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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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1 term
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Biochemical function
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RNA binding
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2 terms
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DOI no:
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Embo J
17:7505-7513
(1998)
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PubMed id:
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Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.
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J.M.Ryter,
S.C.Schultz.
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ABSTRACT
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Protein interactions with double-stranded RNA (dsRNA) are critical for many cell
processes; however, in contrast to protein-dsDNA interactions, surprisingly
little is known about the molecular basis of protein-dsRNA interactions. A large
and diverse class of proteins that bind dsRNA do so by utilizing an
approximately 70 amino acid motif referred to as the dsRNA-binding domain
(dsRBD). We have determined a 1.9 A resolution crystal structure of the second
dsRBD of Xenopus laevis RNA-binding protein A complexed with dsRNA. The
structure shows that the protein spans 16 bp of dsRNA, interacting with two
successive minor grooves and across the intervening major groove on one face of
a primarily A-form RNA helix. The nature of these interactions explains dsRBD
specificity for dsRNA (over ssRNA or dsDNA) and the apparent lack of sequence
specificity. Interestingly, the dsRBD fold resembles a portion of the conserved
core structure of a family of polynucleotidyl transferases that includes RuvC,
MuA transposase, retroviral integrase and RNase H. Structural comparisons of the
dsRBD-dsRNA complex and models proposed for polynucleotidyl transferase-nucleic
acid complexes suggest that similarities in nucleic acid binding also exist
between these families of proteins.
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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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A.Pindel,
and
A.Sadler
(2011).
The role of protein kinase R in the interferon response.
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| |
J Interferon Cytokine Res, 31,
59-70.
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C.Dominguez,
M.Schubert,
O.Duss,
S.Ravindranathan,
and
F.H.Allain
(2011).
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
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| |
Prog Nucl Magn Reson Spectrosc, 58,
1.
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S.R.Nallagatla,
R.Toroney,
and
P.C.Bevilacqua
(2011).
Regulation of innate immunity through RNA structure and the protein kinase PKR.
|
| |
Curr Opin Struct Biol, 21,
119-127.
|
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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.
|
| |
Protein Sci, 20,
118-130.
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|
A.Harashima,
T.Guettouche,
and
G.N.Barber
(2010).
Phosphorylation of the NFAR proteins by the dsRNA-dependent protein kinase PKR constitutes a novel mechanism of translational regulation and cellular defense.
|
| |
Genes Dev, 24,
2640-2653.
|
|
|
|
|
|
|
A.J.Sadler
(2010).
Orchestration of the activation of protein kinase R by the RNA-binding motif.
|
| |
J Interferon Cytokine Res, 30,
195-204.
|
|
|
|
|
|
|
B.E.Wulff,
and
K.Nishikura
(2010).
Substitutional A-to-I RNA editing.
|
| |
WIREs RNA, 1,
90.
|
|
|
|
|
|
|
B.R.Anderson,
H.Muramatsu,
S.R.Nallagatla,
P.C.Bevilacqua,
L.H.Sansing,
D.Weissman,
and
K.Karikó
(2010).
Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation.
|
| |
Nucleic Acids Res, 38,
5884-5892.
|
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|
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|
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C.Martel,
S.Dugré-Brisson,
K.Boulay,
B.Breton,
G.Lapointe,
S.Armando,
V.Trépanier,
T.Duchaîne,
M.Bouvier,
and
L.Desgroseillers
(2010).
Multimerization of Staufen1 in live cells.
|
| |
RNA, 16,
585-597.
|
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|
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|
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G.A.Mueller,
M.T.Miller,
E.F.Derose,
M.Ghosh,
R.E.London,
and
T.M.Hall
(2010).
Solution structure of the Drosha double-stranded RNA-binding domain.
|
| |
Silence, 1,
2.
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H.Peacock,
O.Maydanovych,
and
P.A.Beal
(2010).
N(2)-Modified 2-aminopurine ribonucleosides as minor-groove-modulating adenosine replacements in duplex RNA.
|
| |
Org Lett, 12,
1044-1047.
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H.Qin,
F.Chen,
X.Huan,
S.Machida,
J.Song,
and
Y.A.Yuan
(2010).
Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction.
|
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RNA, 16,
474-481.
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PDB code:
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K.Nishikura
(2010).
