARN with and without the m(7)GpppG cap analog. The structure of the
cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic
alpha-helical extension at its C-terminus, which covers the beta-sheet surface
(hereafter referred to as PARN RRM). In the complex structure of PARN RRM with
the cap analog, the base of the N(7)-methyl guanosine (m(7)G) of the cap analog
stacks with the solvent-exposed aromatic side chain of the distinctive
tryptophan residue 468, located at the C-terminal end of the second beta-strand.
These unique structural features in PARN RRM reveal a novel cap-binding mode,
which is distinct from the nucleotide recognition mode of the canonical RRM
domains.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Yamashita,
T.Nagata,
M.Kawazoe,
C.Takemoto,
T.Kigawa,
P.Güntert,
N.Kobayashi,
T.Terada,
M.Shirouzu,
M.Wakiyama,
Y.Muto,
and
S.Yokoyama
(2011).
Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.
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Protein Sci,
20,
118-130.
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J.Chang,
B.Schwer,
and
S.Shuman
(2010).
Mutational analyses of trimethylguanosine synthase (Tgs1) and Mud2: proteins implicated in pre-mRNA splicing.
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RNA,
16,
1018-1031.
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N.Henriksson,
P.Nilsson,
M.Wu,
H.Song,
and
A.Virtanen
(2010).
Recognition of adenosine residues by the active site of poly(A)-specific ribonuclease.
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J Biol Chem,
285,
163-170.
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T.Nagata,
E.Niyada,
N.Fujimoto,
Y.Nagasaki,
K.Noto,
Y.Miyanoiri,
J.Murata,
K.Hiratsuka,
and
M.Katahira
(2010).
Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.
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Proteins,
78,
3033-3047.
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PDB codes:
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G.J.He,
A.Zhang,
W.F.Liu,
Y.Cheng,
and
Y.B.Yan
(2009).
Conformational stability and multistate unfolding of poly(A)-specific ribonuclease.
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FEBS J,
276,
2849-2860.
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M.Wu,
P.Nilsson,
N.Henriksson,
A.Niedzwiecka,
M.K.Lim,
Z.Cheng,
K.Kokkoris,
A.Virtanen,
and
H.Song
(2009).
Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.
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Structure,
17,
276-286.
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S.S.Bradrick,
and
M.Gromeier
(2009).
Identification of gemin5 as a novel 7-methylguanosine cap-binding protein.
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PLoS One,
4,
e7030.
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T.Monecke,
A.Dickmanns,
and
R.Ficner
(2009).
Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1.
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Nucleic Acids Res,
37,
3865-3877.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
