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PDBsum entry 1elh
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DOI no:
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Biochemistry
31:1610-1621
(1992)
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PubMed id:
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NMR analysis of helix I from the 5S RNA of Escherichia coli.
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S.A.White,
M.Nilges,
A.Huang,
A.T.Brünger,
P.B.Moore.
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ABSTRACT
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The structure of helix I of the 5S rRNA from Escherichia coli has been
determined using a nucleolytic digest fragment of the intact molecule. The
fragment analyzed, which corresponds to bases (-1)-11 and 108-120 of intact 5S
rRNA, contains a G-U pair and has unpaired bases at its termini. Its proton
resonances were assigned by two-dimensional NMR methods, and both NOE distance
and coupling constant information have been used to calculate structural models
for it using the full relaxation matrix algorithm of the molecular dynamics
program XPLOR. Helix I has A-type helical geometry, as expected. Its most
striking departure from regular helical geometry occurs at its G-U, which stacks
on the base pair to the 5' side of its G but not on the base pair to its 3'
side. This stacking pattern maximizes interstrand guanine-guanine interactions
and explains why the G-U in question fails to give imino proton NOE's to the
base pair to 5' side of its G. These results are consistent with the crystal
structures that have been obtained for wobble base pairs in tRNAPhe [Mizuno, H.,
& Sundaralingam, M. (1978) Nucleic Acids Res. 5, 4451-4461] and A-form DNA
[Rabbinovich, D., Haran, T., Eisenstein, M., & Shakked, Z. (1988) J. Mol.
Biol. 200, 151-161]. The conformations of the terminal residues of helix I,
which corresponds to bases (-1)-11 and 108-120 of native 5S RNA, are less
well-determined, and their sugar puckers are intermediate between C2' and
C3'-endo, on average.
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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.Smirnov,
I.Tarassov,
A.M.Mager-Heckel,
M.Letzelter,
R.P.Martin,
I.A.Krasheninnikov,
and
N.Entelis
(2008).
Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria.
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RNA,
14,
749-759.
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F.Joli,
N.Bouchemal,
A.Laigle,
B.Hartmann,
and
E.Hantz
(2006).
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.
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Nucleic Acids Res,
34,
5740-5751.
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PDB code:
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H.Arthanari,
K.J.McConnell,
R.Beger,
M.A.Young,
D.L.Beveridge,
and
P.H.Bolton
(2003).
Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants.
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Biopolymers,
68,
3.
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B.Masquida,
and
E.Westhof
(2000).
On the wobble GoU and related pairs.
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RNA,
6,
9.
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S.T.Hsu,
M.T.Chou,
and
J.W.Cheng
(2000).
The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes.
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Nucleic Acids Res,
28,
1322-1331.
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X.Chen,
J.A.McDowell,
R.Kierzek,
T.R.Krugh,
and
D.H.Turner
(2000).
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
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Biochemistry,
39,
8970-8982.
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PDB codes:
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J.P.Rife,
S.C.Stallings,
C.C.Correll,
A.Dallas,
T.A.Steitz,
and
P.B.Moore
(1999).
Comparison of the crystal and solution structures of two RNA oligonucleotides.
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Biophys J,
76,
65-75.
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E.Jabri,
and
T.R.Cech
(1998).
In vitro selection of the Naegleria GIR1 ribozyme identifies three base changes that dramatically improve activity.
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RNA,
4,
1481-1492.
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L.Bénard,
N.Mathy,
M.Grunberg-Manago,
B.Ehresmann,
C.Ehresmann,
and
C.Portier
(1998).
Identification in a pseudoknot of a U.G motif essential for the regulation of the expression of ribosomal protein S15.
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Proc Natl Acad Sci U S A,
95,
2564-2567.
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M.Stoldt,
J.Wöhnert,
M.Görlach,
and
L.R.Brown
(1998).
The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
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EMBO J,
17,
6377-6384.
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PDB code:
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P.B.Moore
(1998).
The three-dimensional structure of the ribosome and its components.
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Annu Rev Biophys Biomol Struct,
27,
35-58.
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P.Zheng,
C.J.Burrows,
and
S.E.Rokita
(1998).