Functions and regulation of RNA editing by ADAR deaminases.
|
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Annu Rev Biochem, 79,
321-349.
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M.D.Miller,
L.Aravind,
C.Bakolitsa,
C.L.Rife,
D.Carlton,
P.Abdubek,
T.Astakhova,
H.L.Axelrod,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
J.Feuerhelm,
J.C.Grant,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
S.S.Krishna,
A.Kumar,
D.Marciano,
D.McMullan,
A.T.Morse,
E.Nigoghossian,
L.Okach,
R.Reyes,
H.van den Bedem,
D.Weekes,
Q.Xu,
K.O.Hodgson,
J.Wooley,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2010).
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 66,
1167-1173.
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PDB code:
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M.Guo,
P.Schimmel,
and
X.L.Yang
(2010).
Functional expansion of human tRNA synthetases achieved by structural inventions.
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FEBS Lett, 584,
434-442.
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R.Stefl,
F.C.Oberstrass,
J.L.Hood,
M.Jourdan,
M.Zimmermann,
L.Skrisovska,
C.Maris,
L.Peng,
C.Hofr,
R.B.Emeson,
and
F.H.Allain
(2010).
The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove.
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Cell, 143,
225-237.
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PDB codes:
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S.W.Yang,
H.Y.Chen,
J.Yang,
S.Machida,
N.H.Chua,
and
Y.A.Yuan
(2010).
Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing.
|
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Structure, 18,
594-605.
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PDB codes:
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A.Eguchi,
B.R.Meade,
Y.C.Chang,
C.T.Fredrickson,
K.Willert,
N.Puri,
and
S.F.Dowdy
(2009).
Efficient siRNA delivery into primary cells by a peptide transduction domain-dsRNA binding domain fusion protein.
|
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Nat Biotechnol, 27,
567-571.
|
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A.J.Sadler,
O.Latchoumanin,
D.Hawkes,
J.Mak,
and
B.R.Williams
(2009).
An antiviral response directed by PKR phosphorylation of the RNA helicase A.
|
| |
PLoS Pathog, 5,
e1000311.
|
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|
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B.Zinshteyn,
and
K.Nishikura
(2009).
Adenosine-to-inosine RNA editing.
|
| |
Wiley Interdiscip Rev Syst Biol Med, 1,
202-209.
|
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|
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C.Okada,
E.Yamashita,
S.J.Lee,
S.Shibata,
J.Katahira,
A.Nakagawa,
Y.Yoneda,
and
T.Tsukihara
(2009).
A High-Resolution Structure of the Pre-microRNA Nuclear Export Machinery.
|
| |
Science, 326,
1275-1279.
|
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J.Fritz,
A.Strehblow,
A.Taschner,
S.Schopoff,
P.Pasierbek,
and
M.F.Jantsch
(2009).
RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.
|
| |
Mol Cell Biol, 29,
1487-1497.
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J.P.Palavicini,
M.A.O'Connell,
and
J.J.Rosenthal
(2009).
An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme.
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| |
RNA, 15,
1208-1218.
|
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M.Nowotny,
and
W.Yang
(2009).
Structural and functional modules in RNA interference.
|
| |
Curr Opin Struct Biol, 19,
286-293.
|
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Y.Huang,
L.Ji,
Q.Huang,
D.G.Vassylyev,
X.Chen,
and
J.B.Ma
(2009).
Structural insights into mechanisms of the small RNA methyltransferase HEN1.
|
| |
Nature, 461,
823-827.
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PDB code:
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A.Ebihara,
M.Manzoku,
H.Iino,
M.Kanagawa,
A.Shinkai,
S.Yokoyama,
and
S.Kuramitsu
(2008).
Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins.
|
| |
Proteins, 71,
2097-2101.
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PDB code:
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C.L.Li,
W.Z.Yang,
Y.P.Chen,
and
H.S.Yuan
(2008).
Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing.
|
| |
Nucleic Acids Res, 36,
3579-3589.
|
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PDB code:
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M.Nowotny,
S.M.Cerritelli,
R.Ghirlando,
S.A.Gaidamakov,
R.J.Crouch,
and
W.Yang
(2008).
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
|
| |
EMBO J, 27,
1172-1181.
|
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PDB code:
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P.A.Lemaire,
E.Anderson,
J.Lary,
and
J.L.Cole
(2008).
