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PDBsum entry 1ex2
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Structural genomics
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PDB id
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1ex2
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Functional implications from crystal structures of the conserved bacillus subtilis protein maf with and without dutp.
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Authors
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G.Minasov,
M.Teplova,
G.C.Stewart,
E.V.Koonin,
W.F.Anderson,
M.Egli.
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Ref.
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Proc Natl Acad Sci U S A, 2000,
97,
6328-6333.
[DOI no: ]
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PubMed id
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Abstract
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Three-dimensional structures of functionally uncharacterized proteins may
furnish insight into their functions. The potential benefits of
three-dimensional structural information regarding such proteins are
particularly obvious when the corresponding genes are conserved during
evolution, implying an important function, and no functional classification can
be inferred from their sequences. The Bacillus subtilis Maf protein is
representative of a family of proteins that has homologs in many of the
completely sequenced genomes from archaea, prokaryotes, and eukaryotes, but
whose function is unknown. As an aid in exploring function, we determined the
crystal structure of this protein at a resolution of 1.85 A. The structure, in
combination with multiple sequence alignment, reveals a putative active site.
Phosphate ions present at this site and structural similarities between a
portion of Maf and the anticodon-binding domains of several tRNA synthetases
suggest that Maf may be a nucleic acid-binding protein. The crystal structure of
a Maf-nucleoside triphosphate complex provides support for this hypothesis and
hints at di- or oligonucleotides with either 5'- or 3'-terminal phosphate groups
as ligands or substrates of Maf. A further clue comes from the observation that
the structure of the Maf monomer bears similarity to that of the recently
reported Methanococcus jannaschii Mj0226 protein. Just as for Maf, the structure
of this predicted NTPase was determined as part of a structural genomics pilot
project. The structural relation between Maf and Mj0226 was not apparent from
sequence analysis approaches. These results emphasize the potential of
structural genomics to reveal new unexpected connections between protein
families previously considered unrelated.
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Figure 1.
Fig. 1. (A) Final (2 F[o]  F[c])
electron density at 1.85 Å resolution [1  level,
drawn with TURBO FRODO (37)], depicting the phosphate ion bound
at the Maf putative active site. Atoms of selected side chains
are colored yellow, blue, and red for carbon, nitrogen, and
oxygen, respectively, and oxygen atoms of water molecules are
shown as small red spheres. (B) Overall structure of the Maf
protein drawn with the program RIBBONS (38). The  helices and
 strands are
colored cyan and green, respectively, and are numbered. Loop
regions are colored orange, N and C termini are labeled, and a
yellow dot indicates the location of the disulfide bridge.
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Figure 3.
Fig. 3. (A) Arrangement of conserved residues on the 3D
surface of Maf. Green, yellow, and cyan patches indicate the
locations of amino acids that are conserved in 18 or more, in 17
or 16 of 19, and in 15 of 19 analyzed proteins, respectively
(see Fig. 2). All other residues are white. (B) Electrostatic
surface potential of Maf calculated with the program GRASP (39).
Blue and red patches indicate regions of positive and negative
charge, respectively. The views in A and B are similar to that
in Fig. 1B.
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