Nickel- and cobalt-dependent reagents identify structural features of RNA that are not detected by dimethyl sulfate or RNase T1.
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Biochemistry,
37,
2207-2214.
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A.Liljas,
and
S.al-Karadaghi
(1997).
Structural aspects of protein synthesis.
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Nat Struct Biol,
4,
767-771.
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J.A.McDowell,
L.He,
X.Chen,
and
D.H.Turner
(1997).
Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2.
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Biochemistry,
36,
8030-8038.
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PDB codes:
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R.Green,
and
H.F.Noller
(1997).
Ribosomes and translation.
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Annu Rev Biochem,
66,
679-716.
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T.Hermann,
B.Schmid,
H.Heumann,
and
H.U.Göringer
(1997).
A three-dimensional working model for a guide RNA from Trypanosoma brucei.
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Nucleic Acids Res,
25,
2311-2318.
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V.J.Cannistraro,
and
D.Kennell
(1997).
RNase YI* and RNA structure studies.
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Nucleic Acids Res,
25,
1405-1412.
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X.Huang,
P.Yu,
E.LeProust,
and
X.Gao
(1997).
An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences.
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Nucleic Acids Res,
25,
4758-4763.
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A.Földesi,
S.I.Yamakage,
F.P.Nilsson,
T.V.Maltseva,
and
J.Chattopadhyaya
(1996).
The use of non-uniform deuterium labelling ['NMR-window'] to study the NMR structure of a 21mer RNA hairpin.
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Nucleic Acids Res,
24,
1187-1194.
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C.Glemarec,
J.Kufel,
A.Földesi,
T.Maltseva,
A.Sandström,
L.A.Kirsebom,
and
J.Chattopadhyaya
(1996).
The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept].
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Nucleic Acids Res,
24,
2022-2035.
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J.A.McDowell,
and
D.H.Turner
(1996).
Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing.
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Biochemistry,
35,
14077-14089.
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PDB code:
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J.Rudinger,
R.Hillenbrandt,
M.Sprinzl,
and
R.Giegé
(1996).
Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu.
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EMBO J,
15,
650-657.
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M.Z.Barciszewska,
V.A.Erdmann,
and
J.Barciszewski
(1996).
Ribosomal 5S RNA: tertiary structure and interactions with proteins.
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Biol Rev Camb Philos Soc,
71,
1.
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N.L.Greenbaum,
I.Radhakrishnan,
D.J.Patel,
and
D.Hirsh
(1996).
Solution structure of the donor site of a trans-splicing RNA.
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Structure,
4,
725-733.
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PDB codes:
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S.A.White,
and
H.Li
(1996).
Yeast ribosomal protein L32 recognizes an RNA G:U juxtaposition.
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RNA,
2,
226-234.
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S.Zinn-Justin,
M.Guenneugues,
E.Drakopoulou,
B.Gilquin,
C.Vita,
and
A.Ménez
(1996).
Transfer of a beta-hairpin from the functional site of snake curaremimetic toxins to the alpha/beta scaffold of scorpion toxins: three-dimensional solution structure of the chimeric protein.
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Biochemistry,
35,
8535-8543.
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PDB code:
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A.Dallas,
R.Rycyna,
and
P.Moore
(1995).
A proposal for the conformation of loop E in Escherichia coli 5S rRNA.
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Biochem Cell Biol,
73,
887-897.
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A.Liljas,
and
M.Garber
(1995).
Ribosomal proteins and elongation factors.
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Curr Opin Struct Biol,
5,
721-727.
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S.Y.Le,
N.Pattabiraman,
and
J.V.Maizel
(1994).
RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies.
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Nucleic Acids Res,
22,
3966-3976.
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A.T.Brünger,
and
M.Nilges
(1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
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Q Rev Biophys,
26,
49.
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M.Riley
(1993).
Functions of the gene products of Escherichia coli.
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Microbiol Rev,
57,
862-952.
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D.Khare,
and
J.Orban
(1992).
Synthesis of backbone deuterium labelled [r(CGCGAAUUCGCG)]2 and HPLC purification of synthetic RNA.
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Nucleic Acids Res,
20,
5131-5136.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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