Mechanism of PKR Activation by dsRNA.
|
| |
J Mol Biol, 381,
351-360.
|
|
|
|
|
|
|
S.R.Nallagatla,
and
P.C.Bevilacqua
(2008).
Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner.
|
| |
RNA, 14,
1201-1213.
|
|
|
|
|
|
|
S.R.Nallagatla,
R.Toroney,
and
P.C.Bevilacqua
(2008).
A brilliant disguise for self RNA: 5'-end and internal modifications of primary transcripts suppress elements of innate immunity.
|
| |
RNA Biol, 5,
140-144.
|
|
|
|
|
|
|
B.M.Lunde,
C.Moore,
and
G.Varani
(2007).
RNA-binding proteins: modular design for efficient function.
|
| |
Nat Rev Mol Cell Biol, 8,
479-490.
|
|
|
|
|
|
|
H.K.Kini,
and
S.P.Walton
(2007).
In vitro binding of single-stranded RNA by human Dicer.
|
| |
FEBS Lett, 581,
5611-5616.
|
|
|
|
|
|
|
L.V.Loukachevitch,
and
M.Egli
(2007).
Crystallization and preliminary X-ray analysis of Escherichia coli RNase HI-dsRNA complexes.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun, 63,
84-88.
|
|
|
|
|
|
|
L.Valente,
and
K.Nishikura
(2007).
RNA binding-independent dimerization of adenosine deaminases acting on RNA and dominant negative effects of nonfunctional subunits on dimer functions.
|
| |
J Biol Chem, 282,
16054-16061.
|
|
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|
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|
|
M.Singh,
R.A.Kesterson,
M.M.Jacobs,
J.M.Joers,
J.C.Gore,
and
R.B.Emeson
(2007).
Hyperphagia-mediated obesity in transgenic mice misexpressing the RNA-editing enzyme ADAR2.
|
| |
J Biol Chem, 282,
22448-22459.
|
|
|
|
|
|
|
N.Okazaki,
M.Kumei,
M.Manzoku,
S.Kuramitsu,
M.Shirouzu,
A.Shinkai,
and
S.Yokoyama
(2007).
Structure of a UPF0150-family protein from Thermus thermophilus HB8.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun, 63,
173-177.
|
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PDB code:
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S.Y.Sohn,
W.J.Bae,
J.J.Kim,
K.H.Yeom,
V.N.Kim,
and
Y.Cho
(2007).
Crystal structure of human DGCR8 core.
|
| |
Nat Struct Mol Biol, 14,
847-853.
|
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PDB code:
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T.Katoh,
and
T.Suzuki
(2007).
Specific residues at every third position of siRNA shape its efficient RNAi activity.
|
| |
Nucleic Acids Res, 35,
e27.
|
|
|
|
|
|
|
Y.Yuan,
S.A.Compton,
K.Sobczak,
M.G.Stenberg,
C.A.Thornton,
J.D.Griffith,
and
M.S.Swanson
(2007).
Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs.
|
| |
Nucleic Acids Res, 35,
5474-5486.
|
|
|
|
|
|
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B.L.Bass
(2006).
How does RNA editing affect dsRNA-mediated gene silencing?
|
| |
Cold Spring Harb Symp Quant Biol, 71,
285-292.
|
|
|
|
|
|
|
F.Li,
and
S.W.Ding
(2006).
Virus counterdefense: diverse strategies for evading the RNA-silencing immunity.
|
| |
Annu Rev Microbiol, 60,
503-531.
|
|
|
|
|
|
|
H.Poulsen,
R.Jorgensen,
A.Heding,
F.C.Nielsen,
B.Bonven,
and
J.Egebjerg
(2006).
Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain.
|
| |
RNA, 12,
1350-1360.
|
|
|
|
|
|
|
J.Gan,
J.E.Tropea,
B.P.Austin,
D.L.Court,
D.S.Waugh,
and
X.Ji
(2006).
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.
|
| |
Cell, 124,
355-366.
|
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PDB code:
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J.K.Bell,
J.Askins,
P.R.Hall,
D.R.Davies,
and
D.M.Segal
(2006).
