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PDBsum entry 2fcj
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Structural genomics, unknown function
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PDB id
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2fcj
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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 and putative function of small toprim domain-Containing protein from bacillus stearothermophilus.
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Authors
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P.Rezácová,
D.Borek,
S.F.Moy,
A.Joachimiak,
Z.Otwinowski.
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Ref.
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Proteins, 2008,
70,
311-319.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the Midwest Center for Structural Genomics target
APC35832, a 14.7-kDa cytosolic protein from Bacillus stearothermophilus, has
been determined at 1.3 A resolution by the single anomalous diffraction method
from a mercury soaked crystal. The APC35832 protein is a representative of large
group of bacterial and archeal proteins entirely consisting of the Toprim
(topoisomerase-primase) domain. This domain is found in the catalytic centers of
many enzymes catalyzing phosphodiester bond formation or cleavage, but the
function of small Toprim domain proteins remains unknown. Consistent with the
sequence analysis, the APC35832 structure shows a conserved Toprim fold, with a
central 4-stranded parallel beta-sheet surrounded by four alpha-helixes.
Comparison of the APC35832 structure with its closest structural homolog, the
catalytic core of bacteriophage T7 primase, revealed structural conservation of
a metal binding site and isothermal titration calorimetry indicates that
APC35832 binds Mg2+ with a sub-millimolar dissociation constant (K(d)). The
APC35832-Mg2+ complex structure was determined at 1.65 A and reveals the role of
conserved acidic residues in Mg2+ ion coordination. The structural similarities
to other Toprim domain containing proteins and potential function and substrates
of APC35832 are discussed in this article.
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Figure 2.
Figure 2. A: A stereo diagram showing the overall APC35832
structure. B: Superimposition of APC35832 and the Toprim domain
of T7 DNA primase (PDB entry 1NUI), showing conserved acidic
residue positions. APC35832 is colored pink, 1NUI is blue and
conserved acidic residues are highlighted in green and yellow.
C: The solvent-accessible surface colored according to
electrostatic potential (blue positive, red negative, calculated
with DS ViewerPro 6.0 [Accelerys Software]). The acidic surface
pocket is visible, with the MES molecule shown as sticks.
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Figure 4.
Figure 4. A: Detail of octahedral coordination of Mg^2+ ion
with 2F[o]-F[c] electron density map contoured at the 1.3  level
of the map. B: Schematic of Mg^2+ ion binding by APC35832. Mg^2+
is shown as a yellow sphere, water molecules are represented
with turquoise spheres, ion coordination is shown by violet
lines, and hydrogen bonds as green dotted lines with their
length in Å. Figure was prepared using the program
Ligplot.[20] C: A stereo view of the superimposed Mg^2+ binding
sites in APC35832 (pink) and T7 primase, PDB entry 1NUI (blue),
Mg^2+ ions are colored accordingly. Residues numbers are for the
APC35832 protein.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
70,
311-319)
copyright 2008.
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