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PDBsum entry 1imu
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RNA binding protein
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PDB id
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1imu
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
40:10979-10986
(2001)
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PubMed id:
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Solution structure of HI0257, a bacterial ribosome binding protein.
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L.Parsons,
E.Eisenstein,
J.Orban.
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ABSTRACT
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A novel bacterial ribosome binding protein, protein Y (also known as YfiA), was
recently shown to reside at the 30S/50S subunit interface and to stabilize the
ribosomal 70S complex against dissociation at low magnesium ion concentrations.
We report here the three-dimensional NMR structure in solution of a homologue
from Haemophilus influenzae, HI0257, that has 64% sequence identity to protein
Y. The 107 residue protein has a beta-alpha-beta-beta-beta-alpha folding
topology with two parallel alpha-helices packed against the same side of a
four-stranded beta-sheet. The closest structural relatives are proteins with the
double-stranded RNA-binding domain (dsRBD) motif although there is little
(<10%) sequence homology. The most immediate differences between the dsRBD
and HI0257 structures are that (1) HI0257 has a larger beta-sheet motif with an
extra beta-strand at the N-terminus, (2) the helices are parallel in HI0257 but
at an angle of about 30 degrees to each other in the dsRBD, and (3) HI0257 lacks
the extended loop commonly seen between the first and second beta-strands of the
dsRBD. Further, an analysis of the surface electrostatic potential in HI0257 and
the dsRBD family reveals significant differences in the location of contiguous
positively (and negatively) charged regions. The structural data, in combination
with sequence analysis of HI0257 and its homologues, suggest that the most
likely mode of RNA recognition for HI0257 may be distinct from that of the dsRBD
family 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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M.R.Sharma,
A.Dönhöfer,
C.Barat,
V.Marquez,
P.P.Datta,
P.Fucini,
D.N.Wilson,
and
R.K.Agrawal
(2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
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J Biol Chem,
285,
4006-4014.
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D.C.Yeh,
L.M.Parsons,
J.F.Parsons,
F.Liu,
E.Eisenstein,
and
J.Orban
(2005).
NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog.
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Protein Sci,
14,
424-430.
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PDB code:
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D.N.Wilson,
and
K.H.Nierhaus
(2004).
The how and Y of cold shock.
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Nat Struct Mol Biol,
11,
1026-1028.
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L.M.Parsons,
D.C.Yeh,
and
J.Orban
(2004).
Solution structure of the highly acidic protein HI1450 from Haemophilus influenzae, a putative double-stranded DNA mimic.
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Proteins,
54,
375-383.
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PDB code:
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K.Ye,
A.Serganov,
W.Hu,
M.Garber,
and
D.J.Patel
(2002).
Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.
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Eur J Biochem,
269,
5182-5191.
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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
code is
shown on the right.
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Links
