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PDBsum entry 2e12
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References listed in PDB file
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Key reference
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Title
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Xc5848, An orfan protein from xanthomonas campestris, Adopts a novel variant of sm-Like motif.
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Authors
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K.H.Chin,
S.K.Ruan,
A.H.Wang,
S.H.Chou.
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Ref.
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Proteins, 2007,
68,
1006-1010.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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Figure 1.
Figure 1. (a) The monomer structure of XC5848 color-coded from
blue (N-terminal) to red (C-terminal). Distinct interactions
between the N-terminal residues with the extended  3/
2
 hairpin
were circled in red and shown expanded in (b). (b) The 10
N-terminal residues were marked in blue, while other residues in
red. The conventional H-bonds/salt-bridges were annotated in
dotted green lines, while unconventional CH   bonds
in dotted gray lines. The unique bonding force at the N-terminal
region are: (1) K3C  O
R55H^N;
(2) Y4OH R55NH;
(3) Y4OH R59O^
 ;
(4) A5H^N R55C
O;
(5) H7C O
N64N^
 ;
(6) Y9H^N S63C
O;
(7) Y9C O
S63H^N;
(8) Y9OH D84O^
;
(9) T10C O
Q12H^N;
(10) W82C^  3H
Y54;
(11) P6C^ H
W82.
(c) The dimer structure of XC5858. The interface is mainly
comprised of helix-helix interactions, which were shown expanded
in (d). (d) The interaction forces at this interface: (1) K23N^
E19O^
;
(2) H20N^ E19O^
;
(3) H20N^ Q12O^
and
vice versa.
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Figure 2.
Figure 2. (a) Multiple superimposition of Sm-like protein
structures produced from the MUSTANG program.[15] While the core
-sheet
structure of these Sm-like proteins superimposed very well, the
 -helices
and loops 4 vary to a great extent. XC5858 (shown in red)
contains an extra N-terminal structure that interacts
substantially with the extended 2
/
3
structure. (b) Multiple sequence alignments of XC5848 with the
two bacterial Sm-like Hfq proteins (1HK9/1KQ1), the six archaeal
Sm-like proteins (1H64, 1I4K, 1I81, 1I8F, 1LJ0, 1M8V), the two
human Sm-like proteins (1B34, DD3B), and the yeast Sm-like
protein (1N9S) produced from same program. Colors indicate the
chemical nature of the amino acid (small hydrophobic including
aromatic, red; acidic, blue; basic, magenta; basic amino acids
with hydroxyl group and/or amino groups, black). The secondary
structure elements for -helix
(green tube) and -strand
(red arrows) were also shown for the top and bottom sequences,
along with their annotations. The -helices
and -strands
for each individual sequence were boxed in green and red,
respectively. The essential residues responsible for subunit
interactions and/or protein-RNA interactions were further marked
with unique symbols in blue.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2007,
68,
1006-1010)
copyright 2007.
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