The dsRNA binding site of human Toll-like receptor 3.
|
| |
Proc Natl Acad Sci U S A, 103,
8792-8797.
|
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J.O.Langland,
J.M.Cameron,
M.C.Heck,
J.K.Jancovich,
and
B.L.Jacobs
(2006).
Inhibition of PKR by RNA and DNA viruses.
|
| |
Virus Res, 119,
100-110.
|
|
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|
|
|
|
J.Y.Min,
and
R.M.Krug
(2006).
The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2'-5' oligo (A) synthetase/RNase L pathway.
|
| |
Proc Natl Acad Sci U S A, 103,
7100-7105.
|
|
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|
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|
|
K.A.Chilibeck,
T.Wu,
C.Liang,
M.J.Schellenberg,
E.M.Gesner,
J.M.Lynch,
and
A.M.MacMillan
(2006).
FRET analysis of in vivo dimerization by RNA-editing enzymes.
|
| |
J Biol Chem, 281,
16530-16535.
|
|
|
|
|
|
|
K.Nishikura
(2006).
Editor meets silencer: crosstalk between RNA editing and RNA interference.
|
| |
Nat Rev Mol Cell Biol, 7,
919-931.
|
|
|
|
|
|
|
M.Dlakić
(2006).
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold.
|
| |
Bioinformatics, 22,
2711-2714.
|
|
|
|
|
|
|
M.Hallegger,
A.Taschner,
and
M.F.Jantsch
(2006).
RNA aptamers binding the double-stranded RNA-binding domain.
|
| |
RNA, 12,
1993-2004.
|
|
|
|
|
|
|
M.Terribilini,
J.H.Lee,
C.Yan,
R.L.Jernigan,
V.Honavar,
and
D.Dobbs
(2006).
Prediction of RNA binding sites in proteins from amino acid sequence.
|
| |
RNA, 12,
1450-1462.
|
|
|
|
|
|
|
M.Xu,
K.S.Wells,
and
R.B.Emeson
(2006).
Substrate-dependent contribution of double-stranded RNA-binding motifs to ADAR2 function.
|
| |
Mol Biol Cell, 17,
3211-3220.
|
|
|
|
|
|
|
R.E.Collins,
and
X.Cheng
(2006).
Structural and biochemical advances in mammalian RNAi.
|
| |
J Cell Biochem, 99,
1251-1266.
|
|
|
|
|
|
|
R.P.van Rij,
M.C.Saleh,
B.Berry,
C.Foo,
A.Houk,
C.Antoniewski,
and
R.Andino
(2006).
The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster.
|
| |
Genes Dev, 20,
2985-2995.
|
|
|
|
|
|
|
S.Puthenveetil,
L.Whitby,
J.Ren,
K.Kelnar,
J.F.Krebs,
and
P.A.Beal
(2006).
Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification.
|
| |
Nucleic Acids Res, 34,
4900-4911.
|
|
|
|
|
|
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Y.Feng,
C.L.Sansam,
M.Singh,
and
R.B.Emeson
(2006).
Altered RNA editing in mice lacking ADAR2 autoregulation.
|
| |
Mol Cell Biol, 26,
480-488.
|
|
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|
|
A.Hiraguri,
R.Itoh,
N.Kondo,
Y.Nomura,
D.Aizawa,
Y.Murai,
H.Koiwa,
M.Seki,
K.Shinozaki,
and
T.Fukuhara
(2005).
Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana.
|
| |
Plant Mol Biol, 57,
173-188.
|
|
|
|
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|
|
A.K.Henras,
M.Sam,
S.L.Hiley,
H.Wu,
T.R.Hughes,
J.Feigon,
and
G.F.Chanfreau
(2005).
Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III.
|
| |
RNA, 11,
1225-1237.
|
|
|
|
|
|
|
F.V.Rivas,
N.H.Tolia,
J.J.Song,
J.P.Aragon,
J.Liu,
G.J.Hannon,
and
L.Joshua-Tor
(2005).
Purified Argonaute2 and an siRNA form recombinant human RISC.
|
| |
Nat Struct Mol Biol, 12,
340-349.
|
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PDB codes:
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J.A.Chao,
J.H.Lee,
B.R.Chapados,
E.W.Debler,
A.Schneemann,
and
J.R.Williamson
(2005).
