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PDBsum entry 2ba2
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Structural genomics, unknown function
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PDB id
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2ba2
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the duf16 domain of mpn010 from mycoplasma pneumoniae.
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Authors
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D.H.Shin,
J.S.Kim,
H.Yokota,
R.Kim,
S.H.Kim.
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Ref.
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Protein Sci, 2006,
15,
921-928.
[DOI no: ]
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PubMed id
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Abstract
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We have determined the crystal structure of the DUF16 domain of unknown function
encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 A resolution. The
crystal structure revealed that this domain is composed of two separated
homotrimeric coiled-coils. The shorter one consists of 11 highly conserved
residues. The sequence comprises noncanonical heptad repeats that induce a
right-handed coiled-coil structure. The longer one is composed of approximately
nine heptad repeats. In this coiled-coil structure, there are three
distinguishable regions that confer unique structural properties compared with
other known homotrimeric coiled-coils. The first part, containing one stutter,
is an unusual phenylalanine-rich region that is not found in any other
coiled-coil structures. The second part is a highly conserved glutamine-rich
region, frequently found in other trimeric coiled-coil structures. The last part
is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16
family together with a secondary structure prediction shows that the DUF16
family can be classified into five subclasses according to N-terminal sequences.
Based on the structural comparison with other coiled-coil structures, a probable
molecular function of the DUF16 family is discussed.
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Figure 1.
Sequence comparisons of the DUF16 family in M. pneumoniae.
The yellow region indicates the short helical bundle of the
DUF16 domain based on the MPNOIO structure. The front of this
region is the approximate N-terminal domain of the DUF 16 family
and the back is the long helical bundle region of the DUF 16
domain based on the MPNOIO structure. Except for the secondary
structure of MPNOIO, the other secondary structures are
predictions obtained with PSIPRED
(http://bioinf.cs.ucl.ac.uk/psipred). Blue, [alpha]-helix; red,
[beta]-strand; minus symbol ([minus sign]), a gap; period (.),
less than mean value plus 1 SD; plus symbol (+), less than mean
value plus 2 SD; and asterisk (*), less than mean value plus 3
SD. "TWISTER" represents each position of the heptad repeats of
the DUF16 domain of MPN010 obtained using the program TWISTER.
In here, "z" indicates a potential location of stutters. The
percent sequence identities against MPN010 are also shown.
Members of each subclass are as follows: (1) subfamily I:
MPN104, MPN675, MPN038, MPN287, MPN484, and MPN151; (2)
subfamily II: MPN010, MPN137, and MPN145; (3) subfamily III:
MPN283, MPN504, and MPN524; (4) subfamily IV: MPN501, MPN100,
MPN204, MPN410, MPN094, MPN130, MPN368, MPN138, and MPN139; and
(5) subfamily V: MPN655, MPN344, MPN013, and MPN127. The
insertions are abbreviated with the number of amino acids. The
proline-rich regions are in these abbreviations.
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Figure 2.
Diagrams of the DUF16 domain of MPN010. (A) A stereo view of
a refined electron-density map around a phenyalanine-rich region
countered at 1.5[sigma]. The 2Fo-Fc map from finally refined
phases was calculated using all reflection data between 20 A and
1.8 A. The figure was generated using the program RIBBONS
(Carson 1991). The residues around the phenylalanine-rich region
are represented by ball-and-stick models (blue, nitrogen atoms;
red, oxygen; green, carbon). The front phenylalanines are Phe75
and the ones below are Phe72. (B) A stereo drawing of a C[alpha]
atom trace of the DUF16 domain of MPN010. Each model was colored
differently. Every 20th residue is numbered and represented by a
dot. The phenylalanine (blue) and glutamine (pink) residues that
occupy trimer interfaces are represented by a ball-and-stick
model. The figure was generated by MOLSCRIPT (Kraulis 1991). (C)
The electrostatic surface potential of the DUF16 domain of
MPN010. A molecular surface is created by the program GRASP
(red, negative; blue, positive; white, uncharged) (Nicholls et
al. 1991). (D) Local coiled-coil parameters plotted against the
residue numbers. The gray squares represent a coiled-coil radius
and the black diamonds indicate coiled-coil pitch. "SH" and "LH"
represent the range of the short and the long helical bundles,
respectively. The small arrows indicate the positions showing
properties of stutters.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(2006,
15,
921-928)
copyright 2006.
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