Dual modes of RNA-silencing suppression by Flock House virus protein B2.
|
| |
Nat Struct Mol Biol, 12,
952-957.
|
|
|
PDB codes:
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|
J.Choe,
M.S.Kelker,
and
I.A.Wilson
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J.Gan,
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PDB code:
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J.Blaszczyk,
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PDB codes:
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J.W.Ucci,
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T.C.Leeper,
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EMBO J, 23,
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PDB codes:
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S.Puthenveetil,
E.A.Véliz,
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Chembiochem, 5,
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T.Miki,
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Alternative splicing of Staufen2 creates the nuclear export signal for CRM1 (Exportin 1).
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J Biol Chem, 279,
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Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails.
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RNA, 10,
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L.P.Keegan,
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A stem structure in fibroblast growth factor receptor 2 transcripts mediates cell-type-specific splicing by approximating intronic control elements.
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Mol Cell Biol, 23,
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B.R.Szymczyna,
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Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
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Genes Dev, 17,
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PDB code:
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C.B.Carlson,
M.Vuyisich,
B.D.Gooch,
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Biopolymers, 70,
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C.L.Sansam,
K.S.Wells,
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Modulation of RNA editing by functional nucleolar sequestration of ADAR2.
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Proc Natl Acad Sci U S A, 100,
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Recognition of small interfering RNA by a viral suppressor of RNA silencing.
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Nature, 426,
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PDB code:
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|
M.Doyle,
and
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Distinct in vivo roles for double-stranded RNA-binding domains of the Xenopus RNA-editing enzyme ADAR1 in chromosomal targeting.
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J Cell Biol, 161,
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M.L.Hung,
P.Chao,
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dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA.
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Nucleic Acids Res, 31,
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R.S.Dave,
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Secondary structures common to chloroplast mRNA 3'-untranslated regions direct cleavage by CSP41, an endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.
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J Biol Chem, 278,
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T.W.Reichman,
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RNA binding and intramolecular interactions modulate the regulation of gene expression by nuclear factor 110.
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RNA, 9,
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V.G.Kolupaeva,
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Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site.
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Mol Cell Biol, 23,
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A.M.Brownawell,
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Exportin-5, a novel karyopherin, mediates nuclear export of double-stranded RNA binding proteins.
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J Cell Biol, 156,
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B.L.Bass
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RNA editing by adenosine deaminases that act on RNA.
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C.Conrad,
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Ribonuclease III: new sense from nuisance.
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Int J Biochem Cell Biol, 34,
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M.T.Wilhelm,
F.Hellborg,
W.Qian,
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The p53-induced mouse zinc finger protein wig-1 binds double-stranded RNA with high affinity.
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Nucleic Acids Res, 30,
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H.Tabara,
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The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans.
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Cell, 109,
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K.Wild,
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I.Sinning,
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Towards the structure of the mammalian signal recognition particle.
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Curr Opin Struct Biol, 12,
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K.Ye,
A.Serganov,
W.Hu,
M.Garber,
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Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.
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Eur J Biochem, 269,
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PDB code:
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|
M.Vuyisich,
R.J.Spanggord,
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The binding site of the RNA-dependent protein kinase (PKR) on EBER1 RNA from Epstein-Barr virus.
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EMBO Rep, 3,
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S.J.Muh,
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A Non-sequence-specific double-stranded RNA structural element regulates splicing of two mutually exclusive exons of fibroblast growth factor receptor 2 (FGFR2).
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J Biol Chem, 277,
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T.Castrignanò,
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Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration.
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Biophys J, 83,
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W.Kagawa,
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Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form.
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| |
Mol Cell, 10,
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PDB code:
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|
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|
Y.Ben-Asouli,
Y.Banai,
Y.Pel-Or,
A.Shir,
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Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR.
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Cell, 108,
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A.Herbert,
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Proc Natl Acad Sci U S A, 98,
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A.M.Olland,
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L.A.Schiff,
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Structure of the reovirus outer capsid and dsRNA-binding protein sigma3 at 1.8 A resolution.
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EMBO J, 20,
979-989.
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PDB code:
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C.R.Eckmann,
A.Neunteufl,
L.Pfaffstetter,
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The human but not the Xenopus RNA-editing enzyme ADAR1 has an atypical nuclear localization signal and displays the characteristics of a shuttling protein.
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Mol Biol Cell, 12,
1911-1924.
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D.J.Battle,
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The stem-loop binding protein forms a highly stable and specific complex with the 3' stem-loop of histone mRNAs.
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RNA, 7,
123-132.
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G.A.Peters,
R.Hartmann,
J.Qin,
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Modular structure of PACT: distinct domains for binding and activating PKR.
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Mol Cell Biol, 21,
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G.Z.Yusupova,
M.M.Yusupov,
J.H.Cate,
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The path of messenger RNA through the ribosome.
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| |
Cell, 106,
233-241.
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PDB codes:
|
|
|
|
|
|
|
|
H.Wu,
P.K.Yang,
S.E.Butcher,
S.Kang,
G.Chanfreau,
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A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III.
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| |
EMBO J, 20,
7240-7249.
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PDB codes:
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I.Calin-Jageman,
A.K.Amarasinghe,
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Ethidium-dependent uncoupling of substrate binding and cleavage by Escherichia coli ribonuclease III.
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Nucleic Acids Res, 29,
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I.Lebars,
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S.Yoshizawa,
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Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing.
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| |
EMBO J, 20,
7250-7258.
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PDB codes:
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|
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|
J.Blaszczyk,
J.E.Tropea,
M.Bubunenko,
K.M.Routzahn,
D.S.Waugh,
D.L.Court,
and
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Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.
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| |
Structure, 9,
1225-1236.
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PDB codes:
|
|
|
|
|
|
|
|
J.M.Pérez-Cañadillas,
and
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Recent advances in RNA-protein recognition.
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Curr Opin Struct Biol, 11,
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K.Juneau,
E.Podell,
D.J.Harrington,
and
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(2001).
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
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| |
Structure, 9,
221-231.
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|
PDB code:
|
|
|
|
|
|
|
|
K.M.Vattem,
K.A.Staschke,
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Mechanism of activation of the double-stranded-RNA-dependent protein kinase, PKR: role of dimerization and cellular localization in the stimulation of PKR phosphorylation of eukaryotic initiation factor-2 (eIF2).
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Eur J Biochem, 268,
3674-3684.
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K.M.Vattem,
K.A.Staschke,
S.Zhu,
and
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Inhibitory sequences in the N-terminus of the double-stranded-RNA-dependent protein kinase, PKR, are important for regulating phosphorylation of eukaryotic initiation factor 2alpha (eIF2alpha).
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| |
Eur J Biochem, 268,
1143-1153.
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L.Parsons,
E.Eisenstein,
and
J.Orban
(2001).
Solution structure of HI0257, a bacterial ribosome binding protein.
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| |
Biochemistry, 40,
10979-10986.
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PDB code:
|
|
|
|
|
|
|
|
R.J.Spanggord,
and
P.A.Beal
(2001).
Selective binding by the RNA binding domain of PKR revealed by affinity cleavage.
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Biochemistry, 40,
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T.A.Brandt,
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Both carboxy- and amino-terminal domains of the vaccinia virus interferon resistance gene, E3L, are required for pathogenesis in a mouse model.
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J Virol, 75,
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W.Yuan,
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Influenza B virus NS1 protein inhibits conjugation of the interferon (IFN)-induced ubiquitin-like ISG15 protein.
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EMBO J, 20,
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A.D.Frankel
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Fitting peptides into the RNA world.
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Curr Opin Struct Biol, 10,
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A.Ramos,
S.Grünert,
J.Adams,
D.R.Micklem,
M.R.Proctor,
S.Freund,
M.Bycroft,
D.St Johnston,
and
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RNA recognition by a Staufen double-stranded RNA-binding domain.
|
| |
EMBO J, 19,
997.
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PDB code:
|
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|
|
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|
B.Lamontagne,
A.Tremblay,
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S.Abou Elela
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The N-terminal domain that distinguishes yeast from bacterial RNase III contains a dimerization signal required for efficient double-stranded RNA cleavage.
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Mol Cell Biol, 20,
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C.J.Coolidge,
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A new double-stranded RNA-binding protein that interacts with PKR.
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Nucleic Acids Res, 28,
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G.Chanfreau,
M.Buckle,
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Mol Cell Biol, 20,
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RNA, 6,
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RNA, 6,
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PDB code:
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PDB code:
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The most recent references are shown first.
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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